
seed used = 140030033

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4187.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 477
# site patterns = 152
   10    5   10    8    1    7    1   17    7    4    1    4   10    6    6
    4   19    4   14    7   16    1    5   15    2    7   11   10    3    1
    1   11    3    7   12    3    5    7    9    7    1    1    8    1   10
   11    1    1    1    1    5    1    1    1    2    1   15    2    1    2
    3    1    1    2    9    1    2    1    1    1    1    1    1    1    7
    1    2    1    2    1    2    1    1    1    2    7    1    1    1    1
    2    1    1    1    1    1    1    3    1    2    1    1    1    1    1
    1    1    1    1    1    2    1    1    1    1    2    1    1    2    2
    1    1    1    1    1    1    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    1

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



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

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

#1: K12            
position  1:    T:0.18868    C:0.28721    A:0.18449    G:0.33962
position  2:    T:0.29979    C:0.20545    A:0.26415    G:0.23061
position  3:    T:0.27883    C:0.20755    A:0.15933    G:0.35430

#2: Shig4337       
position  1:    T:0.18722    C:0.28855    A:0.19163    G:0.33260
position  2:    T:0.30396    C:0.20925    A:0.25991    G:0.22687
position  3:    T:0.27093    C:0.22247    A:0.15419    G:0.35242

#3: CFT073         
position  1:    T:0.18658    C:0.29140    A:0.18449    G:0.33753
position  2:    T:0.29769    C:0.20545    A:0.26625    G:0.23061
position  3:    T:0.27044    C:0.22222    A:0.14885    G:0.35849

#4: O157           
position  1:    T:0.18868    C:0.28931    A:0.18239    G:0.33962
position  2:    T:0.29769    C:0.20545    A:0.26625    G:0.23061
position  3:    T:0.26625    C:0.21803    A:0.15723    G:0.35849

#5: EDL933         
position  1:    T:0.18868    C:0.28931    A:0.18239    G:0.33962
position  2:    T:0.29769    C:0.20545    A:0.26625    G:0.23061
position  3:    T:0.26625    C:0.21803    A:0.15723    G:0.35849

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     102 | Ser S TCT      20 | Tyr Y TAT      19 | Cys C TGT      12
      TTC       8 |       TCC      26 |       TAC      25 |       TGC      34
Leu L TTA      63 |       TCA       2 | *** * TAA       0 | *** * TGA       0
      TTG      66 |       TCG      17 |       TAG       0 | Trp W TGG      50
------------------------------------------------------------------------------
Leu L CTT      40 | Pro P CCT      21 | His H CAT      39 | Arg R CGT      73
      CTC      12 |       CCC      15 |       CAC      32 |       CGC      79
      CTA       9 |       CCA      25 | Gln Q CAA      48 |       CGA       9
      CTG     123 |       CCG      44 |       CAG      78 |       CGG      36
------------------------------------------------------------------------------
Ile I ATT      45 | Thr T ACT       5 | Asn N AAT      48 | Ser S AGT      20
      ATC      16 |       ACC      38 |       AAC      32 |       AGC      36
      ATA      11 |       ACA       2 | Lys K AAA      39 | Arg R AGA       1
Met M ATG      85 |       ACG      41 |       AAG      18 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      28 | Ala A GCT      20 | Asp D GAT      83 | Gly G GGT      64
      GTC      10 |       GCC      62 |       GAC      32 |       GGC      57
      GTA      18 |       GCA      36 | Glu E GAA      85 |       GGA      19
      GTG      71 |       GCG     113 |       GAG      47 |       GGG      53
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.18798    C:0.28916    A:0.18501    G:0.33785
position  2:    T:0.29932    C:0.20618    A:0.26461    G:0.22989
position  3:    T:0.27053    C:0.21761    A:0.15538    G:0.35648

Codon frequencies under model, for use in evolver:
  0.01572774  0.01265111  0.00903299  0.02072419
  0.01083367  0.00871441  0.00622216  0.01427536
  0.01390359  0.01118379  0.00000000  0.00000000
  0.01207944  0.00971648  0.00000000  0.01591688
  0.02419379  0.01946105  0.01389534  0.03187977
  0.01666531  0.01340528  0.00957147  0.02195962
  0.02138772  0.01720390  0.01228372  0.02818226
  0.01858165  0.01494675  0.01067209  0.02448475
  0.01547978  0.01245165  0.00889058  0.02039745
  0.01066287  0.00857702  0.00612406  0.01405030
  0.01368439  0.01100747  0.00785942  0.01803169
  0.01188899  0.00956329  0.00682826  0.01566594
  0.02826742  0.02273780  0.01623497  0.03724752
  0.01947133  0.01566239  0.01118307  0.02565706
  0.02498888  0.02010060  0.01435198  0.03292744
  0.02171034  0.01746340  0.01246900  0.02860736



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                 
Shig4337             0.2366 (0.0351 0.1484)
CFT073               0.0567 (0.0046 0.0818) 0.2219 (0.0371 0.1673)
O157                 0.0210 (0.0019 0.0882) 0.2087 (0.0341 0.1633) 0.0391 (0.0037 0.0947)
EDL933               0.0210 (0.0019 0.0882) 0.2087 (0.0341 0.1633) 0.0391 (0.0037 0.0947)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, (4, 5)));   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  8  np: 13):  -2524.585604     +0.000000
   6..7     7..1     7..2     6..8     8..3     8..9     9..4     9..5  
  0.00000  0.02404  0.19243  0.00843  0.04165  0.03916  0.00000  0.00000  2.76611  0.91376  0.00000  0.00000  2.54723
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.30572

((1: 0.024041, 2: 0.192434): 0.000000, (3: 0.041655, (4: 0.000004, 5: 0.000004): 0.039161): 0.008425);

((K12: 0.024041, Shig4337: 0.192434): 0.000000, (CFT073: 0.041655, (O157: 0.000004, EDL933: 0.000004): 0.039161): 0.008425);

Detailed output identifying parameters

kappa (ts/tv) =  2.76611


dN/dS for site classes (K=3)

p:   0.91376  0.00000  0.08624
w:   0.00000  1.00000  2.54723

dN & dS for each branch

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

   6..7       0.000    410.6   1020.4   0.2197   0.0000   0.0000    0.0    0.0
   7..1       0.024    410.6   1020.4   0.2197   0.0040   0.0181    7.4    4.0
   7..2       0.192    410.6   1020.4   0.2197   0.0318   0.1446   59.4   32.4
   6..8       0.008    410.6   1020.4   0.2197   0.0014   0.0063    2.6    1.4
   8..3       0.042    410.6   1020.4   0.2197   0.0069   0.0313   12.9    7.0
   8..9       0.039    410.6   1020.4   0.2197   0.0065   0.0294   12.1    6.6
   9..4       0.000    410.6   1020.4   0.2197   0.0000   0.0000    0.0    0.0
   9..5       0.000    410.6   1020.4   0.2197   0.0000   0.0000    0.0    0.0


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

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

     8 V      1.000**       2.547
    37 G      1.000**       2.547
   135 I      1.000**       2.547
   151 A      1.000**       2.547
   204 E      1.000**       2.547
   283 L      1.000**       2.547
   390 M      1.000**       2.547
   443 A      1.000**       2.547
   444 G      1.000**       2.547
   445 V      1.000**       2.547
   446 Y      1.000**       2.547
   447 D      1.000**       2.547
   450 S      1.000**       2.547
   451 E      1.000**       2.547
   452 A      1.000**       2.547
   453 F      1.000**       2.547
   455 E      1.000**       2.547
   456 V      1.000**       2.547
   457 K      1.000**       2.547
   458 G      1.000**       2.547
   459 Q      1.000**       2.547
   465 R      1.000**       2.547
   471 Q      1.000**       2.547
   472 Q      1.000**       2.547
   475 R      1.000**       2.547
   476 K      1.000**       2.547
   477 P      1.000**       2.547


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

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

   444 G      0.816         4.315 +- 2.144
   445 V      0.637         3.444 +- 2.562
   450 S      0.937         4.831 +- 1.814
   452 A      0.913         4.744 +- 1.905
   457 K      0.536         2.932 +- 2.590
   458 G      0.867         4.552 +- 2.039
   459 Q      0.734         3.929 +- 2.250
   465 R      0.534         2.942 +- 2.634
   471 Q      0.899         4.680 +- 1.940
   472 Q      0.799         4.234 +- 2.167
   476 K      0.693         3.710 +- 2.448
   477 P      0.884         4.626 +- 1.991



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:   0.007  0.059  0.196  0.272  0.222  0.132  0.065  0.029  0.012  0.005

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 0.008
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.017 0.974

sum of density on p0-p1 =   1.000000
