
seed used = 140022889

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3667.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 439
# site patterns = 111
   14    7    7   23   22    7   23    1   12    7    3    8    1    1    6
   14    1    9    4    6   19    7    3    3    7    7   10    6    8    1
    1    9    1    2    5    4    1   16   13    5    5    2    1    1    6
    1    9    4    1    3    5    9    1    1    1    1    1    1    5    3
    1    1    1    2    2    8    1    1    2    1    1    1    1    3    1
    1    1    1    1    3    3    1    1    3    2    3    1    1    1    1
    1    3    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 23 23 23 23 23 | Ser TCT  1  1  1  1  1 | Tyr TAT 11  9  9  9  9 | Cys TGT  3  3  3  3  3
    TTC  6  6  6  6  6 |     TCC  5  4  4  4  4 |     TAC  6  7  7  7  7 |     TGC  3  3  3  3  3
Leu TTA  8  8  8  8  8 |     TCA  4  4  4  3  3 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  9  9  9  8  8 |     TCG  6  7  7  7  7 |     TAG  0  0  0  0  0 | Trp TGG 19 19 19 19 19
--------------------------------------------------------------------------------------------------
Leu CTT  5  5  5  7  5 | Pro CCT  1  1  1  1  1 | His CAT  3  4  4  4  4 | Arg CGT  7 10 10  9  9
    CTC  6  6  6  5  6 |     CCC  2  2  2  2  2 |     CAC  3  3  3  3  3 |     CGC  7  5  5  6  7
    CTA  2  2  2  2  1 |     CCA  4  3  3  3  4 | Gln CAA  3  3  3  3  3 |     CGA  2  0  0  1  1
    CTG 26 26 26 26 28 |     CCG  8  9  9  9  8 |     CAG  5  5  5  5  5 |     CGG  4  5  5  4  3
--------------------------------------------------------------------------------------------------
Ile ATT 15 15 15 17 15 | Thr ACT  1  2  2  1  1 | Asn AAT  5  5  5  5  6 | Ser AGT  1  1  1  1  1
    ATC 12 11 11 11 13 |     ACC  8  7  7  9  8 |     AAC 10 10 10 10  9 |     AGC  5  6  6  6  5
    ATA  2  2  2  1  1 |     ACA  2  1  1  2  1 | Lys AAA  8  8  8  8  7 | Arg AGA  0  0  0  0  0
Met ATG 14 15 15 14 14 |     ACG 10 11 11  9 11 |     AAG  1  1  1  1  2 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT  1  1  1  3  3 | Ala GCT  6  6  5  5  7 | Asp GAT  8  8  8  8  7 | Gly GGT 11 11 11 12 12
    GTC 12 12 12 10 10 |     GCC 17 15 16 16 16 |     GAC  3  3  3  3  4 |     GGC 19 19 19 19 18
    GTA  3  2  2  3  2 |     GCA  9  9  9 10  9 | Glu GAA  7  7  7  6  8 |     GGA  3  3  3  4  3
    GTG 13 14 14 13 14 |     GCG 25 26 26 26 26 |     GAG  5  5  5  6  4 |     GGG 11 11 11  9 11
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.23690    C:0.20046    A:0.21412    G:0.34852
position  2:    T:0.35763    C:0.24829    A:0.17768    G:0.21640
position  3:    T:0.23235    C:0.28246    A:0.12984    G:0.35535

#2: S2457T         
position  1:    T:0.23462    C:0.20273    A:0.21640    G:0.34624
position  2:    T:0.35763    C:0.24601    A:0.17768    G:0.21868
position  3:    T:0.23918    C:0.27107    A:0.11845    G:0.37130

#3: Shig4337       
position  1:    T:0.23462    C:0.20273    A:0.21640    G:0.34624
position  2:    T:0.35763    C:0.24601    A:0.17768    G:0.21868
position  3:    T:0.23690    C:0.27335    A:0.11845    G:0.37130

#4: CFT073         
position  1:    T:0.23007    C:0.20501    A:0.21640    G:0.34852
position  2:    T:0.35763    C:0.24601    A:0.17768    G:0.21868
position  3:    T:0.24829    C:0.27335    A:0.12301    G:0.35535

#5: O157           
position  1:    T:0.23007    C:0.20501    A:0.21412    G:0.35080
position  2:    T:0.35763    C:0.24829    A:0.17768    G:0.21640
position  3:    T:0.24374    C:0.27563    A:0.11617    G:0.36446

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     115 | Ser S TCT       5 | Tyr Y TAT      47 | Cys C TGT      15
      TTC      30 |       TCC      21 |       TAC      34 |       TGC      15
Leu L TTA      40 |       TCA      18 | *** * TAA       0 | *** * TGA       0
      TTG      43 |       TCG      34 |       TAG       0 | Trp W TGG      95
------------------------------------------------------------------------------
Leu L CTT      27 | Pro P CCT       5 | His H CAT      19 | Arg R CGT      45
      CTC      29 |       CCC      10 |       CAC      15 |       CGC      30
      CTA       9 |       CCA      17 | Gln Q CAA      15 |       CGA       4
      CTG     132 |       CCG      43 |       CAG      25 |       CGG      21
------------------------------------------------------------------------------
Ile I ATT      77 | Thr T ACT       7 | Asn N AAT      26 | Ser S AGT       5
      ATC      58 |       ACC      39 |       AAC      49 |       AGC      28
      ATA       8 |       ACA       7 | Lys K AAA      39 | Arg R AGA       0
Met M ATG      72 |       ACG      52 |       AAG       6 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       9 | Ala A GCT      29 | Asp D GAT      39 | Gly G GGT      57
      GTC      56 |       GCC      80 |       GAC      16 |       GGC      94
      GTA      12 |       GCA      46 | Glu E GAA      35 |       GGA      16
      GTG      68 |       GCG     129 |       GAG      25 |       GGG      53
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.23326    C:0.20319    A:0.21549    G:0.34806
position  2:    T:0.35763    C:0.24692    A:0.17768    G:0.21777
position  3:    T:0.24009    C:0.27517    A:0.12118    G:0.36355

Codon frequencies under model, for use in evolver:
  0.02056824  0.02357347  0.01038169  0.03114508
  0.01420126  0.01627620  0.00716800  0.02150399
  0.01021862  0.01171166  0.00000000  0.00000000
  0.01252435  0.01435429  0.00000000  0.01896477
  0.01791686  0.02053470  0.00904343  0.02713028
  0.01237062  0.01417810  0.00624400  0.01873199
  0.00890137  0.01020195  0.00449291  0.01347874
  0.01090989  0.01250393  0.00550670  0.01652009
  0.01900152  0.02177783  0.00959090  0.02877270
  0.01311952  0.01503641  0.00662200  0.01986599
  0.00944024  0.01081956  0.00476491  0.01429472
  0.01157035  0.01326090  0.00584006  0.01752019
  0.03069167  0.03517603  0.01549143  0.04647429
  0.02119094  0.02428714  0.01069599  0.03208798
  0.01524809  0.01747599  0.00769638  0.02308914
  0.01868869  0.02141929  0.00943300  0.02829900



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               0.0883 (0.0041 0.0462)
Shig4337             0.0948 (0.0041 0.0431) 0.0000 (0.0000 0.0030)
CFT073               0.0363 (0.0041 0.1125) 0.0175 (0.0020 0.1164) 0.0180 (0.0020 0.1129)
O157                 0.0193 (0.0020 0.1055) 0.0386 (0.0041 0.1059) 0.0399 (0.0041 0.1024) 0.0176 (0.0020 0.1161)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 65
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  8  np: 13):  -2120.806513     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.11437  0.06751  0.07155  0.00272  0.00000  0.00000  0.17535  0.14163  4.73282  0.99771  0.00000  0.01926 505.29019
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.57313

((1: 0.067512, (2: 0.002716, 3: 0.000004): 0.071553): 0.114365, (4: 0.175350, 5: 0.141630): 0.000000);

((K12: 0.067512, (S2457T: 0.002716, Shig4337: 0.000004): 0.071553): 0.114365, (CFT073: 0.175350, O157: 0.141630): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  4.73282


dN/dS for site classes (K=3)

p:   0.99771  0.00000  0.00229
w:   0.01926  1.00000505.29019

dN & dS for each branch

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

   6..7       0.114    386.6    930.4   1.1771   0.0399   0.0339   13.1   37.1
   7..1       0.068    386.6    930.4   1.1771   0.0235   0.0200    7.7   21.9
   7..8       0.072    386.6    930.4   1.1771   0.0250   0.0212    8.2   23.2
   8..2       0.003    386.6    930.4   1.1771   0.0009   0.0008    0.3    0.9
   8..3       0.000    386.6    930.4   1.1771   0.0000   0.0000    0.0    0.0
   6..9       0.000    386.6    930.4   1.1771   0.0000   0.0000    0.0    0.0
   9..4       0.175    386.6    930.4   1.1771   0.0612   0.0520   20.1   56.9
   9..5       0.142    386.6    930.4   1.1771   0.0494   0.0420   16.2   46.0


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

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

   177 A      1.000**       505.290


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

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

   177 A      0.919         3.347 +- 2.443



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:   0.393  0.211  0.119  0.074  0.052  0.040  0.033  0.029  0.026  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 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 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
