
seed used = 140005785

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2119.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 362
# site patterns = 105
   10    3    9    9    9    1   14   10    5    8   10    9    3   19    1
   19    5    9    4   10    5    1    1    5    4    3    4    8    5    6
    5    9    1    1    1    3    8    1    1    1    9    2    3    1    8
    1   12    1    1    1    4    1    1    1    1    1    1    3    2    4
    1    4    1    2    4    1    3    1    4    1    1    1    1    2    1
    3    1    1    1    1    1    3    1    1    1    2    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    2


1       
K12                   ATG TCA CCG CAG AAT CAT CTG CGT CCT GCT GTG TTA TAC GCC GAT GAA GCA AAA CAA GAT AAC TGC CCC GGT TGG AGT TTG GCG TTT ATC CTT GGC GAC GAA ATC AGC ATT AGC CCC TCC GTC CGT ACT GCT ACC GGC CGC GGG CCG GGT TCT CTT CTT GCT GGG GGG ACC AAG TAT CAT CCG ACG GTC GGA GAC TTC GAG ATA ACA CAG TGT AGG GGG CTC AGT TAT GCG CGA ACC GCT CTA TTC ACG GTT TTG GAA CTG TCG GGT GTA TTC CTG TCC CAT GCT GTG CGC GCG GGG CCT GAC GAA TGT GCG CAC 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T AGC ..T ... ... ..T ... ... ... ... ... ..C ... ..A ... ... ..T ..C ... ..C ..G T.. ... ..C ..T ... ..C ... ..A ... ... ... ... ..T ... ... ... ..A ... ... .T. ... ... ... ... ... ... ... ... ... ..T ..C C.. ..G ..T ... ... ... ... ..A ... ..C ..C ..A ... ..A ..T ..A ... ..C ..C ..T ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T AGC ..T ... ... ..T ... ... ... ... ... ..C ... ..A ... ... ..T ..C ... ..C ..G T.. ... ..C ..T ... ..C ... ..A ... ... ... ... ..T ... ... ... ..A ... ... .T. ... ... ... ... ... ... ... ... ... ..T ..C C.. ..G ..T ... ... ... ... ..A ... ..C ..C ..A ... ..A ..T ..A ... ..C ..C ..T ... 
CFT073                ... ... ... ... ... ..C ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ..T ... ..T ... ..C ... ..C ... ..G ... ... ... ..G ... ..C ..G ... A.. ..C ... ... ..C ... ... ... ..T ... ... ..T ... ... ... ..A ... ... .T. ... ..C ... ..A ..G ..G ..C ... ... ..T ..C C.. ..G ..T ... ..C ... ..T ..A ... ..C ..G ... ..A ..A ..T ..A ..T ..C ... ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T AGC ..T ... ... ..T ... ... ... ... ... ..C ... ..A ... ... ..T ..C ... ..C ..G T.. ... ..C ..T ... ..C ... ..A ... ... ... ... ..T ... ... ... ..A ... ... .T. ... ... ... ... ... ... ... ... ... ..T ..C C.. ..G ..T ... ... ... ... ..A ... ..C ... ... ... ... ... ... ... ..C ... ..T ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T AGC ..T ... ... ..T ... ... ... ... ... ..C ... ..A ... ... ..T ..C ... ..C ..G T.. ... ..C ..T ... ..C ... ..A ... ... ... ... ..T ... ... ... ..A ... ... .T. ... ... ... ... ... ... ... ... ... ..T ..C C.. ..G ..T ... ... ... ... ..A ... ..C ... ... ... ... ... ... ... ..C ... ..T ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  5  6  6  7  6  6 | Ser TCT  4  5  5  5  5  5 | Tyr TAT  5  3  3  3  3  3 | Cys TGT  2  1  1  2  2  2
    TTC  5  4  4  3  4  4 |     TCC  2  2  2  1  2  2 |     TAC  3  5  5  5  5  5 |     TGC  1  2  2  1  1  1
Leu TTA  9  9  9  9  9  9 |     TCA  3  3  3  3  3  3 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  5  4  4  4  4  4 |     TCG  1  1  1  1  1  1 |     TAG  0  0  0  0  0  0 | Trp TGG  4  4  4  4  4  4
--------------------------------------------------------------------------------------------------------------
Leu CTT  7  6  6  6  6  6 | Pro CCT  6  6  6  5  7  7 | His CAT  6  5  5  4  5  5 | Arg CGT 12 12 12 10 12 12
    CTC  2  3  3  3  3  3 |     CCC  2  2  2  1  2  2 |     CAC  2  3  3  4  3  3 |     CGC 13 13 13 14 13 13
    CTA  1  2  2  2  2  2 |     CCA  0  2  2  2  1  1 | Gln CAA  4  5  5  5  5  5 |     CGA  1  1  1  1  1  1
    CTG 16 16 16 16 16 16 |     CCG 11  9  9 11  9  9 |     CAG 10  9  9  9  9  9 |     CGG  0  0  0  1  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT  8  9  9  9  9  9 | Thr ACT  3  5  5  4  5  5 | Asn AAT  9  9  9  9  9  9 | Ser AGT  4  5  5  4  5  5
    ATC  7  6  6  6  6  6 |     ACC 10  9  9  9  9  9 |     AAC  5  5  5  5  5  5 |     AGC  4  4  4  4  4  4
    ATA  1  1  1  1  1  1 |     ACA  4  4  4  4  4  4 | Lys AAA  9  9  9  9  9  9 | Arg AGA  0  0  0  0  0  0
Met ATG 10 10 10 10 10 10 |     ACG  5  4  4  5  4  4 |     AAG  3  3  3  3  3  3 |     AGG  1  1  1  2  1  1
--------------------------------------------------------------------------------------------------------------
Val GTT  1  0  0  2  0  0 | Ala GCT 12 10 10  9 11 11 | Asp GAT 11 12 12 11 12 12 | Gly GGT  7  7  7  6  6  6
    GTC 10 11 11 10 11 11 |     GCC 19 21 21 21 20 20 |     GAC  6  6  6  6  6  6 |     GGC 10 11 11 11 11 11
    GTA  1  2  2  1  1  1 |     GCA  5  6  6  7  5  5 | Glu GAA 23 19 19 20 19 19 |     GGA  2  3  3  2  3  3
    GTG 11 11 11 12 12 12 |     GCG 11  9  9 10 10 10 |     GAG  3  5  5  5  5  5 |     GGG  5  2  2  3  3  3
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13536    C:0.25691    A:0.22928    G:0.37845
position  2:    T:0.27348    C:0.27072    A:0.27348    G:0.18232
position  3:    T:0.28177    C:0.27901    A:0.17403    G:0.26519

#2: S2457T         
position  1:    T:0.13536    C:0.25967    A:0.23204    G:0.37293
position  2:    T:0.27624    C:0.27072    A:0.27072    G:0.18232
position  3:    T:0.27901    C:0.29558    A:0.18232    G:0.24309

#3: Shig4337       
position  1:    T:0.13536    C:0.25967    A:0.23204    G:0.37293
position  2:    T:0.27624    C:0.27072    A:0.27072    G:0.18232
position  3:    T:0.27901    C:0.29558    A:0.18232    G:0.24309

#4: CFT073         
position  1:    T:0.13260    C:0.25967    A:0.23204    G:0.37569
position  2:    T:0.27901    C:0.27072    A:0.27072    G:0.17956
position  3:    T:0.26519    C:0.28729    A:0.18232    G:0.26519

#5: O157           
position  1:    T:0.13536    C:0.25967    A:0.23204    G:0.37293
position  2:    T:0.27624    C:0.27072    A:0.27072    G:0.18232
position  3:    T:0.28453    C:0.29006    A:0.17403    G:0.25138

#6: EDL933         
position  1:    T:0.13536    C:0.25967    A:0.23204    G:0.37293
position  2:    T:0.27624    C:0.27072    A:0.27072    G:0.18232
position  3:    T:0.28453    C:0.29006    A:0.17403    G:0.25138

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      36 | Ser S TCT      29 | Tyr Y TAT      20 | Cys C TGT      10
      TTC      24 |       TCC      11 |       TAC      28 |       TGC       8
Leu L TTA      54 |       TCA      18 | *** * TAA       0 | *** * TGA       0
      TTG      25 |       TCG       6 |       TAG       0 | Trp W TGG      24
------------------------------------------------------------------------------
Leu L CTT      37 | Pro P CCT      37 | His H CAT      30 | Arg R CGT      70
      CTC      17 |       CCC      11 |       CAC      18 |       CGC      79
      CTA      11 |       CCA       8 | Gln Q CAA      29 |       CGA       6
      CTG      96 |       CCG      58 |       CAG      55 |       CGG       1
------------------------------------------------------------------------------
Ile I ATT      53 | Thr T ACT      27 | Asn N AAT      54 | Ser S AGT      28
      ATC      37 |       ACC      55 |       AAC      30 |       AGC      24
      ATA       6 |       ACA      24 | Lys K AAA      54 | Arg R AGA       0
Met M ATG      60 |       ACG      26 |       AAG      18 |       AGG       7
------------------------------------------------------------------------------
Val V GTT       3 | Ala A GCT      63 | Asp D GAT      70 | Gly G GGT      39
      GTC      64 |       GCC     122 |       GAC      36 |       GGC      65
      GTA       8 |       GCA      34 | Glu E GAA     119 |       GGA      16
      GTG      69 |       GCG      59 |       GAG      28 |       GGG      18
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.13490    C:0.25921    A:0.23158    G:0.37431
position  2:    T:0.27624    C:0.27072    A:0.27118    G:0.18186
position  3:    T:0.27901    C:0.28959    A:0.17818    G:0.25322

Codon frequencies under model, for use in evolver:
  0.01061093  0.01101366  0.00677629  0.00963038
  0.01039871  0.01079338  0.00664076  0.00943778
  0.01041640  0.01081174  0.00000000  0.00000000
  0.00698553  0.00725066  0.00000000  0.00634000
  0.02038892  0.02116276  0.01302065  0.01850480
  0.01998115  0.02073951  0.01276024  0.01813470
  0.02001513  0.02077478  0.01278194  0.01816554
  0.01342271  0.01393215  0.00857193  0.01218233
  0.01821604  0.01890740  0.01163301  0.01653271
  0.01785172  0.01852926  0.01140035  0.01620205
  0.01788208  0.01856077  0.01141974  0.01622961
  0.01199222  0.01244737  0.00765840  0.01088403
  0.02944262  0.03056008  0.01880247  0.02672185
  0.02885377  0.02994888  0.01842642  0.02618741
  0.02890284  0.02999981  0.01845775  0.02623195
  0.01938306  0.02011872  0.01237829  0.01759188



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               0.0583 (0.0072 0.1237)
Shig4337             0.0583 (0.0072 0.1237)-1.0000 (0.0000 0.0000)
CFT073               0.0313 (0.0049 0.1581) 0.0736 (0.0072 0.0980) 0.0736 (0.0072 0.0980)
O157                 0.0734 (0.0072 0.0982) 0.0000 (0.0000 0.0223) 0.0000 (0.0000 0.0223) 0.0706 (0.0072 0.1022)
EDL933               0.0734 (0.0072 0.0982) 0.0000 (0.0000 0.0223) 0.0000 (0.0000 0.0223) 0.0706 (0.0072 0.1022)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 65
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1781.585694     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.10114  0.01747  0.00000  0.00000  0.00000  0.10488  0.00000  0.00000  0.00000  2.38226  0.99409  0.00000  0.02653 16.45315
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.22351

((1: 0.101145, (2: 0.000004, 3: 0.000004): 0.017471): 0.000000, (4: 0.104881, (5: 0.000004, 6: 0.000004): 0.000000): 0.000000);

((K12: 0.101145, (S2457T: 0.000004, Shig4337: 0.000004): 0.017471): 0.000000, (CFT073: 0.104881, (O157: 0.000004, EDL933: 0.000004): 0.000000): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  2.38226


dN/dS for site classes (K=3)

p:   0.99409  0.00000  0.00591
w:   0.02653  1.00000 16.45315

dN & dS for each branch

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

   7..8       0.000    320.4    765.6   0.1236   0.0000   0.0000    0.0    0.0
   8..1       0.101    320.4    765.6   0.1236   0.0109   0.0882   28.3    8.3
   8..9       0.017    320.4    765.6   0.1236   0.0019   0.0152    4.9    1.4
   9..2       0.000    320.4    765.6   0.1236   0.0000   0.0000    0.0    0.0
   9..3       0.000    320.4    765.6   0.1236   0.0000   0.0000    0.0    0.0
   7..10      0.000    320.4    765.6   0.1236   0.0000   0.0000    0.0    0.0
  10..4       0.105    320.4    765.6   0.1236   0.0113   0.0915   29.3    8.7
  10..11      0.000    320.4    765.6   0.1236   0.0000   0.0000    0.0    0.0
  11..5       0.000    320.4    765.6   0.1236   0.0000   0.0000    0.0    0.0
  11..6       0.000    320.4    765.6   0.1236   0.0000   0.0000    0.0    0.0


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

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

    51 E      1.000**       16.453
    99 A      0.982*        16.154


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

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

    51 E      0.997**       7.069 +- 2.495
    99 A      0.885         6.443 +- 3.037



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:   1.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.017  0.048  0.075  0.094  0.108  0.118  0.127  0.133  0.138  0.141

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 0.000
 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 1.000

sum of density on p0-p1 =   1.000000
