
seed used = 139994321

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0871.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 572
# site patterns = 161
   19   24    8    5    7    6    6    9   13   20    1    3   25    5    1
   14   13    5    4    7    2   18    8    2   20   10    9    4    1    3
    4    6   10    4    1    1   17    2    8    1    1    2    5    1    1
    8    1    1    8   17    1    9    3   13    7    1   11   10    8    2
    3    1    1    1    1    1    6    1    1    2    9    2    2    4    1
    1    1    1    1    1    1    1    1    1    1    2    4    1    1    1
    1    1    1    2    1    1    1    1    1    1    1    1    2    1    1
    1    3    1    1    1    1    1    1    3    1    1    1    1    2    1
    1    1    1    1    2    1    2    1    1    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    1    1    1    1    1    1    1

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

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

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

#1: K12            
position  1:    T:0.13986    C:0.22552    A:0.24301    G:0.39161
position  2:    T:0.29895    C:0.23077    A:0.28671    G:0.18357
position  3:    T:0.20979    C:0.32343    A:0.19755    G:0.26923

#2: S2457T         
position  1:    T:0.14161    C:0.22378    A:0.24650    G:0.38811
position  2:    T:0.29895    C:0.23252    A:0.28671    G:0.18182
position  3:    T:0.21853    C:0.30944    A:0.19580    G:0.27622

#3: Shig4337       
position  1:    T:0.14161    C:0.22378    A:0.24650    G:0.38811
position  2:    T:0.29895    C:0.23252    A:0.28671    G:0.18182
position  3:    T:0.21853    C:0.30944    A:0.19580    G:0.27622

#4: CFT073         
position  1:    T:0.13811    C:0.22727    A:0.25000    G:0.38462
position  2:    T:0.29720    C:0.23252    A:0.28671    G:0.18357
position  3:    T:0.22378    C:0.30070    A:0.19580    G:0.27972

#5: O157           
position  1:    T:0.13986    C:0.22727    A:0.24476    G:0.38811
position  2:    T:0.29720    C:0.23427    A:0.28671    G:0.18182
position  3:    T:0.21154    C:0.31818    A:0.18531    G:0.28497

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      52 | Ser S TCT      12 | Tyr Y TAT      46 | Cys C TGT      20
      TTC      48 |       TCC      27 |       TAC      24 |       TGC      30
Leu L TTA      48 |       TCA      15 | *** * TAA       0 | *** * TGA       0
      TTG      25 |       TCG      29 |       TAG       0 | Trp W TGG      25
------------------------------------------------------------------------------
Leu L CTT      23 | Pro P CCT      11 | His H CAT      42 | Arg R CGT      36
      CTC      19 |       CCC      12 |       CAC      46 |       CGC      81
      CTA      21 |       CCA      51 | Gln Q CAA      43 |       CGA       1
      CTG     139 |       CCG      61 |       CAG      57 |       CGG       2
------------------------------------------------------------------------------
Ile I ATT      80 | Thr T ACT      11 | Asn N AAT      27 | Ser S AGT      18
      ATC      85 |       ACC      55 |       AAC      60 |       AGC      64
      ATA       1 |       ACA      14 | Lys K AAA     126 | Arg R AGA       0
Met M ATG      99 |       ACG      40 |       AAG      19 |       AGG       5
------------------------------------------------------------------------------
Val V GTT      47 | Ala A GCT      39 | Asp D GAT      90 | Gly G GGT      65
      GTC      46 |       GCC     130 |       GAC      50 |       GGC     116
      GTA      26 |       GCA      46 | Glu E GAA     130 |       GGA      33
      GTG      94 |       GCG     112 |       GAG      60 |       GGG      26
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14021    C:0.22552    A:0.24615    G:0.38811
position  2:    T:0.29825    C:0.23252    A:0.28671    G:0.18252
position  3:    T:0.21643    C:0.31224    A:0.19406    G:0.27727

Codon frequencies under model, for use in evolver:
  0.00927252  0.01337699  0.00831381  0.01187901
  0.00722887  0.01042872  0.00648146  0.00926089
  0.00891379  0.01285948  0.00000000  0.00000000
  0.00567439  0.00818615  0.00000000  0.00726945
  0.01491465  0.02151661  0.01337258  0.01910713
  0.01162748  0.01677438  0.01042528  0.01489595
  0.01433764  0.02068419  0.01285524  0.01836793
  0.00912713  0.01316726  0.00818346  0.01169276
  0.01627893  0.02348479  0.01459581  0.02085492
  0.01269108  0.01830878  0.01137892  0.01625852
  0.01564915  0.02257624  0.01403114  0.02004810
  0.00996202  0.01437170  0.00893202  0.01276233
  0.02566707  0.03702858  0.02301328  0.03288204
  0.02001008  0.02886753  0.01794119  0.02563489
  0.02467408  0.03559605  0.02212297  0.03160993
  0.01570716  0.02265993  0.01408316  0.02012242



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               0.0272 (0.0056 0.2058)
Shig4337             0.0272 (0.0056 0.2058)-1.0000 (0.0000 0.0000)
CFT073               0.0207 (0.0042 0.2050) 0.0324 (0.0052 0.1610) 0.0324 (0.0052 0.1610)
O157                 0.0271 (0.0044 0.1639) 0.0317 (0.0031 0.0973) 0.0317 (0.0031 0.0973) 0.0206 (0.0033 0.1592)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 146
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -2973.330971     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00044  0.14254  0.06080  0.00000  0.00000  0.00680  0.11658  0.03631  5.05440  0.97964  0.01858  0.00700 74.62627
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.36348

((1: 0.142537, (2: 0.000004, 3: 0.000004): 0.060803): 0.000439, (4: 0.116582, 5: 0.036308): 0.006799);

((K12: 0.142537, (S2457T: 0.000004, Shig4337: 0.000004): 0.060803): 0.000439, (CFT073: 0.116582, O157: 0.036308): 0.006799);

Detailed output identifying parameters

kappa (ts/tv) =  5.05440


dN/dS for site classes (K=3)

p:   0.97964  0.01858  0.00178
w:   0.00700  1.00000 74.62627

dN & dS for each branch

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

   6..7       0.000    524.7   1191.3   0.1585   0.0001   0.0004    0.2    0.1
   7..1       0.143    524.7   1191.3   0.1585   0.0181   0.1143   60.0   21.6
   7..8       0.061    524.7   1191.3   0.1585   0.0077   0.0487   25.6    9.2
   8..2       0.000    524.7   1191.3   0.1585   0.0000   0.0000    0.0    0.0
   8..3       0.000    524.7   1191.3   0.1585   0.0000   0.0000    0.0    0.0
   6..9       0.007    524.7   1191.3   0.1585   0.0009   0.0055    2.9    1.0
   9..4       0.117    524.7   1191.3   0.1585   0.0148   0.0934   49.0   17.6
   9..5       0.036    524.7   1191.3   0.1585   0.0046   0.0291   15.3    5.5


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

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

    64 S      1.000**       74.626


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

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

    64 S      0.940         4.484 +- 3.330
   327 A      0.559         2.692 +- 2.802



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:   0.378  0.128  0.069  0.051  0.046  0.047  0.053  0.062  0.075  0.092

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000

sum of density on p0-p1 =   1.000000
