
seed used = 140009353

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2244.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 316
# site patterns = 120
    9   11   16    3    3    4    4    8   10    1    1   10    4    1    3
    2    2    6    1    2    1    2    1    1   12    6    4    3    3    2
   10    4    1    2   10    5    6    2    2    6    3    6    2    1    2
    7    6    5    5    1    3    1    5    3    5    1    1    1    1    3
    1    1    1    1    1    4    1    1    1    1    4    1    1    1    1
    1    1    1    3    1    1    1    1    1    1    1    1    2    1    1
    1    1    1    2    1    1    1    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 ACC GAA TCA ACA TCC CCG CAT GAT GCG GTA TTT AAA ATG TTC CCC GCA CGG CTC ATA TTA CCA GAA CCA CTG CGC AAG CTT TGC AAC CAA TTA ACT AGT ATT GCT TAC TCG GTT TTG TGG GTG AGC GAC GGT GAC GGC TAT ATC TCT AAT CTA GCC ACT CAG CGT CAC CAG GAC AGA GTC CCG ACC CCT CTC GAG CTG ATC GTA CCT CGT CTG CGC GGC GTC AGG ACG AGC CTA CGT GAG GGG GGC CAG --- --- --- --- --- --- --- --- --- --- --- --- --- --- GCC GCT GAG TTT GAA GAG ATT CTG GCG ACA ACC CAA CTC ACT GAT GCT ATT CCG --- AAC TGT CAT 
S2457T                               ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... A.. ... .TA ..T ... ..T ..A ..A ..C ..T ... .C. ... ... ... ... ... .A. ... ... ... ... ... ... ... C.. ..A ... ..A AAA TTA GTA GGT TTG CAG CAA AAA TTA GAA GGT TTG CAG GGT ... ... ..A A.. ..T ..C CAA ..C ... G.C ... ..G ..A .GC ..A ..C C.G G.A GCG ..T AAC ..C 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... A.. ... .TA ..T ... ..T ..A ..A ..C ..T ... .C. ... ... ... ... ... .A. ... ... ... ... ... ... ... C.. ..A ... ..A AAA TTA GTA GGT TTG CAG CAA AAA TTA GAA GGT TTG CAG GGT ... ... ..A A.. ..T ..C CAA ..C ... G.C ... ..G ..A .GC ..A ..C C.G G.A GCG ..T AAC ..C 
CFT073                               ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ..G ... C.. ... ..G ..G ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ..T ... ..T ..A G.. ..C ... ... .C. ... ... ... ... ... ... ..T ... ... ... ..T ... ..C C.. ..A ... ... --- --- --- --- --- --- --- AAA TTA GAA GGT TTG CAG GGC ... ... ... A.. ..T ..C CAG ..C ... G.C ..T ..G ..A .GC ..A ..C C.G G.A GCG ..T AAC ..C 
O157                                 ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ..C ... ... .C. ..T ... ... ... ..T ... ..T ... ... ... ... ... ... C.. ..A ..T ... --- --- --- --- --- --- --- AAA TTA GAA GGT TTG CAG GGC ..T ..C ..A ... ..T ..C C.G ..C ... G.C ... ..G ..A .GC ..A ..C C.G G.A GCG ..T AAC ..C 
EDL933                               ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ..C ... ... .C. ..T ... ... ... ..T ... ..T ... ... ... ... ... ... C.. ..A ..T ... --- --- --- --- --- --- --- AAA TTA GAA GGT TTG CAG GGC ..T ..C ..A ... ..T ..C C.G ..C ... G.C ... ..G ..A .GC ..A ..C C.G G.A GCG ..T AAC ..C 



Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 11 10 10 10 11 11 | Ser TCT  1  1  1  1  1  1 | Tyr TAT  5  5  5  5  5  5 | Cys TGT  1  0  0  0  0  0
    TTC  3  3  3  3  3  3 |     TCC  4  4  4  4  4  4 |     TAC  6  6  6  6  6  6 |     TGC  3  3  3  3  3  3
Leu TTA  5  7  7  5  6  6 |     TCA  3  3  3  3  3  3 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  6  8  8  7  7  7 |     TCG  2  2  2  2  2  2 |     TAG  0  0  0  0  0  0 | Trp TGG  3  3  3  3  3  3
--------------------------------------------------------------------------------------------------------------
Leu CTT  3  4  4  3  4  4 | Pro CCT  2  1  1  1  1  1 | His CAT  9  8  8  8  8  8 | Arg CGT  6  5  5  5  6  6
    CTC  3  2  2  2  3  3 |     CCC  2  3  3  3  3  3 |     CAC  1  3  3  2  2  2 |     CGC  7  6  6  8  7  7
    CTA  4  5  5  6  5  5 |     CCA  3  5  5  3  3  3 | Gln CAA 11 13 13 10 10 10 |     CGA  0  0  0  0  0  0
    CTG 15 14 14 16 15 15 |     CCG  6  5  5  6  6  6 |     CAG  7  9  9 10  9  9 |     CGG  6  6  6  6  6  6
--------------------------------------------------------------------------------------------------------------
Ile ATT 12 11 11 11 11 11 | Thr ACT  5  4  4  4  4  4 | Asn AAT  3  4  4  4  4  4 | Ser AGT  2  3  3  3  2  2
    ATC  6  6  6  6  5  5 |     ACC 13 12 12 12 13 13 |     AAC  3  3  3  3  3  3 |     AGC  3  4  4  3  4  4
    ATA  2  3  3  2  2  2 |     ACA  4  4  4  3  3  3 | Lys AAA  4  6  6  5  5  5 | Arg AGA  3  3  3  3  3  3
Met ATG 10  9  9 10 10 10 |     ACG  1  1  1  1  1  1 |     AAG  4  4  4  4  4  4 |     AGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------
Val GTT  2  3  3  3  2  2 | Ala GCT  7  6  6  6  6  6 | Asp GAT 11 12 12 12 11 11 | Gly GGT  2  6  6  4  5  5
    GTC  2  1  1  1  2  2 |     GCC  6  8  8  9  8  8 |     GAC  9  9  9  8 10 10 |     GGC  8  8  8  8  7  7
    GTA  2  3  3  1  2  2 |     GCA  2  3  3  3  4  4 | Glu GAA 18 21 21 19 21 21 |     GGA  0  1  1  1  1  1
    GTG  6  6  6  7  6  6 |     GCG  2  3  3  3  2  2 |     GAG  7  4  4  7  4  4 |     GGG  1  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.17726    C:0.28428    A:0.25418    G:0.28428
position  2:    T:0.30769    C:0.21070    A:0.32776    G:0.15385
position  3:    T:0.27425    C:0.26421    A:0.20401    G:0.25753

#2: S2457T         
position  1:    T:0.17405    C:0.28165    A:0.24684    G:0.29747
position  2:    T:0.30063    C:0.20570    A:0.33861    G:0.15506
position  3:    T:0.26266    C:0.25633    A:0.24367    G:0.23734

#3: Shig4337       
position  1:    T:0.17405    C:0.28165    A:0.24684    G:0.29747
position  2:    T:0.30063    C:0.20570    A:0.33861    G:0.15506
position  3:    T:0.26266    C:0.25633    A:0.24367    G:0.23734

#4: CFT073         
position  1:    T:0.16883    C:0.28896    A:0.24351    G:0.29870
position  2:    T:0.30195    C:0.20779    A:0.33442    G:0.15584
position  3:    T:0.25974    C:0.26299    A:0.20779    G:0.26948

#5: O157           
position  1:    T:0.17532    C:0.28571    A:0.24351    G:0.29545
position  2:    T:0.30519    C:0.20779    A:0.33117    G:0.15584
position  3:    T:0.26299    C:0.26948    A:0.22078    G:0.24675

#6: EDL933         
position  1:    T:0.17532    C:0.28571    A:0.24351    G:0.29545
position  2:    T:0.30519    C:0.20779    A:0.33117    G:0.15584
position  3:    T:0.26299    C:0.26948    A:0.22078    G:0.24675

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      63 | Ser S TCT       6 | Tyr Y TAT      30 | Cys C TGT       1
      TTC      18 |       TCC      24 |       TAC      36 |       TGC      18
Leu L TTA      36 |       TCA      18 | *** * TAA       0 | *** * TGA       0
      TTG      43 |       TCG      12 |       TAG       0 | Trp W TGG      18
------------------------------------------------------------------------------
Leu L CTT      22 | Pro P CCT       7 | His H CAT      49 | Arg R CGT      33
      CTC      15 |       CCC      17 |       CAC      13 |       CGC      41
      CTA      30 |       CCA      22 | Gln Q CAA      67 |       CGA       0
      CTG      89 |       CCG      34 |       CAG      53 |       CGG      36
------------------------------------------------------------------------------
Ile I ATT      67 | Thr T ACT      25 | Asn N AAT      23 | Ser S AGT      15
      ATC      34 |       ACC      75 |       AAC      18 |       AGC      22
      ATA      14 |       ACA      21 | Lys K AAA      31 | Arg R AGA      18
Met M ATG      58 |       ACG       6 |       AAG      24 |       AGG       6
------------------------------------------------------------------------------
Val V GTT      15 | Ala A GCT      37 | Asp D GAT      69 | Gly G GGT      28
      GTC       9 |       GCC      47 |       GAC      55 |       GGC      46
      GTA      13 |       GCA      19 | Glu E GAA     121 |       GGA       5
      GTG      37 |       GCG      15 |       GAG      30 |       GGG       1
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.17412    C:0.28464    A:0.24636    G:0.29488
position  2:    T:0.30350    C:0.20755    A:0.33369    G:0.15526
position  3:    T:0.26415    C:0.26307    A:0.22372    G:0.24906

Codon frequencies under model, for use in evolver:
  0.01444380  0.01438485  0.01223302  0.01361844
  0.00987720  0.00983689  0.00836538  0.00931279
  0.01588049  0.01581567  0.00000000  0.00000000
  0.00738866  0.00735850  0.00000000  0.00696645
  0.02361092  0.02351455  0.01999701  0.02226173
  0.01614601  0.01608011  0.01367468  0.01522338
  0.02595943  0.02585348  0.02198605  0.02447604
  0.01207806  0.01202876  0.01022937  0.01138788
  0.02043597  0.02035256  0.01730801  0.01926820
  0.01397486  0.01391782  0.01183585  0.01317630
  0.02246868  0.02237697  0.01902959  0.02118475
  0.01045392  0.01041125  0.00885383  0.00985656
  0.02446056  0.02436072  0.02071659  0.02306281
  0.01672702  0.01665875  0.01416677  0.01577119
  0.02689358  0.02678381  0.02277722  0.02535680
  0.01251268  0.01246161  0.01059748  0.01179767



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                 
S2457T               0.2774 (0.0297 0.1071)
Shig4337             0.2774 (0.0297 0.1071)-1.0000 (0.0000 0.0000)
CFT073               0.2056 (0.0272 0.1325) 0.1034 (0.0085 0.0826) 0.1034 (0.0085 0.0826)
O157                 0.1938 (0.0207 0.1068) 0.1100 (0.0085 0.0776) 0.1100 (0.0085 0.0776) 0.0614 (0.0057 0.0926)
EDL933               0.1938 (0.0207 0.1068) 0.1100 (0.0085 0.0776) 0.1100 (0.0085 0.0776) 0.0614 (0.0057 0.0926)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1636.118948     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00976  0.67378  0.23567  0.00000  0.00000  0.00418  0.29183  0.19114  0.00000  0.00000  2.81848  0.81939  0.17734  0.02138 998.99997
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.40636

((1: 0.673776, (2: 0.000004, 3: 0.000004): 0.235666): 0.009760, (4: 0.291827, (5: 0.000004, 6: 0.000004): 0.191136): 0.004183);

((K12: 0.673776, (S2457T: 0.000004, Shig4337: 0.000004): 0.235666): 0.009760, (CFT073: 0.291827, (O157: 0.000004, EDL933: 0.000004): 0.191136): 0.004183);

Detailed output identifying parameters

kappa (ts/tv) =  2.81848


dN/dS for site classes (K=3)

p:   0.81939  0.17734  0.00327
w:   0.02138  1.00000998.99997

dN & dS for each branch

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

   7..8       0.010    276.2    671.8   3.4634   0.0041   0.0012    0.3    2.8
   8..1       0.674    276.2    671.8   3.4634   0.2833   0.0818   22.6  190.3
   8..9       0.236    276.2    671.8   3.4634   0.0991   0.0286    7.9   66.6
   9..2       0.000    276.2    671.8   3.4634   0.0000   0.0000    0.0    0.0
   9..3       0.000    276.2    671.8   3.4634   0.0000   0.0000    0.0    0.0
   7..10      0.004    276.2    671.8   3.4634   0.0018   0.0005    0.1    1.2
  10..4       0.292    276.2    671.8   3.4634   0.1227   0.0354    9.8   82.4
  10..11      0.191    276.2    671.8   3.4634   0.0804   0.0232    6.4   54.0
  11..5       0.000    276.2    671.8   3.4634   0.0000   0.0000    0.0    0.0
  11..6       0.000    276.2    671.8   3.4634   0.0000   0.0000    0.0    0.0


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

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

   299 I      0.991**       990.202


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

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

   295 F      0.735         3.997 +- 2.738
   299 I      0.957*        4.936 +- 2.432
   311 I      0.550         3.077 +- 2.834
   315 C      0.731         3.980 +- 2.740



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:   0.705  0.289  0.006  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.084  0.138  0.171  0.163  0.134  0.102  0.076  0.056  0.042  0.032

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 0.016
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.009 0.307
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.020 0.117 0.528

sum of density on p0-p1 =   1.000000
