
seed used = 139992301

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0662.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 391
# site patterns = 144
   13    1    8    3    2    4    9    8    8    4    9    5    5   21   19
    1   19    1    1    9    1    4    1    1    1    1    1    1    1    1
   12    1    1    1    5    1    4    9    2    4    6    4    1    6    6
    4    5    1    1    9    9    9    1    8    2    3    3    1    1    4
    2    1    1    1    1    1    3    1    1    1    1    4    1    1    2
    1    1    1    1    1    1    1    1    4    1    1    1    1    1    1
    2    1    5    1    1    1    1    1    2    2    1    1    1    1    1
    1    1    1    1    1    1    1    3    1    1    1    1    1    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       
K12                   ATG ACA AAT CAA CCA ACG GAA ATT GCC GTC GGC GGA GCA CTG GCG GGG CAG CAC GGA TTT GCG GTA GTG ATC GAG CAC GCA GAA CCA GCG CCG GTC GCT GAT AGC CAA GAC GTG CGG ATC TCG GCT TCA TTG CTT AAA GGG TTA GTC TGG GAT CGT TGC CAT CCT TAC CGC AGA ACG GAG GCG GTG GTG GCC GCT CTT AAG CTA CTG TAT GTG AAC ACT GCG TTA GGC GCG CTG CGC CAT GAT GAG AAA GGT GTG ATT CGC AAG TCG CGG GTT GCA TAT TGC TTG GTC TGC CCC GAC ACC ACT CGT TTG TAT TCT GCG CGT GCA CAG CTC GCG GCG TTC CTG GGT TAC GTT ACA GGT ACG CGT CGC TAC CCA GGC CAT GGA GAT GTC AAC GGC AGT GTC CTC CGC ATT CAA AGC AGC CCA ATG CTC GGG TTA 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ... ... ... ... ... ..T ..A ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ..A ... ..A ..A ..C T.A ... T.G T.. ..C ... ... ..A ... ... AC. ..A T.A ..A G.. A.. ..A ..G ... AC. ..C ... ..A ..T ... ... ..C ... ... ... ..A ..T ... ... ... ..C ... ... ... ... A.. ... ..G ..A ... ... ... ... ... ... ... ... ... ... ... ..C ..A ..T ..G ... ... ..G ... ..G ..T ..T ... ... ... ... ... ... ..T ..T ..G G.. ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ... ... ... ... ... ..T ..A ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ..A ... ..A ..A ..C T.A ... T.G T.. ..C ... ... ..A ... ... AC. ..A T.A ..A G.. A.. ..A ..G ... AC. ..C ... ..A ..T ... ... ..C ... ... ... ..A ..T ... ... ... ..C ... ... ... ... A.. ... ..G ..A ... ... ... ... ... ... ... ... ... ... ... ..C ..A ..T ..G ... ... ..G ... ..G ..T ..T ... ... ... ... ... ... ..T ..T ..G G.. ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ..G ... A.. ... ..T ..T ..A ..T ..C C.G ..T ... ... ..T ..G ..C ... ..G ... ... ... ... ... ... ... ... ... ... ... G.. .C. ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... T.. ..C ... ... ... ... ... ... ..A ... ... ... A.. ..A ..G ... AC. ..C .T. ... ... ..A ... ..C ... ..T ..A ..A ..T ... ... ... ..C ... ... ... ... ... ..C ..G ... ..A ... .T. ... ..T ..G ..T ..A .T. ..C .TA ... ... ..T ..G ... ... ..G ..C ..G ... ... ... ..G ... ..T ..G ... ..T ... ... G.. ..T ..T ..G 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ..T ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..A ..C T.A ... T.G T.. ... ..A ... ... ..A ... AC. ..A T.A ..A G.. A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ..C ..C C.. ..C ... ... ..C ..G ... T.A .T. ... ... ... ... ... ... ... ... ..A ..C ... ..T ..G ..T ..C ..G ... ..G ..T ... ... ... ... ... ... ..G ... ..T ..G G.. ..T ..T ..G 

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  9  9  9  9  9 | Ser TCT  1  2  2  1  1 | Tyr TAT  7  7  7  8  7 | Cys TGT  0  1  1  2  0
    TTC  3  3  3  3  3 |     TCC  0  0  0  0  0 |     TAC  5  5  5  4  5 |     TGC  3  2  2  1  3
Leu TTA  4  6  6  3  6 |     TCA  1  1  1  1  1 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  8 10 10  9 10 |     TCG  7  7  7  7  7 |     TAG  0  0  0  0  0 | Trp TGG  9  9  9  9  9
--------------------------------------------------------------------------------------------------
Leu CTT  7  6  6  9  7 | Pro CCT  2  3  3  3  3 | His CAT 10  9  9 11  8 | Arg CGT 12 11 11 12  9
    CTC  3  3  3  2  1 |     CCC  1  1  1  1  1 |     CAC  2  2  2  1  3 |     CGC  7  6  6  6  9
    CTA  1  0  0  2  0 |     CCA  6  2  2  3  2 | Gln CAA  5  6  6  4  4 |     CGA  0  2  2  1  1
    CTG 24 22 22 22 23 |     CCG 12 15 15 14 15 |     CAG 20 19 19 22 21 |     CGG  3  3  3  2  3
--------------------------------------------------------------------------------------------------
Ile ATT 10  9  9  9 10 | Thr ACT  2  0  0  1  1 | Asn AAT  8 10 10  9 10 | Ser AGT  1  3  3  2  2
    ATC  5  6  6  5  5 |     ACC  2  5  5  3  4 |     AAC  5  4  4  5  4 |     AGC  7  5  5  6  6
    ATA  0  0  0  2  0 |     ACA  2  3  3  1  3 | Lys AAA  5  5  5  4  5 | Arg AGA  1  1  1  1  1
Met ATG 14 13 13 14 13 |     ACG  6  7  7  7  6 |     AAG  4  4  4  5  4 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT  3  3  3  4  3 | Ala GCT  6  5  5  5  5 | Asp GAT 12 11 11  9 14 | Gly GGT  6  7  7  5  8
    GTC  9  7  7  5  8 |     GCC  9 10 10 12  9 |     GAC  6  7  7  8  4 |     GGC 12 10 10 13 10
    GTA  4  6  6  7  6 |     GCA  8 11 11  6 11 | Glu GAA 10 11 11 11 10 |     GGA  7  6  6  6  6
    GTG 14 14 14 15 15 |     GCG 28 23 23 27 24 |     GAG  6  5  5  4  6 |     GGG  7  8  8  8  7
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.14578    C:0.29412    A:0.18414    G:0.37596
position  2:    T:0.30179    C:0.23785    A:0.26854    G:0.19182
position  3:    T:0.24552    C:0.20205    A:0.13811    G:0.41432

#2: S2457T         
position  1:    T:0.15857    C:0.28133    A:0.19182    G:0.36829
position  2:    T:0.29923    C:0.24297    A:0.26854    G:0.18926
position  3:    T:0.24552    C:0.19437    A:0.15345    G:0.40665

#3: Shig4337       
position  1:    T:0.15857    C:0.28133    A:0.19182    G:0.36829
position  2:    T:0.29923    C:0.24297    A:0.26854    G:0.18926
position  3:    T:0.24552    C:0.19437    A:0.15345    G:0.40665

#4: CFT073         
position  1:    T:0.14578    C:0.29412    A:0.18926    G:0.37084
position  2:    T:0.30691    C:0.23529    A:0.26854    G:0.18926
position  3:    T:0.25320    C:0.19182    A:0.13299    G:0.42199

#5: O157           
position  1:    T:0.15601    C:0.28133    A:0.18926    G:0.37340
position  2:    T:0.30435    C:0.23785    A:0.26854    G:0.18926
position  3:    T:0.24808    C:0.19182    A:0.14322    G:0.41688

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      45 | Ser S TCT       7 | Tyr Y TAT      36 | Cys C TGT       4
      TTC      15 |       TCC       0 |       TAC      24 |       TGC      11
Leu L TTA      25 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG      47 |       TCG      35 |       TAG       0 | Trp W TGG      45
------------------------------------------------------------------------------
Leu L CTT      35 | Pro P CCT      14 | His H CAT      47 | Arg R CGT      55
      CTC      12 |       CCC       5 |       CAC      10 |       CGC      34
      CTA       3 |       CCA      15 | Gln Q CAA      25 |       CGA       6
      CTG     113 |       CCG      71 |       CAG     101 |       CGG      14
------------------------------------------------------------------------------
Ile I ATT      47 | Thr T ACT       4 | Asn N AAT      47 | Ser S AGT      11
      ATC      27 |       ACC      19 |       AAC      22 |       AGC      29
      ATA       2 |       ACA      12 | Lys K AAA      24 | Arg R AGA       5
Met M ATG      67 |       ACG      33 |       AAG      21 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      16 | Ala A GCT      26 | Asp D GAT      57 | Gly G GGT      33
      GTC      36 |       GCC      50 |       GAC      32 |       GGC      55
      GTA      29 |       GCA      47 | Glu E GAA      53 |       GGA      31
      GTG      72 |       GCG     125 |       GAG      26 |       GGG      38
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15294    C:0.28645    A:0.18926    G:0.37136
position  2:    T:0.30230    C:0.23939    A:0.26854    G:0.18977
position  3:    T:0.24757    C:0.19488    A:0.14425    G:0.41330

Codon frequencies under model, for use in evolver:
  0.01176492  0.00926123  0.00685477  0.01964062
  0.00931639  0.00733377  0.00542814  0.01555297
  0.01045107  0.00822698  0.00000000  0.00000000
  0.00738543  0.00581373  0.00000000  0.01232939
  0.02203464  0.01734545  0.01283836  0.03678510
  0.01744875  0.01373548  0.01016642  0.02912932
  0.01957392  0.01540839  0.01140464  0.03267712
  0.01383223  0.01088860  0.00805928  0.02309183
  0.01455860  0.01146039  0.00848249  0.02430444
  0.01152864  0.00907523  0.00671710  0.01924616
  0.01293277  0.01018055  0.00753521  0.02159024
  0.00913916  0.00719425  0.00532488  0.01525710
  0.02856633  0.02248714  0.01664402  0.04768925
  0.02262106  0.01780707  0.01318004  0.03776408
  0.02537619  0.01997588  0.01478530  0.04236355
  0.01793250  0.01411629  0.01044828  0.02993691



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               0.0721 (0.0115 0.1589)
Shig4337             0.0721 (0.0115 0.1589)-1.0000 (0.0000 0.0000)
CFT073               0.0848 (0.0155 0.1827) 0.0831 (0.0167 0.2004) 0.0831 (0.0167 0.2004)
O157                 0.0684 (0.0103 0.1506) 0.0544 (0.0069 0.1260) 0.0544 (0.0069 0.1260) 0.0765 (0.0172 0.2253)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 120
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -2150.251402     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00034  0.09780  0.05933  0.00000  0.00000  0.01523  0.17450  0.05356  4.36716  0.96218  0.02858  0.02686  7.96117
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.40077

((1: 0.097799, (2: 0.000004, 3: 0.000004): 0.059329): 0.000338, (4: 0.174504, 5: 0.053559): 0.015228);

((K12: 0.097799, (S2457T: 0.000004, Shig4337: 0.000004): 0.059329): 0.000338, (CFT073: 0.174504, O157: 0.053559): 0.015228);

Detailed output identifying parameters

kappa (ts/tv) =  4.36716


dN/dS for site classes (K=3)

p:   0.96218  0.02858  0.00924
w:   0.02686  1.00000  7.96117

dN & dS for each branch

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

   6..7       0.000    336.3    836.7   0.1280   0.0000   0.0003    0.1    0.0
   7..1       0.098    336.3    836.7   0.1280   0.0110   0.0862   29.0    9.2
   7..8       0.059    336.3    836.7   0.1280   0.0067   0.0523   17.6    5.6
   8..2       0.000    336.3    836.7   0.1280   0.0000   0.0000    0.0    0.0
   8..3       0.000    336.3    836.7   0.1280   0.0000   0.0000    0.0    0.0
   6..9       0.015    336.3    836.7   0.1280   0.0017   0.0134    4.5    1.4
   9..4       0.175    336.3    836.7   0.1280   0.0197   0.1539   51.8   16.5
   9..5       0.054    336.3    836.7   0.1280   0.0060   0.0472   15.9    5.1


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

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

   100 L      0.589         4.728
   134 G      0.992**       7.904
   155 V      0.816         6.678


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

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

   100 L      0.672         4.297 +- 3.469
   134 G      0.982*        5.648 +- 2.490
   142 H      0.675         4.062 +- 2.950
   155 V      0.922         5.350 +- 2.644



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:   0.046  0.104  0.140  0.148  0.138  0.120  0.101  0.082  0.067  0.053

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
