
seed used = 140007141

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2215.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 381
# site patterns = 118
    4   15   11    7   21    6    1    1    2   11    6   12   23   11   20
    3   21    1    6   20    1    4   14    5    1    1    1   20   10   10
    1    6    4    7    1    1    1    1    2    1    1    1    1    1    1
    2    1    1    1    1    2    1    2    1    1    2    1    1    1    1
    1    2    1    2    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    2    1    1    1    1    1    1    2
    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

K12                                  ATG AAA GTT GTA CTG TCC CTC GTC CCA GCT GCA GGC AAC GAA TAC AAC GAC TTA GAT GGT CAC TAT TTC TCT AAC AAA GAT CAG ACC CGT CTT ACT TGG ATC AGC GCT AAC GTG TTC GCA GAT GTG GTT TAT GTA GGT ACC GGC GCG AAC ACT TTC GGC TTT TAC GGT AAA GGC AAC CCA TCT GGT GGC --- --- --- TTT ACT AGT GTA GAC GCA CAA GGC GTC GGT ATC ATC GGT GCG ATC AGC ACT GAT GCT ACC GCT GCT --- --- --- --- --- TAC AAC CGT ACT GCT TAC CTG CGC GGT TCC CTG GCG CCG TCC CTG GCT --- --- --- --- GGC GCT CGT GAC AAC 
S2457T                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ..G TC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..A ..C ... ... ..T ... ..A .G. ..C ..T ..T ..C ..T ..C ... ..T .G. ..G GAA ... --- --- --- --- --- --- --- A.G ..A ..T ..G ... ..T ... ..T ... .C. ..A G.T ... ... ... .AC TT. .G. CTG AAC CGT TAT GAT GAG ... ..T ..C ..C ..G ... ..A ... ..C AA. T.. ... ... ... ... ... GGT GTC ATC AAT AA. ..G ... ... ... 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ..G TC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..A ..C ... ... ..T ... ..A .G. ..C ..T ..T ..C ..T ..C ... ..T .G. ..G GAA ... --- --- --- --- --- --- --- A.G ..A ..T ..G ... ..T ... ..T ... .C. ..A G.T ... ... ... .AC TT. .G. CTG AAC CGT TAT GAT GAG ... ..T ..C ..C ..G ... ..A ... ..C AA. T.. ... ... ... ... ... GGT GTC ATC AAT AA. ..G ... ... ... 
CFT073                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... G.. ..G TC. ... ... ... ... ... ... ... GCT C.G .G. ... ..T ..T ..C A.C ... ..C ..T ..C ... ... ... ... ..C ... ... ... ... ..C C.G ... .G. GT. AGC ... AAT GAT CCG TTC AC. GG. CA. A.C A.A ..T ..G ..T ... ..A ... G.T .C. ..A G.T ... ..C TGG .A. .A. A.. .GC --- --- --- --- --- CTG .CT ... ... ... ... ... ... ... ... ... ... ... ..T G.A ..A GGT GTC GTT GCT AA. ... ..C .CT G.. 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ..G TC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..A ..C ..T ... ... ..T ... ... ... ... ... ... ... ..C ... ..T .G. GT. AGC ..C --- --- --- --- --- --- --- A.G ..A ... ..G ... ..T ..A ... ... .C. ..A G.T ... ... ... .A. .G. C.G CTG --- --- --- --- --- ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... GGT GTC ATC AAT AA. ..G ... ... ... 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ..G TC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..A ..C ..T ... ... ..T ... ... ... ... ... ... ... ..C ... ..T .G. GT. AGC ..C --- --- --- --- --- --- --- A.G ..A ... ..G ... ..T ..A ... ... .C. ..A G.T ... ... ... .A. .G. C.G CTG --- --- --- --- --- ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... GGT GTC ATC AAT AA. ..G ... ... ... 



Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  2  1  1  3  1  1 | Ser TCT  6  6  6  7  6  6 | Tyr TAT  5  6  6  4  6  6 | Cys TGT  0  0  0  0  0  0
    TTC 17 18 18 16 17 17 |     TCC  8  7  7  7  8  8 |     TAC 24 24 24 24 23 23 |     TGC  0  0  0  0  0  0
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  4  4  4  5  4  4
--------------------------------------------------------------------------------------------------------------
Leu CTT  1  1  1  1  1  1 | Pro CCT  0  0  0  0  0  0 | His CAT  0  0  0  1  0  0 | Arg CGT 12 13 13 11 12 12
    CTC  1  1  1  1  1  1 |     CCC  0  0  0  0  0  0 |     CAC  1  1  1  1  1  1 |     CGC  1  2  2  2  1  1
    CTA  0  1  1  0  0  0 |     CCA  3  2  2  2  2  2 | Gln CAA  1  0  0  0  0  0 |     CGA  0  0  0  0  0  0
    CTG 24 23 23 24 25 25 |     CCG  1  2  2  3  2  2 |     CAG 20 21 21 22 21 21 |     CGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT  0  1  1  0  0  0 | Thr ACT 12  9  9 10 11 11 | Asn AAT  0  2  2  4  1  1 | Ser AGT  1  0  0  0  0  0
    ATC 10  9  9 10 10 10 |     ACC 12 13 13 15 11 11 |     AAC 32 31 31 26 31 31 |     AGC  2  4  4  4  5  5
    ATA  0  0  0  0  0  0 |     ACA  0  0  0  0  0  0 | Lys AAA 17 16 16 16 16 16 | Arg AGA  0  0  0  0  0  0
Met ATG  4  5  5  4  5  5 |     ACG  0  0  0  0  0  0 |     AAG  0  1  1  1  1  1 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT 12 13 13 16 14 14 | Ala GCT 18 15 15 19 15 15 | Asp GAT  9  9  9  9  9  9 | Gly GGT 29 30 30 26 26 26
    GTC  2  2  2  3  2  2 |     GCC  0  0  0  0  0  0 |     GAC 23 24 24 24 23 23 |     GGC 19 17 17 21 19 19
    GTA  9 10 10  9 10 10 |     GCA  8  9  9  8  9  9 | Glu GAA 11 13 13 11 12 12 |     GGA  0  0  0  1  1  1
    GTG  2  1  1  1  1  1 |     GCG  3  3  3  2  3  3 |     GAG  0  1  1  0  0  0 |     GGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.18256    C:0.17711    A:0.24523    G:0.39510
position  2:    T:0.23161    C:0.19346    A:0.38965    G:0.18529
position  3:    T:0.29155    C:0.41417    A:0.13624    G:0.15804

#2: S2457T         
position  1:    T:0.18231    C:0.17962    A:0.24397    G:0.39410
position  2:    T:0.23592    C:0.17694    A:0.39946    G:0.18767
position  3:    T:0.28418    C:0.41019    A:0.13941    G:0.16622

#3: Shig4337       
position  1:    T:0.18231    C:0.17962    A:0.24397    G:0.39410
position  2:    T:0.23592    C:0.17694    A:0.39946    G:0.18767
position  3:    T:0.28418    C:0.41019    A:0.13941    G:0.16622

#4: CFT073         
position  1:    T:0.17867    C:0.18133    A:0.24000    G:0.40000
position  2:    T:0.23733    C:0.19467    A:0.38133    G:0.18667
position  3:    T:0.29600    C:0.41067    A:0.12800    G:0.16533

#5: O157           
position  1:    T:0.17984    C:0.17984    A:0.24796    G:0.39237
position  2:    T:0.23978    C:0.18256    A:0.39237    G:0.18529
position  3:    T:0.27793    C:0.41417    A:0.13896    G:0.16894

#6: EDL933         
position  1:    T:0.17984    C:0.17984    A:0.24796    G:0.39237
position  2:    T:0.23978    C:0.18256    A:0.39237    G:0.18529
position  3:    T:0.27793    C:0.41417    A:0.13896    G:0.16894

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       9 | Ser S TCT      37 | Tyr Y TAT      33 | Cys C TGT       0
      TTC     103 |       TCC      45 |       TAC     142 |       TGC       0
Leu L TTA       6 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG       2 |       TCG       0 |       TAG       0 | Trp W TGG      25
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       0 | His H CAT       1 | Arg R CGT      73
      CTC       6 |       CCC       0 |       CAC       6 |       CGC       9
      CTA       2 |       CCA      13 | Gln Q CAA       1 |       CGA       0
      CTG     144 |       CCG      12 |       CAG     126 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       2 | Thr T ACT      62 | Asn N AAT      10 | Ser S AGT       1
      ATC      58 |       ACC      75 |       AAC     182 |       AGC      24
      ATA       0 |       ACA       0 | Lys K AAA      97 | Arg R AGA       0
Met M ATG      28 |       ACG       0 |       AAG       5 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      82 | Ala A GCT      97 | Asp D GAT      54 | Gly G GGT     167
      GTC      13 |       GCC       0 |       GAC     141 |       GGC     112
      GTA      58 |       GCA      52 | Glu E GAA      72 |       GGA       3
      GTG       7 |       GCG      17 |       GAG       2 |       GGG       0
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.18092    C:0.17957    A:0.24482    G:0.39469
position  2:    T:0.23672    C:0.18452    A:0.39244    G:0.18632
position  3:    T:0.28533    C:0.41224    A:0.13681    G:0.16562

Codon frequencies under model, for use in evolver:
  0.01254722  0.01812816  0.00601633  0.00728293
  0.00978015  0.01413031  0.00468954  0.00567681
  0.02080071  0.03005276  0.00000000  0.00000000
  0.00987557  0.01426817  0.00000000  0.00573219
  0.01245358  0.01799287  0.00597143  0.00722858
  0.00970716  0.01402486  0.00465454  0.00563444
  0.02064548  0.02982849  0.00989941  0.01198350
  0.00980187  0.01416169  0.00469995  0.00568941
  0.01697932  0.02453164  0.00814150  0.00985550
  0.01323483  0.01912162  0.00634604  0.00768205
  0.02814823  0.04066842  0.01349694  0.01633840
  0.01336395  0.01930817  0.00640795  0.00775699
  0.02737291  0.03954824  0.01312518  0.01588838
  0.02133630  0.03082658  0.01023065  0.01238448
  0.04537867  0.06556287  0.02175886  0.02633967
  0.02154446  0.03112732  0.01033047  0.01250530



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               0.1862 (0.0270 0.1448)
Shig4337             0.1862 (0.0270 0.1448)-1.0000 (0.0000 0.0000)
CFT073               0.3208 (0.0538 0.1677) 0.2074 (0.0427 0.2059) 0.2074 (0.0427 0.2059)
O157                 0.2583 (0.0239 0.0924) 0.1214 (0.0142 0.1170) 0.1214 (0.0142 0.1170) 0.1839 (0.0304 0.1655)
EDL933               0.2583 (0.0239 0.0924) 0.1214 (0.0142 0.1170) 0.1214 (0.0142 0.1170) 0.1839 (0.0304 0.1655)-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):  -2126.242514     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00196  0.30911  0.24327  0.00000  0.00000  0.01984  0.61978  0.06227  0.00000  0.00000  2.46667  0.82609  0.15229  0.00000 62.96004
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.25625

((1: 0.309110, (2: 0.000004, 3: 0.000004): 0.243274): 0.001957, (4: 0.619781, (5: 0.000004, 6: 0.000004): 0.062273): 0.019843);

((K12: 0.309110, (S2457T: 0.000004, Shig4337: 0.000004): 0.243274): 0.001957, (CFT073: 0.619781, (O157: 0.000004, EDL933: 0.000004): 0.062273): 0.019843);

Detailed output identifying parameters

kappa (ts/tv) =  2.46667


dN/dS for site classes (K=3)

p:   0.82609  0.15229  0.02162
w:   0.00000  1.00000 62.96004

dN & dS for each branch

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

   7..8       0.002    288.2    854.8   1.5135   0.0007   0.0005    0.1    0.6
   8..1       0.309    288.2    854.8   1.5135   0.1127   0.0744   21.5   96.3
   8..9       0.243    288.2    854.8   1.5135   0.0887   0.0586   16.9   75.8
   9..2       0.000    288.2    854.8   1.5135   0.0000   0.0000    0.0    0.0
   9..3       0.000    288.2    854.8   1.5135   0.0000   0.0000    0.0    0.0
   7..10      0.020    288.2    854.8   1.5135   0.0072   0.0048    1.4    6.2
  10..4       0.620    288.2    854.8   1.5135   0.2259   0.1493   43.0  193.1
  10..11      0.062    288.2    854.8   1.5135   0.0227   0.0150    4.3   19.4
  11..5       0.000    288.2    854.8   1.5135   0.0000   0.0000    0.0    0.0
  11..6       0.000    288.2    854.8   1.5135   0.0000   0.0000    0.0    0.0


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

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

   177 P      0.982*        61.815
   178 S      1.000**       62.944
   186 F      0.558         35.603
   187 T      0.502         32.116
   229 D      0.508         32.485
   233 T      0.944         59.469
   234 A      0.992**       62.446
   235 A      1.000**       62.957


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

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

    49 D      0.800         7.176 +- 3.398
   177 P      0.983*        8.666 +- 1.779
   178 S      0.999**       8.783 +- 1.506
   181 G      0.769         6.960 +- 3.560
   186 F      0.916         8.130 +- 2.599
   187 T      0.899         7.994 +- 2.749
   188 S      0.883         7.867 +- 2.880
   190 V      0.846         7.553 +- 3.132
   229 D      0.912         8.092 +- 2.631
   233 T      0.989*        8.702 +- 1.694
   234 A      0.971*        8.565 +- 1.965
   235 A      0.999**       8.786 +- 1.498
   242 Y      0.790         7.104 +- 3.441
   280 S      0.638         5.851 +- 3.905
   320 *      0.759         6.858 +- 3.582



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:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.001  0.008  0.037  0.090  0.152  0.206  0.242  0.264

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 0.103
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.303 0.594

sum of density on p0-p1 =   1.000000
