
seed used = 141402385

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


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b0957.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 350
# site patterns = 91
    5   14    3    1   19   14    3    1    9    2   20   21    6   10    7
   14    1   13    5   15    5   13    9    7    6    1   15    1    1    1
    1    2    1    9    1    1    2   15    1    4    1   10    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    2    1    3    1    2    3    2    1    1    1    3    1    2    1    1
    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1
    1

K12                                  ATG AAA AAG ACA GCT ATC GCG ATT GCA GTG CTG GGT TTC ACC GTA CAG GCC CCG GAT AAC TGG TAC ACT GGC TCC CAT GAC TTC ATC AAC AAT GGC CAT GAA CAA GCT TTT GTT TAT GGC TTA CGT AGC GTT GAA GGT CAA CCA GAC GGC ACT AAA TCC GTT TAT --- --- --- --- AAC CAC ACC TCT GTC GCT GAG TAC CCT CAC ATG AGC GCA CCA CCG GCA CCG AAC CTG ACC CGC GGT CGC TCT TCC AAG TGT GAC TGC CTG GGT CAG 
S2457T                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..T CCT ... ..T ..C ... ... ..A ... ... ... ..T ... ... GA. AAC ATC ..C ..G ... ..T ..T ..C ..G G.T ..A CC. GGC GCA TCC TTT G.. ... ..T ... ..T ..A ... ... ... A.. C.. ... ... ..G ..A --- --- ... ..A ..T ... ... ... ... ... ... ... ... ... T.. ... ... 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..T CCT ... ..T ..C ... ... ..A ... ... ... ..T ... ... GA. AAC ATC ..C ..G ... ..T ..T ..C ..G G.T ..A CC. GGC GCA TCC TTT G.. ... ..T ... ..T ..A ... ... ... A.. C.. ... ... ..G ..A --- --- ... ..A ..T ... ... ... ... ... ... ... ... ... T.. ... ... 
CFT073                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..T CCT ... ..T ..C ... ... ..A ... ... ... ... ... ... GA. AAC ATC ..C ..G ... ..T ..T ..C ..G G.T ..A CC. GGC GCA TCC TTT G.. ... ... ... ... ... ... ..T ... ... ... ... .T. ... ... ... ... .C. ... ..T ... .C. ..T ..C ..T ..A ... ..T ... ... ..C ... 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A 



Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  2  4  4  4  2  2 | Ser TCT  4  4  4  4  4  4 | Tyr TAT  2  1  1  3  2  2 | Cys TGT  1  1  1  1  1  1
    TTC  7  6  6  6  7  7 |     TCC  8  8  8  8  8  8 |     TAC 15 15 15 13 15 15 |     TGC  1  1  1  1  1  1
Leu TTA  1  1  1  1  1  1 |     TCA  0  0  0  0  0  0 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  0  1  1  0  0  0 |     TCG  0  0  0  0  0  0 |     TAG  0  0  0  0  0  0 | Trp TGG  5  5  5  5  5  5
--------------------------------------------------------------------------------------------------------------
Leu CTT  0  0  0  0  0  0 | Pro CCT  1  3  3  3  1  1 | His CAT  2  1  1  1  2  2 | Arg CGT 10 10 10 11 10 10
    CTC  0  0  0  0  0  0 |     CCC  0  0  0  0  0  0 |     CAC  3  3  3  4  3  3 |     CGC  3  3  3  2  3  3
    CTA  0  1  1  0  0  0 |     CCA  3  2  2  3  3  3 | Gln CAA  2  1  1  1  3  3 |     CGA  0  0  0  0  0  0
    CTG 22 21 21 22 22 22 |     CCG 15 15 15 15 15 15 |     CAG 15 16 16 16 14 14 |     CGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT  1  2  2  2  1  1 | Thr ACT 10 11 11 10 10 10 | Asn AAT  1  1  1  1  1  1 | Ser AGT  0  0  0  0  0  0
    ATC 15 15 15 15 15 15 |     ACC 12 11 11 13 12 12 |     AAC 18 18 18 16 18 18 |     AGC  4  3  3  3  4  4
    ATA  0  0  0  0  0  0 |     ACA  1  1  1  1  1  1 | Lys AAA 15 14 14 15 15 15 | Arg AGA  0  0  0  0  0  0
Met ATG  6  5  5  6  6  6 |     ACG  0  0  0  0  0  0 |     AAG  4  5  5  4  4  4 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT 17 16 16 15 17 17 | Ala GCT 22 20 20 23 22 22 | Asp GAT  5  6  6  7  5  5 | Gly GGT 24 30 30 24 25 25
    GTC  1  0  0  1  1  1 |     GCC  1  1  1  1  1  1 |     GAC 17 18 18 17 17 17 |     GGC 14  9  9 14 13 13
    GTA  7  8  8  9  7  7 |     GCA 11 14 14 12 11 11 | Glu GAA 10  9  9  9 10 10 |     GGA  0  0  0  0  0  0
    GTG  2  2  2  2  2  2 |     GCG  3  3  3  3  3  3 |     GAG  3  3  3  3  3  3 |     GGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13295    C:0.21965    A:0.25145    G:0.39595
position  2:    T:0.23410    C:0.26301    A:0.32370    G:0.17919
position  3:    T:0.29480    C:0.34393    A:0.14451    G:0.21676

#2: S2457T         
position  1:    T:0.13506    C:0.21839    A:0.24713    G:0.39943
position  2:    T:0.23563    C:0.26724    A:0.31897    G:0.17816
position  3:    T:0.31609    C:0.31897    A:0.14655    G:0.21839

#3: Shig4337       
position  1:    T:0.13506    C:0.21839    A:0.24713    G:0.39943
position  2:    T:0.23563    C:0.26724    A:0.31897    G:0.17816
position  3:    T:0.31609    C:0.31897    A:0.14655    G:0.21839

#4: CFT073         
position  1:    T:0.13143    C:0.22286    A:0.24571    G:0.40000
position  2:    T:0.23714    C:0.27429    A:0.31429    G:0.17429
position  3:    T:0.31143    C:0.32571    A:0.14571    G:0.21714

#5: O157           
position  1:    T:0.13295    C:0.21965    A:0.25145    G:0.39595
position  2:    T:0.23410    C:0.26301    A:0.32370    G:0.17919
position  3:    T:0.29769    C:0.34104    A:0.14740    G:0.21387

#6: EDL933         
position  1:    T:0.13295    C:0.21965    A:0.25145    G:0.39595
position  2:    T:0.23410    C:0.26301    A:0.32370    G:0.17919
position  3:    T:0.29769    C:0.34104    A:0.14740    G:0.21387

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      18 | Ser S TCT      24 | Tyr Y TAT      11 | Cys C TGT       6
      TTC      39 |       TCC      48 |       TAC      88 |       TGC       6
Leu L TTA       6 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG       2 |       TCG       0 |       TAG       0 | Trp W TGG      30
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT      12 | His H CAT       9 | Arg R CGT      61
      CTC       0 |       CCC       0 |       CAC      19 |       CGC      17
      CTA       2 |       CCA      16 | Gln Q CAA      11 |       CGA       0
      CTG     130 |       CCG      90 |       CAG      91 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       9 | Thr T ACT      62 | Asn N AAT       6 | Ser S AGT       0
      ATC      90 |       ACC      71 |       AAC     106 |       AGC      21
      ATA       0 |       ACA       6 | Lys K AAA      88 | Arg R AGA       0
Met M ATG      34 |       ACG       0 |       AAG      26 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      98 | Ala A GCT     129 | Asp D GAT      34 | Gly G GGT     158
      GTC       4 |       GCC       6 |       GAC     104 |       GGC      72
      GTA      46 |       GCA      73 | Glu E GAA      57 |       GGA       0
      GTG      12 |       GCG      18 |       GAG      18 |       GGG       0
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.13340    C:0.21977    A:0.24904    G:0.39779
position  2:    T:0.23512    C:0.26631    A:0.32054    G:0.17802
position  3:    T:0.30566    C:0.33157    A:0.14635    G:0.21641

Codon frequencies under model, for use in evolver:
  0.00977265  0.01060110  0.00467921  0.00691910
  0.01106902  0.01200737  0.00529992  0.00783694
  0.01332272  0.01445211  0.00000000  0.00000000
  0.00739929  0.00802655  0.00000000  0.00523875
  0.01610027  0.01746512  0.00770892  0.01139909
  0.01823602  0.01978193  0.00873153  0.01291121
  0.02194893  0.02380960  0.01050930  0.01553998
  0.01219020  0.01322359  0.00583675  0.00863074
  0.01824462  0.01979126  0.00873565  0.01291731
  0.02066483  0.02241664  0.00989446  0.01463083
  0.02487226  0.02698074  0.01190901  0.01760972
  0.01381379  0.01498481  0.00661414  0.00978025
  0.02914218  0.03161264  0.01395348  0.02063285
  0.03300798  0.03580615  0.01580445  0.02336986
  0.03972853  0.04309641  0.01902229  0.02812805
  0.02206480  0.02393528  0.01056478  0.01562201



Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
S2457T               0.1482 (0.0190 0.1282)
Shig4337             0.1482 (0.0190 0.1282)-1.0000 (0.0000 0.0000)
CFT073               0.1930 (0.0202 0.1047) 0.0761 (0.0064 0.0844) 0.0761 (0.0064 0.0844)
O157                 0.0000 (0.0000 0.0077) 0.1482 (0.0190 0.1282) 0.1482 (0.0190 0.1282) 0.1930 (0.0202 0.1047)
EDL933               0.0000 (0.0000 0.0077) 0.1482 (0.0190 0.1282) 0.1482 (0.0190 0.1282) 0.1930 (0.0202 0.1047)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1739.615826     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.00288  0.79605  0.00000  0.00000  0.00000  0.68041  0.00290  0.00000  0.00000  4.75892  0.92269  0.05994  0.00000 209.07593
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.48225

((1: 0.002881, (2: 0.000004, 3: 0.000004): 0.796047): 0.000000, (4: 0.680407, (5: 0.000004, 6: 0.000004): 0.002895): 0.000000);

((K12: 0.002881, (S2457T: 0.000004, Shig4337: 0.000004): 0.796047): 0.000000, (CFT073: 0.680407, (O157: 0.000004, EDL933: 0.000004): 0.002895): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  4.75892


dN/dS for site classes (K=3)

p:   0.92269  0.05994  0.01737
w:   0.00000  1.00000209.07593

dN & dS for each branch

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

   7..8       0.000    319.7    730.3   3.6917   0.0000   0.0000    0.0    0.0
   8..1       0.003    319.7    730.3   3.6917   0.0012   0.0003    0.1    0.9
   8..9       0.796    319.7    730.3   3.6917   0.3411   0.0924   29.5  249.1
   9..2       0.000    319.7    730.3   3.6917   0.0000   0.0000    0.0    0.0
   9..3       0.000    319.7    730.3   3.6917   0.0000   0.0000    0.0    0.0
   7..10      0.000    319.7    730.3   3.6917   0.0000   0.0000    0.0    0.0
  10..4       0.680    319.7    730.3   3.6917   0.2915   0.0790   25.2  212.9
  10..11      0.003    319.7    730.3   3.6917   0.0012   0.0003    0.1    0.9
  11..5       0.000    319.7    730.3   3.6917   0.0000   0.0000    0.0    0.0
  11..6       0.000    319.7    730.3   3.6917   0.0000   0.0000    0.0    0.0


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

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

    46 N      1.000**       209.075
    87 S      0.897         187.682
    88 V      1.000**       209.037
    89 E      1.000**       209.075
   129 S      0.985*        205.908
   132 Y      0.998**       208.671


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

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

    46 N      1.000**       9.901 +- 0.870
    87 S      0.996**       9.869 +- 1.022
    88 V      0.999**       9.893 +- 0.910
    89 E      1.000**       9.904 +- 0.858
   129 S      0.941         9.377 +- 2.273
   132 Y      0.999**       9.898 +- 0.887
   139 N      0.740         7.548 +- 4.016



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:   0.000  0.000  0.000  0.000  0.001  0.007  0.031  0.102  0.267  0.592

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 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.998

sum of density on p0-p1 =   1.000000
