
seed used = 140001141

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1658.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 311
# site patterns = 98
   15    7    3    1    9    8    1   11    1    8    3    1    3    9    1
    3   10    4    5    4    5   17    2   11    1    7    4    2    1    1
    4    2    3    5   14    3    4    2   10    2    1    7    4    5    5
    1    1    3    1    6    1    3    1    3    2    3    2    5    2    1
    3    8    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    1    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  4  4  4  4  4  4 | Ser TCT  2  2  3  2  2  2 | Tyr TAT  7  7  7  7  7  7 | Cys TGT  3  3  3  3  3  3
    TTC  6  6  6  6  6  6 |     TCC  3  3  3  2  3  3 |     TAC  4  4  5  4  4  4 |     TGC  1  1  1  1  1  1
Leu TTA  1  1  1  1  1  1 |     TCA  1  1  2  2  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  3  3  2  3  5  5 |     TCG  4  4  3  5  4  4 |     TAG  0  0  0  0  0  0 | Trp TGG  4  4  4  4  4  4
--------------------------------------------------------------------------------------------------------------
Leu CTT  3  3  3  3  3  3 | Pro CCT  3  3  3  4  3  3 | His CAT  3  3  2  4  3  3 | Arg CGT  5  5  4  5  5  5
    CTC  0  0  0  0  0  0 |     CCC  1  1  1  0  1  1 |     CAC  4  4  5  3  4  4 |     CGC 11 11 13 11 11 11
    CTA  0  0  0  0  1  1 |     CCA  3  3  3  3  3  3 | Gln CAA  2  2  2  3  2  2 |     CGA  1  1  1  1  1  1
    CTG 17 17 15 17 14 14 |     CCG  6  6  6  5  6  6 |     CAG  7  7  6  7  7  7 |     CGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------
Ile ATT  6  6  6  5  5  5 | Thr ACT  3  3  3  3  4  4 | Asn AAT  3  3  3  4  3  3 | Ser AGT  0  0  0  0  0  0
    ATC 12 12 10 13 12 12 |     ACC  6  6  6  6  4  4 |     AAC 11 11 10 10 11 11 |     AGC  5  5  5  5  5  5
    ATA  1  1  1  1  2  2 |     ACA  4  4  3  4  6  6 | Lys AAA 10 10 10 11 10 10 | Arg AGA  0  0  1  0  0  0
Met ATG 16 16 15 16 16 16 |     ACG  3  3  4  3  2  2 |     AAG  4  4  4  3  4  4 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  4  4  4  4  5  5 | Ala GCT  5  5  8  5  5  5 | Asp GAT 10 10  9 10 10 10 | Gly GGT 11 12 11 11 12 12
    GTC  8  7  6  6  6  6 |     GCC  7  7  9  8  8  8 |     GAC  3  3  4  3  3  3 |     GGC 10  9 10 10  8  8
    GTA  1  1  1  1  1  1 |     GCA  8  8  8  9  9  9 | Glu GAA 19 19 18 18 19 19 |     GGA  0  0  0  0  0  0
    GTG  9 10 11 11 10 10 |     GCG 16 16 15 14 14 14 |     GAG  5  5  5  5  5  5 |     GGG  1  1  2  1  2  2
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13826    C:0.21543    A:0.27010    G:0.37621
position  2:    T:0.29260    C:0.24116    A:0.29582    G:0.17042
position  3:    T:0.23151    C:0.29582    A:0.16399    G:0.30868

#2: S2457T         
position  1:    T:0.13826    C:0.21543    A:0.27010    G:0.37621
position  2:    T:0.29260    C:0.24116    A:0.29582    G:0.17042
position  3:    T:0.23473    C:0.28939    A:0.16399    G:0.31190

#3: Shig4337       
position  1:    T:0.14148    C:0.20900    A:0.26045    G:0.38907
position  2:    T:0.27331    C:0.25723    A:0.28939    G:0.18006
position  3:    T:0.23473    C:0.30225    A:0.16399    G:0.29904

#4: CFT073         
position  1:    T:0.14148    C:0.21543    A:0.27010    G:0.37299
position  2:    T:0.29260    C:0.24116    A:0.29582    G:0.17042
position  3:    T:0.23794    C:0.28296    A:0.17363    G:0.30547

#5: O157           
position  1:    T:0.14469    C:0.20900    A:0.27010    G:0.37621
position  2:    T:0.29260    C:0.24116    A:0.29582    G:0.17042
position  3:    T:0.23794    C:0.27974    A:0.18006    G:0.30225

#6: EDL933         
position  1:    T:0.14469    C:0.20900    A:0.27010    G:0.37621
position  2:    T:0.29260    C:0.24116    A:0.29582    G:0.17042
position  3:    T:0.23794    C:0.27974    A:0.18006    G:0.30225

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      24 | Ser S TCT      13 | Tyr Y TAT      42 | Cys C TGT      18
      TTC      36 |       TCC      17 |       TAC      25 |       TGC       6
Leu L TTA       6 |       TCA       8 | *** * TAA       0 | *** * TGA       0
      TTG      21 |       TCG      24 |       TAG       0 | Trp W TGG      24
------------------------------------------------------------------------------
Leu L CTT      18 | Pro P CCT      19 | His H CAT      18 | Arg R CGT      29
      CTC       0 |       CCC       5 |       CAC      24 |       CGC      68
      CTA       2 |       CCA      18 | Gln Q CAA      13 |       CGA       6
      CTG      94 |       CCG      35 |       CAG      41 |       CGG       6
------------------------------------------------------------------------------
Ile I ATT      33 | Thr T ACT      20 | Asn N AAT      19 | Ser S AGT       0
      ATC      71 |       ACC      32 |       AAC      64 |       AGC      30
      ATA       8 |       ACA      27 | Lys K AAA      61 | Arg R AGA       1
Met M ATG      95 |       ACG      17 |       AAG      23 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      26 | Ala A GCT      33 | Asp D GAT      59 | Gly G GGT      69
      GTC      39 |       GCC      47 |       GAC      19 |       GGC      55
      GTA       6 |       GCA      51 | Glu E GAA     112 |       GGA       0
      GTG      61 |       GCG      89 |       GAG      30 |       GGG       9
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14148    C:0.21222    A:0.26849    G:0.37781
position  2:    T:0.28939    C:0.24384    A:0.29475    G:0.17203
position  3:    T:0.23580    C:0.28832    A:0.17095    G:0.30493

Codon frequencies under model, for use in evolver:
  0.00989163  0.01209477  0.00717143  0.01279168
  0.00833462  0.01019096  0.00604260  0.01077818
  0.01007481  0.01231875  0.00000000  0.00000000
  0.00588003  0.00718967  0.00000000  0.00760394
  0.01483745  0.01814216  0.01075715  0.01918752
  0.01250193  0.01528645  0.00906390  0.01616726
  0.01511222  0.01847812  0.01095636  0.01954285
  0.00882004  0.01078450  0.00639453  0.01140592
  0.01877162  0.02295258  0.01360943  0.02427512
  0.01581683  0.01933967  0.01146720  0.02045404
  0.01911925  0.02337762  0.01386145  0.02472466
  0.01115869  0.01364403  0.00809005  0.01443021
  0.02641516  0.03229853  0.01915099  0.03415960
  0.02225722  0.02721451  0.01613648  0.02878263
  0.02690433  0.03289666  0.01950564  0.03479219
  0.01570234  0.01919968  0.01138420  0.02030599



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               0.0000 (0.0000 0.0090)
Shig4337             0.6791 (0.0490 0.0721) 0.7854 (0.0490 0.0623)
CFT073               0.0375 (0.0028 0.0753) 0.0375 (0.0028 0.0753) 0.3899 (0.0520 0.1333)
O157                 0.0000 (0.0000 0.0657) 0.0000 (0.0000 0.0560) 0.4680 (0.0485 0.1037) 0.0280 (0.0028 0.1008)
EDL933               0.0000 (0.0000 0.0657) 0.0000 (0.0000 0.0560) 0.4680 (0.0485 0.1037) 0.0280 (0.0028 0.1008)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 51
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1637.709229     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.00662  0.00000  0.00000  0.19804  0.01069  0.05223  0.03183  0.00000  0.00000  2.25465  0.90974  0.00000  0.00000  5.68022
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.29944

((1: 0.006623, (2: 0.000004, 3: 0.198039): 0.000000): 0.000000, (4: 0.052233, (5: 0.000004, 6: 0.000004): 0.031834): 0.010694);

((K12: 0.006623, (S2457T: 0.000004, Shig4337: 0.198039): 0.000000): 0.000000, (CFT073: 0.052233, (O157: 0.000004, EDL933: 0.000004): 0.031834): 0.010694);

Detailed output identifying parameters

kappa (ts/tv) =  2.25465


dN/dS for site classes (K=3)

p:   0.90974  0.00000  0.09026
w:   0.00000  1.00000  5.68022

dN & dS for each branch

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

   7..8       0.000    255.2    677.8   0.5127   0.0000   0.0000    0.0    0.0
   8..1       0.007    255.2    677.8   0.5127   0.0018   0.0034    0.9    1.2
   8..9       0.000    255.2    677.8   0.5127   0.0000   0.0000    0.0    0.0
   9..2       0.000    255.2    677.8   0.5127   0.0000   0.0000    0.0    0.0
   9..3       0.198    255.2    677.8   0.5127   0.0524   0.1022   26.1   35.5
   7..10      0.011    255.2    677.8   0.5127   0.0028   0.0055    1.4    1.9
  10..4       0.052    255.2    677.8   0.5127   0.0138   0.0270    6.9    9.4
  10..11      0.032    255.2    677.8   0.5127   0.0084   0.0164    4.2    5.7
  11..5       0.000    255.2    677.8   0.5127   0.0000   0.0000    0.0    0.0
  11..6       0.000    255.2    677.8   0.5127   0.0000   0.0000    0.0    0.0


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

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

   213 E      1.000**       5.680
   237 P      1.000**       5.680
   290 I      1.000**       5.680
   291 H      1.000**       5.680
   292 Q      1.000**       5.680
   293 P      1.000**       5.680
   294 K      1.000**       5.680
   295 D      1.000**       5.680
   297 L      1.000**       5.680
   298 G      1.000**       5.680
   299 E      1.000**       5.680
   300 T      1.000**       5.680
   301 A      1.000**       5.680
   302 F      1.000**       5.680
   303 N      1.000**       5.680
   304 M      1.000**       5.680
   305 L      1.000**       5.680
   306 L      1.000**       5.680
   307 D      1.000**       5.680
   308 R      0.654         3.712
   309 I      1.000**       5.680
   310 V      1.000**       5.680
   311 N      1.000**       5.680


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

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

   291 H      0.974*        7.714 +- 2.003
   292 Q      0.769         6.196 +- 3.351
   293 P      0.532         4.409 +- 3.830
   294 K      0.982*        7.769 +- 1.915
   297 L      0.976*        7.731 +- 1.983
   299 E      0.753         6.077 +- 3.382
   301 A      0.674         5.477 +- 3.618
   302 F      0.883         7.063 +- 2.737
   304 M      0.922         7.345 +- 2.468
   305 L      0.885         7.088 +- 2.787
   306 L      0.955*        7.589 +- 2.189
   307 D      0.810         6.518 +- 3.105
   308 R      0.541         4.365 +- 4.044
   311 N      0.949         7.531 +- 2.243



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:   0.967  0.033  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.001  0.008  0.038  0.099  0.165  0.202  0.197  0.165  0.124

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 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.017 0.114
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.011 0.609 0.244

sum of density on p0-p1 =   1.000000
