
seed used = 139993845

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0829.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 612
# site patterns = 108
   19   26   25    9   24    7    1   24   10   12   20   29    1   13    3
    7   12   18    6    3    1   13   14   16    6   13    1   17    6    2
    5    3    1   17    2    8    1    4   18    1    7    4    1    1    6
    1    1   13    1    1   10    1   10    4    1    7    1    1   15    1
    8    6    1    7    5    1    1    6   13    3    1    1    1    3    3
    1    1    1    5    1    1    1    3    3    1    1    1    1    1    1
    4    4    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 12 12 12 13 13 | Ser TCT  4  4  4  5  3 | Tyr TAT  6  6  6  7  6 | Cys TGT  0  0  0  1  0
    TTC  5  5  5  4  4 |     TCC  6  6  6  6  6 |     TAC  5  5  5  4  5 |     TGC  4  5  5  4  4
Leu TTA  9  8  8  8  8 |     TCA  6  7  7  5  7 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG 18 18 18 19 18 |     TCG 10 11 11 10 10 |     TAG  0  0  0  0  0 | Trp TGG  3  3  3  3  3
--------------------------------------------------------------------------------------------------
Leu CTT  7  8  8  6  7 | Pro CCT  8  8  8  6  6 | His CAT 13 13 13 13 13 | Arg CGT 16 18 18 15 17
    CTC  6  6  6  6  6 |     CCC  5  4  4  4  6 |     CAC  3  3  3  3  3 |     CGC 21 18 18 23 21
    CTA  1  1  1  1  1 |     CCA  7  8  8 10  9 | Gln CAA 13 13 13 13 13 |     CGA  6  5  5  5  5
    CTG 28 28 28 29 29 |     CCG 14 12 12 14 13 |     CAG 30 29 29 30 29 |     CGG  8 10 10  8  9
--------------------------------------------------------------------------------------------------
Ile ATT 25 25 25 25 24 | Thr ACT  5  5  5  3  5 | Asn AAT  7  7  7  8  7 | Ser AGT  5  5  5  6  5
    ATC 13 13 13 13 13 |     ACC  9  9  9  9  9 |     AAC  6  5  5  4  5 |     AGC  4  5  5  5  5
    ATA  3  3  3  3  4 |     ACA  1  1  1  1  1 | Lys AAA 13 13 13 13 13 | Arg AGA  1  1  1  1  1
Met ATG 20 20 20 20 20 |     ACG  6  6  6  6  6 |     AAG  2  2  2  2  2 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT 12 10 10 12 12 | Ala GCT  8  9  9  9  8 | Asp GAT 18 19 19 18 19 | Gly GGT 15 15 15 14 15
    GTC 12 12 12 13 12 |     GCC 11 10 10 11 11 |     GAC  6  6  6  4  5 |     GGC 18 18 18 17 18
    GTA  9 10 10  8  8 |     GCA 13 13 13 13 14 | Glu GAA 25 25 25 26 25 |     GGA  0  0  0  0  0
    GTG 21 22 22 21 23 |     GCG 27 26 26 26 25 |     GAG 16 16 16 18 16 |     GGG  7  7  7  8  7
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.14379    C:0.30392    A:0.19608    G:0.35621
position  2:    T:0.32843    C:0.22876    A:0.26634    G:0.17647
position  3:    T:0.26307    C:0.21895    A:0.17484    G:0.34314

#2: S2457T         
position  1:    T:0.14706    C:0.30065    A:0.19608    G:0.35621
position  2:    T:0.32843    C:0.22712    A:0.26471    G:0.17974
position  3:    T:0.26797    C:0.21242    A:0.17647    G:0.34314

#3: Shig4337       
position  1:    T:0.14706    C:0.30065    A:0.19608    G:0.35621
position  2:    T:0.32843    C:0.22712    A:0.26471    G:0.17974
position  3:    T:0.26797    C:0.21242    A:0.17647    G:0.34314

#4: CFT073         
position  1:    T:0.14542    C:0.30392    A:0.19444    G:0.35621
position  2:    T:0.32843    C:0.22549    A:0.26634    G:0.17974
position  3:    T:0.26307    C:0.21242    A:0.17484    G:0.34967

#5: O157           
position  1:    T:0.14216    C:0.30556    A:0.19608    G:0.35621
position  2:    T:0.33007    C:0.22712    A:0.26307    G:0.17974
position  3:    T:0.26144    C:0.21732    A:0.17810    G:0.34314

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      62 | Ser S TCT      20 | Tyr Y TAT      31 | Cys C TGT       1
      TTC      23 |       TCC      30 |       TAC      24 |       TGC      22
Leu L TTA      41 |       TCA      32 | *** * TAA       0 | *** * TGA       0
      TTG      91 |       TCG      52 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT      36 | Pro P CCT      36 | His H CAT      65 | Arg R CGT      84
      CTC      30 |       CCC      23 |       CAC      15 |       CGC     101
      CTA       5 |       CCA      42 | Gln Q CAA      65 |       CGA      26
      CTG     142 |       CCG      65 |       CAG     147 |       CGG      45
------------------------------------------------------------------------------
Ile I ATT     124 | Thr T ACT      23 | Asn N AAT      36 | Ser S AGT      26
      ATC      65 |       ACC      45 |       AAC      25 |       AGC      24
      ATA      16 |       ACA       5 | Lys K AAA      65 | Arg R AGA       5
Met M ATG     100 |       ACG      30 |       AAG      10 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      56 | Ala A GCT      43 | Asp D GAT      93 | Gly G GGT      74
      GTC      61 |       GCC      53 |       GAC      27 |       GGC      89
      GTA      45 |       GCA      66 | Glu E GAA     126 |       GGA       0
      GTG     109 |       GCG     130 |       GAG      82 |       GGG      36
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14510    C:0.30294    A:0.19575    G:0.35621
position  2:    T:0.32876    C:0.22712    A:0.26503    G:0.17908
position  3:    T:0.26471    C:0.21471    A:0.17614    G:0.34444

Codon frequencies under model, for use in evolver:
  0.01294546  0.01050021  0.00861432  0.01684508
  0.00894343  0.00725412  0.00595125  0.01163750
  0.01043615  0.00846488  0.00000000  0.00000000
  0.00705180  0.00571979  0.00000000  0.00917605
  0.02702802  0.02192273  0.01798531  0.03516979
  0.01867244  0.01514542  0.01242524  0.02429722
  0.02178899  0.01767329  0.01449909  0.02835259
  0.01472302  0.01194200  0.00979717  0.01915810
  0.01746471  0.01416582  0.01162158  0.02272568
  0.01206558  0.00978652  0.00802882  0.01570015
  0.01407940  0.01141996  0.00936889  0.01832060
  0.00951358  0.00771657  0.00633064  0.01237940
  0.03178052  0.02577753  0.02114778  0.04135391
  0.02195573  0.01780853  0.01461005  0.02856955
  0.02562028  0.02078089  0.01704856  0.03333799
  0.01731185  0.01404184  0.01151986  0.02252678



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               0.1872 (0.0055 0.0294)
Shig4337             0.1872 (0.0055 0.0294)-1.0000 (0.0000 0.0000)
CFT073               0.0834 (0.0055 0.0659) 0.1094 (0.0073 0.0671) 0.1094 (0.0073 0.0671)
O157                 0.0835 (0.0037 0.0439) 0.1913 (0.0048 0.0249) 0.1913 (0.0048 0.0249) 0.0982 (0.0062 0.0635)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 60
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -2846.575160     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00840  0.02476  0.01239  0.00000  0.00000  0.00039  0.05472  0.01254  2.15331  0.91369  0.07640  0.00000 10.21766
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.11321

((1: 0.024762, (2: 0.000004, 3: 0.000004): 0.012389): 0.008403, (4: 0.054721, 5: 0.012536): 0.000391);

((K12: 0.024762, (S2457T: 0.000004, Shig4337: 0.000004): 0.012389): 0.008403, (CFT073: 0.054721, O157: 0.012536): 0.000391);

Detailed output identifying parameters

kappa (ts/tv) =  2.15331


dN/dS for site classes (K=3)

p:   0.91369  0.07640  0.00992
w:   0.00000  1.00000 10.21766

dN & dS for each branch

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

   6..7       0.008    542.1   1293.9   0.1777   0.0012   0.0067    3.6    1.5
   7..1       0.025    542.1   1293.9   0.1777   0.0035   0.0196   10.6    4.5
   7..8       0.012    542.1   1293.9   0.1777   0.0017   0.0098    5.3    2.3
   8..2       0.000    542.1   1293.9   0.1777   0.0000   0.0000    0.0    0.0
   8..3       0.000    542.1   1293.9   0.1777   0.0000   0.0000    0.0    0.0
   6..9       0.000    542.1   1293.9   0.1777   0.0001   0.0003    0.2    0.1
   9..4       0.055    542.1   1293.9   0.1777   0.0077   0.0434   23.5   10.0
   9..5       0.013    542.1   1293.9   0.1777   0.0018   0.0099    5.4    2.3


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

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

    70 Q      0.707         7.515
    75 E      0.679         7.257
   288 A      0.993**       10.155


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

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

    70 Q      0.893         4.832 +- 2.358
    75 E      0.888         4.809 +- 2.370
    83 N      0.517         2.972 +- 2.893
   241 T      0.530         3.038 +- 2.892
   288 A      0.981*        5.159 +- 2.108
   383 G      0.517         2.962 +- 2.881
   536 P      0.542         3.107 +- 2.906
   538 R      0.525         3.010 +- 2.889



The grid (see ternary graph for p0-p1)

w0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
w2:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

w0:   0.997  0.003  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.029  0.105  0.183  0.200  0.168  0.123  0.083  0.054  0.034  0.021

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 0.007
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.007 0.986

sum of density on p0-p1 =   1.000000
