
seed used = 140014073

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2901.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 477
# site patterns = 134
   18   23    3   12    2   13   15    7   11    3   21    2    5    9    3
    7   11    6   23   16    1    1    9    6    4    9    1    1    1    4
    7    1    1    1    1    1   18   11    3   13    7    1    7    2    6
    1   14    1    1    3    1    1    1    2   15    2    1    1    1    1
    1    1    7    1    1    4    2    1    2    1    1    1    5    1    1
    7    1    2    1    1    1    1    2    1    1    1    1    2    2    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    2    1    1    2    1    1    1    1    2    1    1    1
    2    1    1    2    1    1    1    1    1    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 15 16 16 14 15 | Ser TCT  2  3  3  2  3 | Tyr TAT 16 13 13 13 14 | Cys TGT  4  5  5  5  4
    TTC 11 11 11 11 11 |     TCC  5  4  4  5  3 |     TAC 18 21 21 21 20 |     TGC  6  7  7  5  6
Leu TTA  2  2  2  2  2 |     TCA  1  3  3  1  2 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  2  2  2  3  2 |     TCG  3  2  2  3  4 |     TAG  0  0  0  0  0 | Trp TGG 11 11 11 11 11
--------------------------------------------------------------------------------------------------
Leu CTT  3  3  3  1  2 | Pro CCT  1  0  0  2  0 | His CAT  7  8  8  8  7 | Arg CGT 11 10 10 11 11
    CTC  3  4  4  4  4 |     CCC  0  1  1  0  1 |     CAC  5  4  4  5  5 |     CGC 12 11 11 11 12
    CTA  2  2  2  1  2 |     CCA  6  5  5  3  5 | Gln CAA  1  1  1  1  1 |     CGA  0  0  0  0  0
    CTG 17 17 17 17 19 |     CCG 14 15 15 16 14 |     CAG 11 11 11 11 11 |     CGG  0  1  1  0  0
--------------------------------------------------------------------------------------------------
Ile ATT  9  8  8  9 10 | Thr ACT  2  4  4  3  3 | Asn AAT  2  2  2  4  2 | Ser AGT  0  0  0  0  0
    ATC 10  9  9 11  8 |     ACC 13 12 12 14 12 |     AAC 19 19 19 18 20 |     AGC  9  9  9  9 10
    ATA  0  2  2  0  1 |     ACA  2  1  1  0  2 | Lys AAA 23 23 23 23 23 | Arg AGA  0  0  0  0  0
Met ATG 15 14 14 15 14 |     ACG  2  2  2  2  2 |     AAG  8  8  8  8  8 |     AGG  1  1  1  0  0
--------------------------------------------------------------------------------------------------
Val GTT  5  5  5  7  5 | Ala GCT  5  4  4  3  4 | Asp GAT 18 16 16 20 17 | Gly GGT  9 11 11 10  9
    GTC  7  8  8  7  7 |     GCC  9 12 12 11 10 |     GAC 12 14 14 11 12 |     GGC 27 25 25 28 27
    GTA  4  5  5  3  5 |     GCA  6  4  4  4  8 | Glu GAA 27 27 27 26 28 |     GGA  3  3  3  1  2
    GTG 22 19 19 22 21 |     GCG  6  6  6  8  4 |     GAG 10  9  9 10  9 |     GGG  3  2  2  3  3
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.20126    C:0.19497    A:0.24109    G:0.36268
position  2:    T:0.26625    C:0.16143    A:0.37107    G:0.20126
position  3:    T:0.22851    C:0.34801    A:0.16143    G:0.26205

#2: S2457T         
position  1:    T:0.20964    C:0.19497    A:0.23899    G:0.35639
position  2:    T:0.26625    C:0.16352    A:0.36897    G:0.20126
position  3:    T:0.22642    C:0.35849    A:0.16352    G:0.25157

#3: Shig4337       
position  1:    T:0.20964    C:0.19497    A:0.23899    G:0.35639
position  2:    T:0.26625    C:0.16352    A:0.36897    G:0.20126
position  3:    T:0.22642    C:0.35849    A:0.16352    G:0.25157

#4: CFT073         
position  1:    T:0.20126    C:0.19078    A:0.24319    G:0.36478
position  2:    T:0.26625    C:0.16143    A:0.37526    G:0.19706
position  3:    T:0.23480    C:0.35849    A:0.13627    G:0.27044

#5: O157           
position  1:    T:0.20335    C:0.19706    A:0.24109    G:0.35849
position  2:    T:0.26834    C:0.16143    A:0.37107    G:0.19916
position  3:    T:0.22222    C:0.35220    A:0.16981    G:0.25577

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      76 | Ser S TCT      13 | Tyr Y TAT      69 | Cys C TGT      23
      TTC      55 |       TCC      21 |       TAC     101 |       TGC      31
Leu L TTA      10 |       TCA      10 | *** * TAA       0 | *** * TGA       0
      TTG      11 |       TCG      14 |       TAG       0 | Trp W TGG      55
------------------------------------------------------------------------------
Leu L CTT      12 | Pro P CCT       3 | His H CAT      38 | Arg R CGT      53
      CTC      19 |       CCC       3 |       CAC      23 |       CGC      57
      CTA       9 |       CCA      24 | Gln Q CAA       5 |       CGA       0
      CTG      87 |       CCG      74 |       CAG      55 |       CGG       2
------------------------------------------------------------------------------
Ile I ATT      44 | Thr T ACT      16 | Asn N AAT      12 | Ser S AGT       0
      ATC      47 |       ACC      63 |       AAC      95 |       AGC      46
      ATA       5 |       ACA       6 | Lys K AAA     115 | Arg R AGA       0
Met M ATG      72 |       ACG      10 |       AAG      40 |       AGG       3
------------------------------------------------------------------------------
Val V GTT      27 | Ala A GCT      20 | Asp D GAT      87 | Gly G GGT      50
      GTC      37 |       GCC      54 |       GAC      63 |       GGC     132
      GTA      22 |       GCA      26 | Glu E GAA     135 |       GGA      12
      GTG     103 |       GCG      30 |       GAG      47 |       GGG      13
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.20503    C:0.19455    A:0.24067    G:0.35975
position  2:    T:0.26667    C:0.16226    A:0.37107    G:0.20000
position  3:    T:0.22767    C:0.35514    A:0.15891    G:0.25828

Codon frequencies under model, for use in evolver:
  0.01294319  0.02018947  0.00903401  0.01468325
  0.00787581  0.01228510  0.00549711  0.00893462
  0.01801057  0.02809384  0.00000000  0.00000000
  0.00970739  0.01514210  0.00000000  0.01101244
  0.01228148  0.01915729  0.00857215  0.01393258
  0.00747316  0.01165703  0.00521607  0.00847784
  0.01708979  0.02665755  0.01192823  0.01938731
  0.00921111  0.01436797  0.00642911  0.01044943
  0.01519303  0.02369889  0.01060434  0.01723556
  0.00924482  0.01442055  0.00645264  0.01048767
  0.02114125  0.03297723  0.01475605  0.02398344
  0.01139477  0.01777417  0.00795326  0.01292667
  0.02271014  0.03542447  0.01585109  0.02576325
  0.01381891  0.02155546  0.00964524  0.01567670
  0.03160138  0.04929349  0.02205695  0.03584981
  0.01703261  0.02656836  0.01188832  0.01932244



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               0.0480 (0.0068 0.1407)
Shig4337             0.0480 (0.0068 0.1407)-1.0000 (0.0000 0.0000)
CFT073               0.0302 (0.0054 0.1785) 0.0529 (0.0122 0.2305) 0.0529 (0.0122 0.2305)
O157                 0.0789 (0.0063 0.0800) 0.0546 (0.0077 0.1403) 0.0546 (0.0077 0.1403) 0.0427 (0.0081 0.1901)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 114
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -2471.538815     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00965  0.02679  0.09000  0.00000  0.00000  0.00796  0.12657  0.03000  2.21336  0.97918  0.01838  0.02630 16.50674
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.29097

((1: 0.026788, (2: 0.000004, 3: 0.000004): 0.089999): 0.009651, (4: 0.126568, 5: 0.029996): 0.007964);

((K12: 0.026788, (S2457T: 0.000004, Shig4337: 0.000004): 0.089999): 0.009651, (CFT073: 0.126568, O157: 0.029996): 0.007964);

Detailed output identifying parameters

kappa (ts/tv) =  2.21336


dN/dS for site classes (K=3)

p:   0.97918  0.01838  0.00244
w:   0.02630  1.00000 16.50674

dN & dS for each branch

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

   6..7       0.010    352.1   1078.9   0.0844   0.0009   0.0104    3.7    0.9
   7..1       0.027    352.1   1078.9   0.0844   0.0024   0.0288   10.2    2.6
   7..8       0.090    352.1   1078.9   0.0844   0.0082   0.0969   34.1    8.8
   8..2       0.000    352.1   1078.9   0.0844   0.0000   0.0000    0.0    0.0
   8..3       0.000    352.1   1078.9   0.0844   0.0000   0.0000    0.0    0.0
   6..9       0.008    352.1   1078.9   0.0844   0.0007   0.0086    3.0    0.8
   9..4       0.127    352.1   1078.9   0.0844   0.0115   0.1362   48.0   12.4
   9..5       0.030    352.1   1078.9   0.0844   0.0027   0.0323   11.4    2.9


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

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

   114 D      0.991**       16.364


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

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

   114 D      0.887         2.672 +- 1.989
   115 M      0.678         2.249 +- 1.894



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:   0.523  0.208  0.098  0.055  0.035  0.025  0.019  0.015  0.012  0.011

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
