
seed used = 139995649

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0922.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 440
# site patterns = 89
    9    5   22   11    5   20    1    4    1   26    4   11    7    2   10
    4   12    5    1    4    6    8    1    4    3    2    6    8   10   12
   17   21    4   11    8   11    4   17    8    5    4   12    1    2   11
    6    1    3    1    1    2    6    1    7    1    4    1    7    2    3
    2    2    2    1    1    3    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 AGT GAA TTT TCC CAG ACA GTC CCC CTG GTT GCC TGG AGA AAA AAT GAC TTC ATC TCG CCG GTA CGA CTC TCT GCG ACG AAC GGC GAG CGT GAT GGT GTG GCA CGC CAT GCG CAA ACC AGC ATC AAT GGG ATT TAC ATT ACT TAC ATC CGT CTT CAG TTG AAA CAC GTC TAT CCA GAC AAG CTG CGG TGT TCG GGA ACG GCT AAT TTG ACC GAT TTC CTG GAT GAC CAC ACC GCT TTA CTA ACT GCA CCT GAG CTG GAA ACC TCA 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ..C ... ..T ..T ..C ... ..A ... ..G ... ..T ... ... ..T ... T.. ... ... ..A ... ... ..C ..C ..A ... ..C ..T ..T ..C ... ... ..T ... ... ... ... .T. ... ... ... ..G ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ..T ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ..T ... ... ... ..C ..T ..T ... ... ... ... .G. ... ..G CCA T.. ... ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 11 11 11 12 11 | Ser TCT  3  3  3  3  3 | Tyr TAT  7  7  7  8  8 | Cys TGT  1  1  1  1  1
    TTC  6  6  6  5  6 |     TCC  5  5  5  5  5 |     TAC  7  7  7  6  6 |     TGC  0  0  0  0  0
Leu TTA  1  1  1  2  1 |     TCA  1  1  1  2  1 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  8  8  8  9  9 |     TCG  5  5  5  4  5 |     TAG  0  0  0  0  0 | Trp TGG  7  7  7  7  7
--------------------------------------------------------------------------------------------------
Leu CTT  6  6  6  7  6 | Pro CCT  1  1  1  1  0 | His CAT  4  4  4  4  5 | Arg CGT 19 19 19 17 17
    CTC  4  4  4  4  4 |     CCC  1  1  1  1  1 |     CAC  5  5  5  5  4 |     CGC 11 11 11 13 13
    CTA  1  1  1  1  1 |     CCA  2  2  2  2  3 | Gln CAA  8  8  8  9  8 |     CGA  1  1  1  1  1
    CTG 30 30 30 27 29 |     CCG  6  6  6  6  7 |     CAG 21 21 21 20 21 |     CGG  2  2  2  2  2
--------------------------------------------------------------------------------------------------
Ile ATT 12 12 12 12 13 | Thr ACT  4  4  5  5  4 | Asn AAT  6  6  6  4  5 | Ser AGT  5  5  5  5  6
    ATC 14 14 14 14 13 |     ACC  8  8  7  7  7 |     AAC  8  8  8 10  9 |     AGC  4  4  4  4  4
    ATA  0  0  0  0  0 |     ACA  1  1  1  1  2 | Lys AAA 11 11 11 10 11 | Arg AGA  2  2  2  2  2
Met ATG  9  9  9  9  9 |     ACG  7  7  7  7  6 |     AAG  2  2  2  3  2 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT  4  4  4  5  4 | Ala GCT  2  2  2  1  2 | Asp GAT 23 23 23 24 23 | Gly GGT  4  4  4  4  4
    GTC  5  5  5  4  5 |     GCC 11 11 11 12 11 |     GAC 16 16 16 15 16 |     GGC 10 10 10 10 10
    GTA  8  8  8  9  8 |     GCA  9  9  9  8 11 | Glu GAA 23 23 23 22 23 |     GGA  3  3  3  3  3
    GTG 11 11 11 11 11 |     GCG 19 19 19 19 17 |     GAG 13 13 13 14 12 |     GGG  2  2  2  2  2
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.14091    C:0.27727    A:0.21136    G:0.37045
position  2:    T:0.29545    C:0.19318    A:0.35000    G:0.16136
position  3:    T:0.25455    C:0.26136    A:0.16136    G:0.32273

#2: S2457T         
position  1:    T:0.14091    C:0.27727    A:0.21136    G:0.37045
position  2:    T:0.29545    C:0.19318    A:0.35000    G:0.16136
position  3:    T:0.25455    C:0.26136    A:0.16136    G:0.32273

#3: Shig4337       
position  1:    T:0.14091    C:0.27727    A:0.21136    G:0.37045
position  2:    T:0.29545    C:0.19318    A:0.35000    G:0.16136
position  3:    T:0.25682    C:0.25909    A:0.16136    G:0.32273

#4: CFT073         
position  1:    T:0.14545    C:0.27273    A:0.21136    G:0.37045
position  2:    T:0.29773    C:0.19091    A:0.35000    G:0.16136
position  3:    T:0.25682    C:0.26136    A:0.16364    G:0.31818

#5: O157           
position  1:    T:0.14318    C:0.27727    A:0.21136    G:0.36818
position  2:    T:0.29545    C:0.19318    A:0.34773    G:0.16364
position  3:    T:0.25455    C:0.25909    A:0.17045    G:0.31591

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      56 | Ser S TCT      15 | Tyr Y TAT      37 | Cys C TGT       5
      TTC      29 |       TCC      25 |       TAC      33 |       TGC       0
Leu L TTA       6 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG      42 |       TCG      24 |       TAG       0 | Trp W TGG      35
------------------------------------------------------------------------------
Leu L CTT      31 | Pro P CCT       4 | His H CAT      21 | Arg R CGT      91
      CTC      20 |       CCC       5 |       CAC      24 |       CGC      59
      CTA       5 |       CCA      11 | Gln Q CAA      41 |       CGA       5
      CTG     146 |       CCG      31 |       CAG     104 |       CGG      10
------------------------------------------------------------------------------
Ile I ATT      61 | Thr T ACT      22 | Asn N AAT      27 | Ser S AGT      26
      ATC      69 |       ACC      37 |       AAC      43 |       AGC      20
      ATA       0 |       ACA       6 | Lys K AAA      54 | Arg R AGA      10
Met M ATG      45 |       ACG      34 |       AAG      11 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      21 | Ala A GCT       9 | Asp D GAT     116 | Gly G GGT      20
      GTC      24 |       GCC      56 |       GAC      79 |       GGC      50
      GTA      41 |       GCA      46 | Glu E GAA     114 |       GGA      15
      GTG      55 |       GCG      93 |       GAG      65 |       GGG      10
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14227    C:0.27636    A:0.21136    G:0.37000
position  2:    T:0.29591    C:0.19273    A:0.34955    G:0.16182
position  3:    T:0.25545    C:0.26045    A:0.16364    G:0.32045

Codon frequencies under model, for use in evolver:
  0.01106258  0.01127911  0.00708635  0.01387744
  0.00720512  0.00734615  0.00461538  0.00903845
  0.01306778  0.01332356  0.00000000  0.00000000
  0.00604958  0.00616799  0.00000000  0.00758889
  0.02148898  0.02190958  0.01376518  0.02695681
  0.01399589  0.01426983  0.00896534  0.01755713
  0.02538406  0.02588090  0.01626025  0.03184300
  0.01175127  0.01198128  0.00752750  0.01474136
  0.01643483  0.01675651  0.01052765  0.02061664
  0.01070410  0.01091361  0.00685672  0.01342774
  0.01941380  0.01979378  0.01243588  0.02435361
  0.00898740  0.00916331  0.00575705  0.01127423
  0.02876978  0.02933289  0.01842904  0.03609021
  0.01873792  0.01910468  0.01200294  0.02350576
  0.03398458  0.03464976  0.02176948  0.04263191
  0.01573278  0.01604072  0.01007794  0.01973597



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              -1.0000 (0.0000 0.0000)
Shig4337             0.0000 (0.0000 0.0032) 0.0000 (0.0000 0.0032)
CFT073               0.0123 (0.0010 0.0809) 0.0123 (0.0010 0.0809) 0.0118 (0.0010 0.0844)
O157                 0.0604 (0.0030 0.0495) 0.0604 (0.0030 0.0495) 0.0565 (0.0030 0.0529) 0.0402 (0.0040 0.0990)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 37
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1963.699095     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00454  0.00000  0.00000  0.00000  0.00286  0.02825  0.13640  0.07075 10.59892  0.99769  0.00000  0.02968 433.16875
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.24281

((1: 0.000004, (2: 0.000004, 3: 0.002858): 0.000000): 0.004544, (4: 0.136405, 5: 0.070748): 0.028250);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.002858): 0.000000): 0.004544, (CFT073: 0.136405, O157: 0.070748): 0.028250);

Detailed output identifying parameters

kappa (ts/tv) = 10.59892


dN/dS for site classes (K=3)

p:   0.99769  0.00000  0.00231
w:   0.02968  1.00000433.16875

dN & dS for each branch

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

   6..7       0.005    443.4    876.6   1.0304   0.0015   0.0015    0.7    1.3
   7..1       0.000    443.4    876.6   1.0304   0.0000   0.0000    0.0    0.0
   7..8       0.000    443.4    876.6   1.0304   0.0000   0.0000    0.0    0.0
   8..2       0.000    443.4    876.6   1.0304   0.0000   0.0000    0.0    0.0
   8..3       0.003    443.4    876.6   1.0304   0.0010   0.0009    0.4    0.8
   6..9       0.028    443.4    876.6   1.0304   0.0095   0.0092    4.1    8.3
   9..4       0.136    443.4    876.6   1.0304   0.0459   0.0446   19.8   40.3
   9..5       0.071    443.4    876.6   1.0304   0.0238   0.0231   10.2   20.9


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

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

   344 E      1.000**       433.117


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

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

   344 E      0.775         2.528 +- 1.842



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:   0.994  0.006  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.455  0.243  0.129  0.070  0.040  0.024  0.016  0.011  0.007  0.006

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 0.011
 0.000 0.000 0.000 0.000 0.000 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 0.968

sum of density on p0-p1 =   1.000000
