
seed used = 140023597

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3664.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 430
# site patterns = 158
   15    5   17    9    4    5    4    8    6   17    7   16    4    2    9
    9    4    4    1   14    4    7    9    9    3    4    3    2    1    1
    2    2    4    5    1    2    7    2    6    3    9    3    1    2    6
    7    2    2    1    4    6    1    1    4    3    1    1    1    2    3
    1    1    1    4    1    1    1    1    1    1    1    1    4    2    2
    1    1    1    1    1    1    1    1    2    4    4    2    1    3    2
    1    3    1    5    1    1    1    1    2    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    2    3    3    3    1
    1    1    1    1    1    1    1    1    1    1    2    1    1    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

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



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

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

#1: K12            
position  1:    T:0.22093    C:0.13023    A:0.30233    G:0.34651
position  2:    T:0.42791    C:0.24651    A:0.15581    G:0.16977
position  3:    T:0.30698    C:0.25116    A:0.17209    G:0.26977

#2: S2457T         
position  1:    T:0.22093    C:0.13023    A:0.30698    G:0.34186
position  2:    T:0.42791    C:0.24651    A:0.15581    G:0.16977
position  3:    T:0.30930    C:0.24186    A:0.17674    G:0.27209

#3: Shig4337       
position  1:    T:0.22093    C:0.13023    A:0.30698    G:0.34186
position  2:    T:0.42791    C:0.24651    A:0.15581    G:0.16977
position  3:    T:0.30930    C:0.24186    A:0.17674    G:0.27209

#4: CFT073         
position  1:    T:0.22558    C:0.12791    A:0.30233    G:0.34419
position  2:    T:0.42791    C:0.24651    A:0.15581    G:0.16977
position  3:    T:0.30930    C:0.25116    A:0.17209    G:0.26744

#5: O157           
position  1:    T:0.22409    C:0.15686    A:0.29972    G:0.31933
position  2:    T:0.42857    C:0.21849    A:0.17087    G:0.18207
position  3:    T:0.30252    C:0.22969    A:0.20728    G:0.26050

#6: EDL933         
position  1:    T:0.22409    C:0.15686    A:0.29972    G:0.31933
position  2:    T:0.42857    C:0.21849    A:0.17087    G:0.18207
position  3:    T:0.30252    C:0.22969    A:0.20728    G:0.26050

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     121 | Ser S TCT      31 | Tyr Y TAT      16 | Cys C TGT      12
      TTC      53 |       TCC      24 |       TAC      22 |       TGC       6
Leu L TTA     107 |       TCA      42 | *** * TAA       0 | *** * TGA       0
      TTG      52 |       TCG      30 |       TAG       0 | Trp W TGG      26
------------------------------------------------------------------------------
Leu L CTT      17 | Pro P CCT      34 | His H CAT      24 | Arg R CGT      22
      CTC      18 |       CCC      17 |       CAC       6 |       CGC      14
      CTA      23 |       CCA      12 | Gln Q CAA      24 |       CGA       6
      CTG      57 |       CCG      35 |       CAG      14 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT     119 | Thr T ACT      42 | Asn N AAT      46 | Ser S AGT      37
      ATC      79 |       ACC      81 |       AAC      42 |       AGC      34
      ATA      33 |       ACA      18 | Lys K AAA      56 | Arg R AGA       0
Met M ATG     107 |       ACG      32 |       AAG      12 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      75 | Ala A GCT      20 | Asp D GAT      62 | Gly G GGT      69
      GTC      44 |       GCC      44 |       GAC      24 |       GGC      80
      GTA      15 |       GCA      36 | Glu E GAA      42 |       GGA      34
      GTG     122 |       GCG      82 |       GAG       0 |       GGG      70
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.22268    C:0.13763    A:0.30320    G:0.33648
position  2:    T:0.42810    C:0.23829    A:0.16023    G:0.17338
position  3:    T:0.30690    C:0.24158    A:0.18406    G:0.26746

Codon frequencies under model, for use in evolver:
  0.02995211  0.02357676  0.01796325  0.02610284
  0.01667200  0.01312334  0.00999874  0.01452941
  0.01121048  0.00882432  0.00000000  0.00000000
  0.01213032  0.00954836  0.00000000  0.01057140
  0.01851284  0.01457235  0.01110275  0.01613368
  0.01030465  0.00811129  0.00618003  0.00898036
  0.00692899  0.00545414  0.00415554  0.00603852
  0.00749752  0.00590166  0.00449651  0.00653398
  0.04078350  0.03210268  0.02445918  0.03554225
  0.02270099  0.01786905  0.01361452  0.01978359
  0.01526446  0.01201540  0.00915459  0.01330276
  0.01651693  0.01300128  0.00990573  0.01439427
  0.04525974  0.03562614  0.02714373  0.03944323
  0.02519256  0.01983029  0.01510879  0.02195496
  0.01693983  0.01333416  0.01015936  0.01476282
  0.01832976  0.01442825  0.01099295  0.01597413



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               0.0399 (0.0031 0.0780)
Shig4337             0.0399 (0.0031 0.0780)-1.0000 (0.0000 0.0000)
CFT073               0.0304 (0.0031 0.1024) 0.0145 (0.0021 0.1428) 0.0145 (0.0021 0.1428)
O157                 0.3317 (0.0442 0.1331) 0.3107 (0.0408 0.1314) 0.3107 (0.0408 0.1314) 0.3094 (0.0428 0.1382)
EDL933               0.3317 (0.0442 0.1331) 0.3107 (0.0408 0.1314) 0.3107 (0.0408 0.1314) 0.3094 (0.0428 0.1382)-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):  -2267.659825     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00310  0.02153  0.04577  0.00000  0.00000  0.01340  0.04918  0.19933  0.00000  0.00000  1.66435  0.91383  0.00000  0.00000  2.54723
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.33233

((1: 0.021532, (2: 0.000004, 3: 0.000004): 0.045768): 0.003104, (4: 0.049179, (5: 0.000004, 6: 0.000004): 0.199329): 0.013397);

((K12: 0.021532, (S2457T: 0.000004, Shig4337: 0.000004): 0.045768): 0.003104, (CFT073: 0.049179, (O157: 0.000004, EDL933: 0.000004): 0.199329): 0.013397);

Detailed output identifying parameters

kappa (ts/tv) =  1.66435


dN/dS for site classes (K=3)

p:   0.91383  0.00000  0.08617
w:   0.00000  1.00000  2.54723

dN & dS for each branch

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

   7..8       0.003    371.1    918.9   0.2195   0.0005   0.0023    0.9    0.5
   8..1       0.022    371.1    918.9   0.2195   0.0035   0.0162    6.0    3.3
   8..9       0.046    371.1    918.9   0.2195   0.0075   0.0344   12.8    6.9
   9..2       0.000    371.1    918.9   0.2195   0.0000   0.0000    0.0    0.0
   9..3       0.000    371.1    918.9   0.2195   0.0000   0.0000    0.0    0.0
   7..10      0.013    371.1    918.9   0.2195   0.0022   0.0101    3.7    2.0
  10..4       0.049    371.1    918.9   0.2195   0.0081   0.0369   13.7    7.4
  10..11      0.199    371.1    918.9   0.2195   0.0328   0.1496   55.5   30.2
  11..5       0.000    371.1    918.9   0.2195   0.0000   0.0000    0.0    0.0
  11..6       0.000    371.1    918.9   0.2195   0.0000   0.0000    0.0    0.0


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

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

   149 V      1.000**       2.547
   277 T      1.000**       2.547
   311 G      1.000**       2.547
   353 G      1.000**       2.547
   354 G      1.000**       2.547
   356 T      1.000**       2.547
   357 G      1.000**       2.547
   359 T      1.000**       2.547
   361 V      1.000**       2.547
   378 A      1.000**       2.547
   379 I      1.000**       2.547
   380 V      1.000**       2.547
   417 T      1.000**       2.547
   418 T      1.000**       2.547
   420 M      1.000**       2.547
   421 M      1.000**       2.547
   422 P      1.000**       2.547
   423 F      1.000**       2.547
   424 T      1.000**       2.547
   425 F      1.000**       2.547
   426 S      1.000**       2.547
   427 I      1.000**       2.547
   428 T      1.000**       2.547
   429 E      1.000**       2.547


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

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

   149 V      0.691         3.295 +- 1.988
   354 G      0.548         2.633 +- 2.223
   361 V      0.769         3.596 +- 1.925
   378 A      0.859         3.956 +- 1.808
   379 I      0.684         3.267 +- 1.987
   417 T      0.906         4.108 +- 1.691
   422 P      0.862         3.966 +- 1.803
   423 F      0.699         3.312 +- 1.962
   424 T      0.841         3.884 +- 1.836
   425 F      0.548         2.629 +- 2.142
   426 S      0.808         3.751 +- 1.881
   429 E      0.857         3.947 +- 1.809



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:   0.021  0.126  0.286  0.278  0.165  0.075  0.030  0.012  0.004  0.002

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 0.024
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.070 0.904

sum of density on p0-p1 =   1.000000
