
seed used = 140022809

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3645.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 274
# site patterns = 136
    3    4   12    6    8    2    7    3    2    1    1    1    1    1    1
    1    1    1    1    4    1    2    1    1    1    1    1    7    1    4
    1    1    1    1    1    1    1    5    1    1    2    2    1    1    1
    1    1    1    1    1    1    1    4    2    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    3    1    2
    1    2    2    1    4    9    3    1    3    2    2    1    1    1    3
   10    6    2    2    6    1    5    5    1    1    1    2    2    8    1
    4    3    1    1    1    1    5    1    4    1    1    2    1    1    1
    1    1    1    1    1    3    1    1    1    1    1    1    1    1    1
    1

1       
K12                   ATG AAC GAA CAT CAA CCT TTT GAG ATA AAA CTG ATT AAT GCA AAC GGA GCA CAA TGG TCA GCA AGA CAA CTT GGG AAA CTA CTG GGT TAT TCA GAG TAT CGT CAC ATA CCT GTA TTA ACG CGC GCC AAA GAA TGT AAC AGT GGT CAC ACA ATT GAT GAC TTC GAG ATC CTC GAT GTC AAA ATT GGC AAT GCC AAA AGA GCA TTA AAA GAC ATC GTA CTC TCC GCC TGT TAC GGC CCT GCG AAA CCG GTC ATT GCA GGG CAG ACT GCT ATC CAG ACC CGA CGG GAG CTT GCT GAT GCA TTT AAG CTT CGT AAG CTG AAT TTG TTG GTT GCA GGG ACA ACT GGT CAG GGG GGA TTA GCT ATT CAT CAG CGG AAT GGC GTG GCA AAC CAC GAC CGC AGG ATG GTC AGC AGT 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..C ..C ..A .T. .G. A.. ... ..T ..T ... ... A.. ... ..A ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..C ..C ..A .T. .G. A.. ... ..T ..T ... ... A.. ... ..A ... ... ... 
CFT073                ... ... ... ... ... ... ... ..A ... CGG .AT TA. GGC A.T G.A ..G CA. TTT ... ... ..G ... G.. T.G .CA CCG T.. ... .A. ... CGG ..C .GG ..C A.T CA. AAG ... C.G G.C ... ..G .CT C.. ..C GC. ..C AA. ..A G.C GCA TC. ... ... .TT .C. AC. A.A ..T GT. T.A ..T GGG ..T C.. C.. .A. C.T G.. ..T G.T CAT ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ..A ... ... ... ... ... ... ... ... ..G ... ... ..T ..C .G. ... ... ... ..T ... ... ..A ... ..G ... ... .TC ... .G. ..A ... ... ..C ..C ... ... ... .G. ... ... ..T ..T ... ... ... ... ... ... ... ... 
O157                  ... ... ... ... ... ... ... ..A ... CGG .AT TA. GGC A.T G.A ..G CA. TTT ... ... ..T ... G.. T.G .CA CCG T.. ... .A. ... CGG ..C .GG ..C A.T CA. AAG ... C.G G.C ... ..G .CT C.. ..C GC. ..C AA. ..A G.T GCA TC. ... ... .TT .C. AC. A.A ..T GT. T.A ..T GGG ..T C.. C.. .A. C.T G.. ..T G.T CAT ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ..C ..C ..C ..A .T. .G. ... ... ..T ..T ... ..T A.. ... ... ... ... ... 
EDL933                ... ... ... ... ... ... ... ..A ... CGG .AT TA. GGC A.T G.A ..G CA. TTT ... ... ..T ... G.. T.G .CA CCG T.. ... .A. ... CGG ..C .GG ..C A.T CA. AAG ... C.G G.C ... ..G .CT C.. ..C GC. ..C AA. ..A G.T GCA TC. ... ... .TT .C. AC. A.A ..T GT. T.A ..T GGG ..T C.. C.. .A. C.T G.. ..T G.T CAT ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ..C ..C ..C ..A .T. .G. ... ... ..T ..T ... ..T A.. ... ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.12044    C:0.25182    A:0.28832    G:0.33942
position  2:    T:0.24453    C:0.19343    A:0.41971    G:0.14234
position  3:    T:0.26277    C:0.18978    A:0.28832    G:0.25912

#2: S2457T         
position  1:    T:0.12044    C:0.24818    A:0.29927    G:0.33212
position  2:    T:0.24818    C:0.19343    A:0.41606    G:0.14234
position  3:    T:0.25547    C:0.20073    A:0.28832    G:0.25547

#3: Shig4337       
position  1:    T:0.12044    C:0.24818    A:0.29927    G:0.33212
position  2:    T:0.24818    C:0.19343    A:0.41606    G:0.14234
position  3:    T:0.25547    C:0.20073    A:0.28832    G:0.25547

#4: CFT073         
position  1:    T:0.13139    C:0.26642    A:0.24818    G:0.35401
position  2:    T:0.23358    C:0.20438    A:0.40146    G:0.16058
position  3:    T:0.27007    C:0.18613    A:0.27737    G:0.26642

#5: O157           
position  1:    T:0.13139    C:0.26277    A:0.25182    G:0.35401
position  2:    T:0.23358    C:0.21168    A:0.40876    G:0.14599
position  3:    T:0.27737    C:0.17883    A:0.27737    G:0.26642

#6: EDL933         
position  1:    T:0.13139    C:0.26277    A:0.25182    G:0.35401
position  2:    T:0.23358    C:0.21168    A:0.40876    G:0.14599
position  3:    T:0.27737    C:0.17883    A:0.27737    G:0.26642

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      50 | Ser S TCT       3 | Tyr Y TAT      30 | Cys C TGT       9
      TTC      13 |       TCC       6 |       TAC      12 |       TGC       3
Leu L TTA      19 |       TCA      27 | *** * TAA       0 | *** * TGA       0
      TTG      26 |       TCG       0 |       TAG       0 | Trp W TGG       9
------------------------------------------------------------------------------
Leu L CTT      24 | Pro P CCT      19 | His H CAT      44 | Arg R CGT      15
      CTC      21 |       CCC       2 |       CAC      16 |       CGC      17
      CTA       3 |       CCA       0 | Gln Q CAA      74 |       CGA      15
      CTG      58 |       CCG      21 |       CAG      72 |       CGG      21
------------------------------------------------------------------------------
Ile I ATT      28 | Thr T ACT      19 | Asn N AAT      42 | Ser S AGT      14
      ATC      30 |       ACC      42 |       AAC      31 |       AGC      15
      ATA      17 |       ACA      33 | Lys K AAA      75 | Arg R AGA      15
Met M ATG      22 |       ACG       3 |       AAG      56 |       AGG       7
------------------------------------------------------------------------------
Val V GTT      16 | Ala A GCT      48 | Asp D GAT      44 | Gly G GGT      33
      GTC      14 |       GCC      33 |       GAC      34 |       GGC      22
      GTA      36 |       GCA      41 | Glu E GAA      94 |       GGA      16
      GTG      18 |       GCG      34 |       GAG      53 |       GGG      30
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12591    C:0.25669    A:0.27311    G:0.34428
position  2:    T:0.24027    C:0.20134    A:0.41180    G:0.14659
position  3:    T:0.26642    C:0.18917    A:0.28285    G:0.26156

Codon frequencies under model, for use in evolver:
  0.00833895  0.00592103  0.00885299  0.00818664
  0.00698783  0.00496167  0.00741858  0.00686019
  0.01429232  0.01014820  0.00000000  0.00000000
  0.00508781  0.00361258  0.00000000  0.00499488
  0.01700017  0.01207090  0.01804812  0.01668966
  0.01424571  0.01011511  0.01512387  0.01398552
  0.02913700  0.02068860  0.03093311  0.02860482
  0.01037226  0.00736477  0.01101164  0.01018281
  0.01808786  0.01284320  0.01920286  0.01775749
  0.01515717  0.01076228  0.01609151  0.01488032
  0.03100121  0.02201228  0.03291225  0.03043498
  0.01103588  0.00783598  0.01171618  0.01083431
  0.02280117  0.01618988  0.02420673  0.02238471
  0.01910681  0.01356671  0.02028462  0.01875782
  0.03907948  0.02774822  0.04148849  0.03836570
  0.01391160  0.00987787  0.01476917  0.01365751



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               0.2162 (0.0095 0.0440)
Shig4337             0.2162 (0.0095 0.0440)-1.0000 (0.0000 0.0000)
CFT073               0.3662 (0.1172 0.3202) 0.3883 (0.1246 0.3209) 0.3883 (0.1246 0.3209)
O157                 0.4384 (0.1171 0.2670) 0.4919 (0.1170 0.2378) 0.4919 (0.1170 0.2378) 0.1147 (0.0096 0.0833)
EDL933               0.4384 (0.1171 0.2670) 0.4919 (0.1170 0.2378) 0.4919 (0.1170 0.2378) 0.1147 (0.0096 0.0833)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 92
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1672.091183     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.09539  0.04094  0.01121  0.00000  0.00000  0.44346  0.08343  0.00000  0.00000  0.00000  2.12856  0.76308  0.00000  0.00000  2.48376
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.67446

((1: 0.040941, (2: 0.000004, 3: 0.000004): 0.011215): 0.095393, (4: 0.083433, (5: 0.000004, 6: 0.000004): 0.000000): 0.443464);

((K12: 0.040941, (S2457T: 0.000004, Shig4337: 0.000004): 0.011215): 0.095393, (CFT073: 0.083433, (O157: 0.000004, EDL933: 0.000004): 0.000000): 0.443464);

Detailed output identifying parameters

kappa (ts/tv) =  2.12856


dN/dS for site classes (K=3)

p:   0.76308  0.00000  0.23692
w:   0.00000  1.00000  2.48376

dN & dS for each branch

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

   7..8       0.095    215.1    606.9   0.5885   0.0269   0.0457    9.8   16.3
   8..1       0.041    215.1    606.9   0.5885   0.0115   0.0196    4.2    7.0
   8..9       0.011    215.1    606.9   0.5885   0.0032   0.0054    1.2    1.9
   9..2       0.000    215.1    606.9   0.5885   0.0000   0.0000    0.0    0.0
   9..3       0.000    215.1    606.9   0.5885   0.0000   0.0000    0.0    0.0
   7..10      0.443    215.1    606.9   0.5885   0.1250   0.2123   45.7   75.8
  10..4       0.083    215.1    606.9   0.5885   0.0235   0.0399    8.6   14.3
  10..11      0.000    215.1    606.9   0.5885   0.0000   0.0000    0.0    0.0
  11..5       0.000    215.1    606.9   0.5885   0.0000   0.0000    0.0    0.0
  11..6       0.000    215.1    606.9   0.5885   0.0000   0.0000    0.0    0.0


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

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

    12 K      1.000**       2.484
    13 L      1.000**       2.484
    14 I      1.000**       2.484
    15 N      1.000**       2.484
    16 A      1.000**       2.484
    17 N      1.000**       2.484
    19 A      1.000**       2.484
    21 Q      1.000**       2.484
    26 Q      1.000**       2.484
    28 G      1.000**       2.484
    29 K      1.000**       2.484
    32 G      1.000**       2.484
    34 S      1.000**       2.484
    35 E      1.000**       2.484
    36 Y      1.000**       2.484
    38 H      1.000**       2.484
    40 I      1.000**       2.484
    41 P      1.000**       2.484
    44 T      1.000**       2.484
    47 K      1.000**       2.484
    48 E      1.000**       2.484
    52 N      1.000**       2.484
    54 G      1.000**       2.484
    55 H      1.000**       2.484
    56 T      1.000**       2.484
    57 I      1.000**       2.484
    58 D      1.000**       2.484
    62 E      1.000**       2.484
    64 I      1.000**       2.484
    65 L      1.000**       2.484
    66 D      1.000**       2.484
    69 K      1.000**       2.484
    70 I      1.000**       2.484
    73 N      1.000**       2.484
    75 K      1.000**       2.484
    77 A      1.000**       2.484
    79 K      1.000**       2.484
    81 I      1.000**       2.484
    82 V      1.000**       2.484
   110 A      1.000**       2.484
   125 K      1.000**       2.484
   155 G      1.000**       2.484
   160 T      1.000**       2.484
   171 Q      1.000**       2.484
   185 R      1.000**       2.484
   191 N      1.000**       2.484
   221 G      1.000**       2.484
   237 R      1.000**       2.484
   250 M      1.000**       2.484


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

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

    12 K      0.840         2.989 +- 1.230
    13 L      0.764         2.754 +- 1.338
    14 I      0.873         3.088 +- 1.134
    15 N      0.842         3.004 +- 1.176
    16 A      0.529         2.003 +- 1.532
    17 N      0.766         2.781 +- 1.239
    19 A      0.858         3.045 +- 1.153
    21 Q      0.938         3.272 +- 1.030
    28 G      0.595         2.213 +- 1.505
    29 K      0.885         3.126 +- 1.124
    34 S      0.908         3.192 +- 1.089
    36 Y      0.891         3.145 +- 1.113
    38 H      0.541         2.037 +- 1.535
    40 I      0.850         3.024 +- 1.161
    41 P      0.937         3.269 +- 1.030
    44 T      0.576         2.155 +- 1.527
    47 K      0.750         2.712 +- 1.355
    52 N      0.858         3.048 +- 1.153
    54 G      0.779         2.816 +- 1.228
    56 T      0.534         2.022 +- 1.533
    57 I      0.868         3.078 +- 1.147
    58 D      0.876         3.098 +- 1.131
    62 E      0.729         2.646 +- 1.377
    64 I      0.582         2.168 +- 1.505
    65 L      0.901         3.172 +- 1.097
    66 D      0.742         2.713 +- 1.256
    69 K      0.817         2.928 +- 1.196
    70 I      0.756         2.726 +- 1.391
    73 N      0.905         3.174 +- 1.075
    81 I      0.536         2.020 +- 1.516
    82 V      0.925         3.234 +- 1.050
   110 A      0.676         2.473 +- 1.460
   155 G      0.879         3.107 +- 1.128
   160 T      0.521         1.973 +- 1.513
   185 R      0.894         3.154 +- 1.111
   221 G      0.670         2.453 +- 1.465
   237 R      0.866         3.070 +- 1.143
   250 M      0.525         1.989 +- 1.501



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:   0.983  0.017  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.007  0.323  0.468  0.157  0.033  0.008  0.002  0.001  0.000  0.000

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 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.006 0.016 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.019 0.184 0.037 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005 0.128 0.375 0.219 0.002 0.000

sum of density on p0-p1 =   1.000000
