
seed used = 140006597

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2182.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 396
# site patterns = 103
   14   11    1    6    4   10   17    3   18    5    7    4   11   21    9
   22    4   11    4    3    1   22    2    2    3    1    1    4    3    1
    2    7    4    5   12    1    7   16    6    1    1    1    1    2    1
    3    1    1    1    6    1    1    1    3    4    4    3    1    6    1
    1    3    9    1    1    1    1    1    1    1    3    2    1    1    1
    1    1    1    4    1    1    1    1    1    1    1    3    2    1    1
    1    1    1    1    2    2    1    3    1    1    1    1    2

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

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

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

#1: K12            
position  1:    T:0.22475    C:0.20960    A:0.25505    G:0.31061
position  2:    T:0.42424    C:0.26515    A:0.13131    G:0.17929
position  3:    T:0.24242    C:0.26515    A:0.12121    G:0.37121

#2: S2457T         
position  1:    T:0.22980    C:0.20707    A:0.25253    G:0.31061
position  2:    T:0.42424    C:0.26515    A:0.13131    G:0.17929
position  3:    T:0.25000    C:0.25758    A:0.11869    G:0.37374

#3: Shig4337       
position  1:    T:0.22980    C:0.20707    A:0.25253    G:0.31061
position  2:    T:0.42424    C:0.26515    A:0.13131    G:0.17929
position  3:    T:0.25000    C:0.25758    A:0.11869    G:0.37374

#4: CFT073         
position  1:    T:0.22727    C:0.20707    A:0.25505    G:0.31061
position  2:    T:0.42424    C:0.26515    A:0.13131    G:0.17929
position  3:    T:0.23990    C:0.27020    A:0.11111    G:0.37879

#5: O157           
position  1:    T:0.22475    C:0.20960    A:0.25253    G:0.31313
position  2:    T:0.42424    C:0.26515    A:0.13131    G:0.17929
position  3:    T:0.25000    C:0.26263    A:0.11111    G:0.37626

#6: EDL933         
position  1:    T:0.22475    C:0.20960    A:0.25253    G:0.31313
position  2:    T:0.42424    C:0.26515    A:0.13131    G:0.17929
position  3:    T:0.25000    C:0.26263    A:0.11111    G:0.37626

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     117 | Ser S TCT      18 | Tyr Y TAT      24 | Cys C TGT      12
      TTC     105 |       TCC      12 |       TAC      36 |       TGC      12
Leu L TTA      28 |       TCA      22 | *** * TAA       0 | *** * TGA       0
      TTG      35 |       TCG      64 |       TAG       0 | Trp W TGG      54
------------------------------------------------------------------------------
Leu L CTT      32 | Pro P CCT       4 | His H CAT      24 | Arg R CGT      50
      CTC      16 |       CCC      11 |       CAC      18 |       CGC      28
      CTA      12 |       CCA       8 | Gln Q CAA       9 |       CGA       7
      CTG     145 |       CCG      77 |       CAG      37 |       CGG      17
------------------------------------------------------------------------------
Ile I ATT     123 | Thr T ACT      12 | Asn N AAT      14 | Ser S AGT      32
      ATC      57 |       ACC      66 |       AAC      42 |       AGC      46
      ATA      18 |       ACA       1 | Lys K AAA      27 | Arg R AGA       0
Met M ATG     132 |       ACG      23 |       AAG       9 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      47 | Ala A GCT      29 | Asp D GAT      24 | Gly G GGT      25
      GTC      40 |       GCC      58 |       GAC       6 |       GGC      71
      GTA      12 |       GCA      82 | Glu E GAA      24 |       GGA      24
      GTG      89 |       GCG     143 |       GAG      18 |       GGG      48
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.22685    C:0.20833    A:0.25337    G:0.31145
position  2:    T:0.42424    C:0.26515    A:0.13131    G:0.17929
position  3:    T:0.24705    C:0.26263    A:0.11532    G:0.37500

Codon frequencies under model, for use in evolver:
  0.02424434  0.02577251  0.01131678  0.03680018
  0.01515271  0.01610782  0.00707299  0.02300011
  0.00750420  0.00797721  0.00000000  0.00000000
  0.01024612  0.01089196  0.00000000  0.01555246
  0.02226521  0.02366864  0.01039296  0.03379608
  0.01391575  0.01479290  0.00649560  0.02112255
  0.00689161  0.00732601  0.00321687  0.01046069
  0.00940970  0.01000282  0.00439226  0.01428287
  0.02707809  0.02878489  0.01263952  0.04110150
  0.01692381  0.01799055  0.00789970  0.02568843
  0.00838131  0.00890961  0.00391223  0.01272189
  0.01144372  0.01216504  0.00534170  0.01737028
  0.03328536  0.03538341  0.01553695  0.05052343
  0.02080335  0.02211463  0.00971059  0.03157715
  0.01030261  0.01095201  0.00480906  0.01563821
  0.01406703  0.01495371  0.00656621  0.02135217



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               0.1493 (0.0056 0.0378)
Shig4337             0.1493 (0.0056 0.0378)-1.0000 (0.0000 0.0000)
CFT073               0.0171 (0.0023 0.1315) 0.0661 (0.0079 0.1197) 0.0661 (0.0079 0.1197)
O157                 0.0302 (0.0034 0.1118) 0.0487 (0.0045 0.0927) 0.0487 (0.0045 0.0927) 0.0457 (0.0034 0.0739)
EDL933               0.0302 (0.0034 0.1118) 0.0487 (0.0045 0.0927) 0.0487 (0.0045 0.0927) 0.0457 (0.0034 0.0739)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 55
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1882.373265     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00671  0.03106  0.02040  0.00000  0.00000  0.05557  0.05751  0.02200  0.00000  0.00000  3.96024  0.99732  0.00000  0.03720 48.97913
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.19327

((1: 0.031063, (2: 0.000004, 3: 0.000004): 0.020395): 0.006715, (4: 0.057508, (5: 0.000004, 6: 0.000004): 0.021999): 0.055574);

((K12: 0.031063, (S2457T: 0.000004, Shig4337: 0.000004): 0.020395): 0.006715, (CFT073: 0.057508, (O157: 0.000004, EDL933: 0.000004): 0.021999): 0.055574);

Detailed output identifying parameters

kappa (ts/tv) =  3.96024


dN/dS for site classes (K=3)

p:   0.99732  0.00000  0.00268
w:   0.03720  1.00000 48.97913

dN & dS for each branch

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

   7..8       0.007    345.2    842.8   0.1685   0.0009   0.0055    1.9    0.8
   8..1       0.031    345.2    842.8   0.1685   0.0043   0.0252    8.7    3.6
   8..9       0.020    345.2    842.8   0.1685   0.0028   0.0166    5.7    2.4
   9..2       0.000    345.2    842.8   0.1685   0.0000   0.0000    0.0    0.0
   9..3       0.000    345.2    842.8   0.1685   0.0000   0.0000    0.0    0.0
   7..10      0.056    345.2    842.8   0.1685   0.0076   0.0452   15.6    6.4
  10..4       0.058    345.2    842.8   0.1685   0.0079   0.0467   16.1    6.6
  10..11      0.022    345.2    842.8   0.1685   0.0030   0.0179    6.2    2.5
  11..5       0.000    345.2    842.8   0.1685   0.0000   0.0000    0.0    0.0
  11..6       0.000    345.2    842.8   0.1685   0.0000   0.0000    0.0    0.0


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

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

    96 N      1.000**       48.979


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

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

    96 N      0.968*        5.064 +- 2.827



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:   0.145  0.154  0.135  0.113  0.096  0.084  0.075  0.069  0.065  0.063

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 0.001 0.999

sum of density on p0-p1 =   1.000000
