
seed used = 140022357

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3621.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 309
# site patterns = 106
    2    7   10    8    2    1    5    2    2    9    1    9    8    4    1
    1    7    3    7    4    8    5   16    6    2    3    1    4    7    2
    3    3    4    6   11    2    1    1    1    7    1    3    1    2    7
    1   12    6    4    1    1    1    1    8    1    1    5    1    5    1
    3    1    1    2    1    1    1    2    1    1    1    5    2    2    1
    4    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    1    1
    1

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

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

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

#1: K12            
position  1:    T:0.14887    C:0.24919    A:0.22006    G:0.38188
position  2:    T:0.26537    C:0.24595    A:0.30421    G:0.18447
position  3:    T:0.26537    C:0.19094    A:0.25243    G:0.29126

#2: S2457T         
position  1:    T:0.15210    C:0.25566    A:0.20712    G:0.38511
position  2:    T:0.26214    C:0.25243    A:0.30421    G:0.18123
position  3:    T:0.29126    C:0.18123    A:0.25243    G:0.27508

#3: Shig4337       
position  1:    T:0.15210    C:0.25566    A:0.20712    G:0.38511
position  2:    T:0.26214    C:0.25243    A:0.30421    G:0.18123
position  3:    T:0.29126    C:0.18123    A:0.25243    G:0.27508

#4: CFT073         
position  1:    T:0.13592    C:0.25566    A:0.22006    G:0.38835
position  2:    T:0.25890    C:0.24919    A:0.31068    G:0.18123
position  3:    T:0.26861    C:0.19094    A:0.25243    G:0.28803

#5: O157           
position  1:    T:0.14563    C:0.25890    A:0.20712    G:0.38835
position  2:    T:0.26214    C:0.25243    A:0.30744    G:0.17799
position  3:    T:0.29773    C:0.18123    A:0.24919    G:0.27184

#6: EDL933         
position  1:    T:0.14563    C:0.25890    A:0.20712    G:0.38835
position  2:    T:0.26214    C:0.25243    A:0.30744    G:0.17799
position  3:    T:0.29773    C:0.18123    A:0.24919    G:0.27184

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      51 | Ser S TCT       9 | Tyr Y TAT      42 | Cys C TGT       8
      TTC      14 |       TCC       6 |       TAC       6 |       TGC       0
Leu L TTA      37 |       TCA       8 | *** * TAA       0 | *** * TGA       0
      TTG      31 |       TCG      12 |       TAG       0 | Trp W TGG      48
------------------------------------------------------------------------------
Leu L CTT      20 | Pro P CCT      26 | His H CAT      53 | Arg R CGT      37
      CTC      13 |       CCC      16 |       CAC      25 |       CGC      36
      CTA       6 |       CCA      17 | Gln Q CAA      33 |       CGA      19
      CTG      74 |       CCG      37 |       CAG      50 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      44 | Thr T ACT       6 | Asn N AAT      29 | Ser S AGT      17
      ATC      24 |       ACC      34 |       AAC      15 |       AGC      24
      ATA      18 |       ACA      14 | Lys K AAA      67 | Arg R AGA       7
Met M ATG      22 |       ACG      39 |       AAG      30 |       AGG       2
------------------------------------------------------------------------------
Val V GTT      51 | Ala A GCT      60 | Asp D GAT      64 | Gly G GGT      12
      GTC       0 |       GCC      60 |       GAC      24 |       GGC      45
      GTA      42 |       GCA      65 | Glu E GAA     106 |       GGA      27
      GTG      39 |       GCG      56 |       GAG      24 |       GGG      41
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14671    C:0.25566    A:0.21143    G:0.38619
position  2:    T:0.26214    C:0.25081    A:0.30636    G:0.18069
position  3:    T:0.28533    C:0.18447    A:0.25135    G:0.27886

Codon frequencies under model, for use in evolver:
  0.01131830  0.00731731  0.00997037  0.01106155
  0.01082924  0.00700113  0.00953955  0.01058358
  0.01322797  0.00855192  0.00000000  0.00000000
  0.00780171  0.00504383  0.00000000  0.00762473
  0.01972380  0.01275149  0.01737484  0.01927638
  0.01887154  0.01220050  0.01662408  0.01844345
  0.02305168  0.01490298  0.02030640  0.02252877
  0.01359562  0.00878961  0.01197648  0.01328722
  0.01631167  0.01054554  0.01436907  0.01594165
  0.01560684  0.01008987  0.01374818  0.01525281
  0.01906384  0.01232483  0.01679348  0.01863139
  0.01124364  0.00726904  0.00990460  0.01098858
  0.02979376  0.01926175  0.02624554  0.02911791
  0.02850637  0.01842945  0.02511147  0.02785972
  0.03482069  0.02251167  0.03067380  0.03403080
  0.02053685  0.01327713  0.01809106  0.02007098



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               0.6803 (0.0481 0.0708)
Shig4337             0.6803 (0.0481 0.0708)-1.0000 (0.0000 0.0000)
CFT073               0.4066 (0.0459 0.1128) 0.4156 (0.0534 0.1285) 0.4156 (0.0534 0.1285)
O157                 0.6351 (0.0481 0.0758) 0.1834 (0.0057 0.0313) 0.1834 (0.0057 0.0313) 0.3692 (0.0534 0.1445)
EDL933               0.6351 (0.0481 0.0758) 0.1834 (0.0057 0.0313) 0.1834 (0.0057 0.0313) 0.3692 (0.0534 0.1445)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 71
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 10  np: 15):  -1715.066279     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.31598  0.01647  0.00000  0.00000  0.00000  0.78779  0.02193  0.00000  0.00000  1.75953  0.87277  0.05844  0.02853 56.37370
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.14219

((1: 0.315982, (2: 0.000004, 3: 0.000004): 0.016469): 0.000000, (4: 0.787794, (5: 0.000004, 6: 0.000004): 0.021932): 0.000000);

((K12: 0.315982, (S2457T: 0.000004, Shig4337: 0.000004): 0.016469): 0.000000, (CFT073: 0.787794, (O157: 0.000004, EDL933: 0.000004): 0.021932): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  1.75953


dN/dS for site classes (K=3)

p:   0.87277  0.05844  0.06879
w:   0.02853  1.00000 56.37370

dN & dS for each branch

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

   7..8       0.000    260.2    666.8   3.9611   0.0000   0.0000    0.0    0.0
   8..1       0.316    260.2    666.8   3.9611   0.1333   0.0337    8.8   88.9
   8..9       0.016    260.2    666.8   3.9611   0.0069   0.0018    0.5    4.6
   9..2       0.000    260.2    666.8   3.9611   0.0000   0.0000    0.0    0.0
   9..3       0.000    260.2    666.8   3.9611   0.0000   0.0000    0.0    0.0
   7..10      0.000    260.2    666.8   3.9611   0.0000   0.0000    0.0    0.0
  10..4       0.788    260.2    666.8   3.9611   0.3323   0.0839   21.8  221.6
  10..11      0.022    260.2    666.8   3.9611   0.0093   0.0023    0.6    6.2
  11..5       0.000    260.2    666.8   3.9611   0.0000   0.0000    0.0    0.0
  11..6       0.000    260.2    666.8   3.9611   0.0000   0.0000    0.0    0.0


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

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

   285 M      0.997**       56.184
   286 V      0.997**       56.226
   288 R      0.999**       56.320
   289 A      0.914         51.586
   290 P      0.988*        55.689
   291 R      0.983*        55.409
   292 E      1.000**       56.373
   293 N      1.000**       56.374
   294 L      0.996**       56.128
   295 I      1.000**       56.371
   296 N      0.998**       56.273
   298 N      1.000**       56.372
   299 S      0.992**       55.957
   300 Q      0.670         38.111
   301 A      0.992**       55.923
   303 L      1.000**       56.367
   305 K      0.999**       56.343
   306 L      0.818         46.281
   307 S      1.000**       56.373
   308 S      1.000**       56.374
   309 L      1.000**       56.364


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

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

   120 R      0.553         6.008 +- 4.929
   285 M      0.995**       10.391 +- 0.693
   286 V      0.991**       10.350 +- 0.931
   288 R      0.991**       10.344 +- 0.997
   289 A      0.963*        10.087 +- 1.800
   290 P      0.972*        10.171 +- 1.580
   291 R      0.988*        10.321 +- 1.064
   292 E      1.000**       10.433 +- 0.291
   293 N      1.000**       10.435 +- 0.266
   294 L      0.983*        10.260 +- 1.355
   295 I      0.997**       10.411 +- 0.538
   296 N      0.995**       10.390 +- 0.702
   298 N      1.000**       10.432 +- 0.316
   299 S      0.964*        10.090 +- 1.794
   300 Q      0.943         9.898 +- 2.205
   301 A      0.962*        10.075 +- 1.831
   303 L      1.000**       10.432 +- 0.306
   305 K      0.998**       10.416 +- 0.499
   306 L      0.924         9.696 +- 2.593
   307 S      1.000**       10.434 +- 0.279
   308 S      1.000**       10.435 +- 0.264
   309 L      0.999**       10.430 +- 0.340



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:   0.984  0.016  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.003  0.059  0.938

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 0.003 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 0.000 0.000 0.001 0.348 0.630 0.001

sum of density on p0-p1 =   1.000000
