
seed used = 140001565

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1614.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 491
# site patterns = 104
   13   12   29    8   35    8   15   15    7   13    6    3    5    2    9
    7    6   23   11    4    3    7   23   14   14    1    1    2    6    1
    6    2    7   14    1    1    2    5    1    3    5    1    1    8   13
    6   14    1    4    3    8    3    8    8    1    4    1    2    1    1
    1    3    1    1    1    1    1    2    1    1    1    1    1    1    1
    1    1    1    1    6    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       
K12                   ATG AAT AAA TCG CTG GTA GCG GGC GTC ATT GTT CTA TGG ACA GCA TAT AAG GAA ACC CAT CTC GAC CAG AAC CAA ACA GCT CCT TCC GTG AGT CGC TTC AGC AGC TTG TTG GTG AAA CCC GCC GGG GAA CCG GGT ATC GAT CCG CTT TCA ACG CCA TTT GAG TCG TAC GGT GAT AAG CTG GCC TTA GCT AGA GCC GGG CGG ATA GCA GTG TTG GCA CGT GGA AAT TCA GAA ATC AGC ACT CAG GGT AAC GCC CTG GCC GTA CGT TCT TTT GGG CGT GCT AAT TCG TTA TTT GTT GGC GCG ATG CCA GCT CTT 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ..A ... ... ... ... ... .G. ..C ... ..C ... ... ... ... ... ... ... ..T ... T.. ..G ... ... ... ..G ... ... ... ... ... ... ... ... ... ..T GAT G.C AGC TC. 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ..A ... ... ... ... ... .G. ..C ... ..C ... ... ... ... ... ... ... ..T ... T.. ..G ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... .G. ... ... ..A .T. ... ... ... ... ... ... ... ... ... ... ... ..C ... ..A ..C ... ... ..A ... ..A ... ..T ... ... ... ..G ... ..A ... ..C ... ..C ..G ..G G.. ..T ... ..A ..C ..T ..T ... ..G ..G ..G ... ..A ... ... ... ..C C.A C.G ..C ..G ..T ... ... ..G ..A T.A 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ..T C.. ... ... ... ... ... ..A ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ..G ... ..T ... ... ... ..G ..A ... ... ..C ... ..C ... ... ... ... ... ..A ..C ..T ... T.. ..G ... ... ... ..G ... ... A.. ..C C.A C.G ..C ... ..T ..A ... ..G ..A T.A 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ..T C.. ... ... ... ... ... ..A ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ..G ... ..T ... ... ... ..G ..A ... ... ..C ... ..C ... ... ... ... ... ..A ..C ..T ... T.. ..G ... ... ... ..G ... ... A.. ..C C.A C.G ..C ... ..T ..A ... ..G ..A T.A 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 10  9  9  8  8  8 | Ser TCT  1  2  1  1  1  1 | Tyr TAT  7  7  7  7  7  7 | Cys TGT  0  0  0  0  0  0
    TTC  7  7  7  8  8  8 |     TCC  6  6  6  7  6  6 |     TAC  4  4  4  4  4  4 |     TGC  0  0  0  0  0  0
Leu TTA  4  4  4  6  4  4 |     TCA  4  4  4  3  4  4 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  4  6  6  3  5  5 |     TCG 10 10 10  9  9  9 |     TAG  0  0  0  0  0  0 | Trp TGG  5  5  5  5  5  5
--------------------------------------------------------------------------------------------------------------
Leu CTT  5  4  5  4  4  4 | Pro CCT  2  2  2  2  2  2 | His CAT  4  4  4  4  4  4 | Arg CGT  3  2  2  1  2  2
    CTC  3  3  3  3  3  3 |     CCC  3  3  3  3  4  4 |     CAC  0  0  0  0  0  0 |     CGC  2  3  3  3  3  3
    CTA  3  3  3  3  4  4 |     CCA  4  3  4  4  4  4 | Gln CAA 14 14 14 15 15 15 |     CGA  0  0  0  0  0  0
    CTG 37 36 36 38 37 37 |     CCG  9  9  9 10  9  9 |     CAG 24 24 24 23 23 23 |     CGG  1  1  1  2  1  1
--------------------------------------------------------------------------------------------------------------
Ile ATT 13 13 13 13 13 13 | Thr ACT  6  6  6  6  7  7 | Asn AAT 14 15 15 13 13 13 | Ser AGT  6  6  6  7  7  7
    ATC  7  7  7  6  7  7 |     ACC 11 11 11 11 12 12 |     AAC 15 15 15 16 16 16 |     AGC 16 17 16 15 15 15
    ATA  2  2  2  2  2  2 |     ACA  3  3  3  3  2  2 | Lys AAA 30 30 30 29 30 30 | Arg AGA  1  1  1  2  1  1
Met ATG 14 13 14 14 14 14 |     ACG  8  8  8  8  8  8 |     AAG  7  6  6  7  7  7 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  7  7  7  6  7  7 | Ala GCT  4  4  4  4  2  2 | Asp GAT 16 17 16 14 16 16 | Gly GGT 15 15 15 14 15 15
    GTC  7  7  7  9  7  7 |     GCC  9  9  8  5  7  7 |     GAC  7  7  7  9  7  7 |     GGC 16 16 16 16 16 16
    GTA  9  9  9  9 10 10 |     GCA 11 10 10 13 12 12 | Glu GAA 25 25 25 23 25 25 |     GGA  1  3  3  3  2  2
    GTG  7  7  7  8  6  6 |     GCG 16 16 17 18 18 18 |     GAG  8  8  8  9  8  8 |     GGG  4  3  3  3  3  3
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.12627    C:0.23218    A:0.31161    G:0.32994
position  2:    T:0.28310    C:0.21792    A:0.35642    G:0.14257
position  3:    T:0.23014    C:0.23014    A:0.22607    G:0.31365

#2: S2457T         
position  1:    T:0.13035    C:0.22607    A:0.31161    G:0.33198
position  2:    T:0.27902    C:0.21589    A:0.35845    G:0.14664
position  3:    T:0.23014    C:0.23422    A:0.22607    G:0.30957

#3: Shig4337       
position  1:    T:0.12831    C:0.23014    A:0.31161    G:0.32994
position  2:    T:0.28310    C:0.21589    A:0.35642    G:0.14460
position  3:    T:0.22811    C:0.23014    A:0.22811    G:0.31365

#4: CFT073         
position  1:    T:0.12424    C:0.23422    A:0.30957    G:0.33198
position  2:    T:0.28513    C:0.21792    A:0.35234    G:0.14460
position  3:    T:0.21181    C:0.23422    A:0.23422    G:0.31976

#5: O157           
position  1:    T:0.12424    C:0.23422    A:0.31365    G:0.32790
position  2:    T:0.28310    C:0.21792    A:0.35642    G:0.14257
position  3:    T:0.21996    C:0.23422    A:0.23422    G:0.31161

#6: EDL933         
position  1:    T:0.12424    C:0.23422    A:0.31365    G:0.32790
position  2:    T:0.28310    C:0.21792    A:0.35642    G:0.14257
position  3:    T:0.21996    C:0.23422    A:0.23422    G:0.31161

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      52 | Ser S TCT       7 | Tyr Y TAT      42 | Cys C TGT       0
      TTC      45 |       TCC      37 |       TAC      24 |       TGC       0
Leu L TTA      26 |       TCA      23 | *** * TAA       0 | *** * TGA       0
      TTG      29 |       TCG      57 |       TAG       0 | Trp W TGG      30
------------------------------------------------------------------------------
Leu L CTT      26 | Pro P CCT      12 | His H CAT      24 | Arg R CGT      12
      CTC      18 |       CCC      20 |       CAC       0 |       CGC      17
      CTA      20 |       CCA      23 | Gln Q CAA      87 |       CGA       0
      CTG     221 |       CCG      55 |       CAG     141 |       CGG       7
------------------------------------------------------------------------------
Ile I ATT      78 | Thr T ACT      38 | Asn N AAT      83 | Ser S AGT      39
      ATC      41 |       ACC      68 |       AAC      93 |       AGC      94
      ATA      12 |       ACA      16 | Lys K AAA     179 | Arg R AGA       7
Met M ATG      83 |       ACG      48 |       AAG      40 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      41 | Ala A GCT      20 | Asp D GAT      95 | Gly G GGT      89
      GTC      44 |       GCC      45 |       GAC      44 |       GGC      96
      GTA      56 |       GCA      68 | Glu E GAA     148 |       GGA      14
      GTG      41 |       GCG     103 |       GAG      49 |       GGG      19
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12627    C:0.23184    A:0.31195    G:0.32994
position  2:    T:0.28276    C:0.21724    A:0.35608    G:0.14392
position  3:    T:0.22335    C:0.23286    A:0.23048    G:0.31331

Codon frequencies under model, for use in evolver:
  0.00820984  0.00855920  0.00847186  0.01151624
  0.00630768  0.00657610  0.00650899  0.00884801
  0.01033869  0.01077863  0.00000000  0.00000000
  0.00417884  0.00435666  0.00000000  0.00586181
  0.01507345  0.01571487  0.01555452  0.02114406
  0.01158104  0.01207385  0.01195065  0.01624514
  0.01898205  0.01978980  0.01958786  0.02662680
  0.00767244  0.00799893  0.00791731  0.01076241
  0.02028185  0.02114490  0.02092914  0.02845007
  0.01558269  0.01624578  0.01608001  0.02185839
  0.02554100  0.02662786  0.02635614  0.03582728
  0.01032353  0.01076283  0.01065301  0.01448119
  0.02145153  0.02236436  0.02213615  0.03009082
  0.01648137  0.01718270  0.01700737  0.02311900
  0.02701399  0.02816352  0.02787614  0.03789348
  0.01091891  0.01138354  0.01126738  0.01531634



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               0.3586 (0.0097 0.0270)
Shig4337             0.1520 (0.0027 0.0175) 0.7579 (0.0070 0.0092)
CFT073               0.0527 (0.0053 0.1016) 0.1231 (0.0122 0.0994) 0.0635 (0.0062 0.0983)
O157                 0.0433 (0.0036 0.0823) 0.1546 (0.0104 0.0674) 0.0640 (0.0045 0.0695) 0.0492 (0.0036 0.0724)
EDL933               0.0433 (0.0036 0.0823) 0.1546 (0.0104 0.0674) 0.0640 (0.0045 0.0695) 0.0492 (0.0036 0.0724)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 56
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 10  np: 15):  -2364.307435     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.03351  0.01240  0.00648  0.02427  0.00000  0.00416  0.04433  0.01809  0.00000  0.00000  2.17276  0.98990  0.00000  0.05758 10.66062
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.14325

((1: 0.012405, (2: 0.024271, 3: 0.000004): 0.006476): 0.033507, (4: 0.044327, (5: 0.000004, 6: 0.000004): 0.018088): 0.004161);

((K12: 0.012405, (S2457T: 0.024271, Shig4337: 0.000004): 0.006476): 0.033507, (CFT073: 0.044327, (O157: 0.000004, EDL933: 0.000004): 0.018088): 0.004161);

Detailed output identifying parameters

kappa (ts/tv) =  2.17276


dN/dS for site classes (K=3)

p:   0.98990  0.00000  0.01010
w:   0.05758  1.00000 10.66062

dN & dS for each branch

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

   7..8       0.034    389.4   1083.6   0.1646   0.0048   0.0290   11.3    5.2
   8..1       0.012    389.4   1083.6   0.1646   0.0018   0.0107    4.2    1.9
   8..9       0.006    389.4   1083.6   0.1646   0.0009   0.0056    2.2    1.0
   9..2       0.024    389.4   1083.6   0.1646   0.0035   0.0210    8.2    3.7
   9..3       0.000    389.4   1083.6   0.1646   0.0000   0.0000    0.0    0.0
   7..10      0.004    389.4   1083.6   0.1646   0.0006   0.0036    1.4    0.6
  10..4       0.044    389.4   1083.6   0.1646   0.0063   0.0383   14.9    6.8
  10..11      0.018    389.4   1083.6   0.1646   0.0026   0.0156    6.1    2.8
  11..5       0.000    389.4   1083.6   0.1646   0.0000   0.0000    0.0    0.0
  11..6       0.000    389.4   1083.6   0.1646   0.0000   0.0000    0.0    0.0


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

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

   488 M      0.996**       10.623
   490 A      0.979*        10.440
   491 L      1.000**       10.659


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

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

   416 F      0.507         3.015 +- 3.017
   488 M      0.937         5.165 +- 2.385
   490 A      0.894         5.005 +- 2.507
   491 L      0.976*        5.333 +- 2.271



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:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.033  0.105  0.169  0.182  0.158  0.122  0.090  0.064  0.046  0.033

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 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.996

sum of density on p0-p1 =   1.000000
