
seed used = 140014453

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2917.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 515
# site patterns = 175
    2    3    7    1    5   10    2    5    6    4   12    5    1    3   13
    6    7    1   14   11    1    7    9   10    4    3    1    4    1    6
    1    1    1    1    1    6    9   11    3    5    3    1    1    2    7
    3    9    6    5    1    5    4    6    4    1    3    7    2    6   12
   10    4    1    1    1    1    1    4    1    2    2    1    1    1    6
    1    1    2    2    1    1    1    1    1    1    2    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    5   10
    4    1    2    8    4    1    1    2   10    6    1    2    1    4    1
    1    6    2    1    1    2    6    5   10    1    1    1    1    1    1
    1    1    1    1    2    3    3    3    1    2    1    2    1    1    1
    1    1    1    1    1    2    2    1    2    2    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1

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



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

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

#1: K12            
position  1:    T:0.13204    C:0.22913    A:0.26214    G:0.37670
position  2:    T:0.27573    C:0.27573    A:0.29320    G:0.15534
position  3:    T:0.23107    C:0.36699    A:0.16311    G:0.23883

#2: S2457T         
position  1:    T:0.13204    C:0.22913    A:0.26214    G:0.37670
position  2:    T:0.27573    C:0.27573    A:0.29515    G:0.15340
position  3:    T:0.23107    C:0.36117    A:0.16893    G:0.23883

#3: Shig4337       
position  1:    T:0.13204    C:0.22913    A:0.26214    G:0.37670
position  2:    T:0.27573    C:0.27573    A:0.29515    G:0.15340
position  3:    T:0.23107    C:0.36117    A:0.16893    G:0.23883

#4: CFT073         
position  1:    T:0.16617    C:0.22552    A:0.27003    G:0.33828
position  2:    T:0.28487    C:0.24926    A:0.28487    G:0.18101
position  3:    T:0.25519    C:0.35905    A:0.15134    G:0.23442

#5: O157           
position  1:    T:0.13204    C:0.22913    A:0.26602    G:0.37282
position  2:    T:0.27573    C:0.27573    A:0.29320    G:0.15534
position  3:    T:0.23107    C:0.36505    A:0.16117    G:0.24272

#6: EDL933         
position  1:    T:0.13204    C:0.22913    A:0.26602    G:0.37282
position  2:    T:0.27573    C:0.27573    A:0.29320    G:0.15534
position  3:    T:0.23107    C:0.36505    A:0.16117    G:0.24272

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      52 | Ser S TCT       5 | Tyr Y TAT      55 | Cys C TGT       8
      TTC      34 |       TCC      31 |       TAC      46 |       TGC      22
Leu L TTA      11 |       TCA      41 | *** * TAA       0 | *** * TGA       0
      TTG      27 |       TCG      41 |       TAG       0 | Trp W TGG      23
------------------------------------------------------------------------------
Leu L CTT      27 | Pro P CCT      22 | His H CAT      15 | Arg R CGT      69
      CTC      29 |       CCC       7 |       CAC      33 |       CGC      74
      CTA       6 |       CCA      31 | Gln Q CAA      48 |       CGA      12
      CTG     149 |       CCG      56 |       CAG      81 |       CGG       7
------------------------------------------------------------------------------
Ile I ATT      69 | Thr T ACT      27 | Asn N AAT      26 | Ser S AGT      13
      ATC     147 |       ACC     139 |       AAC      99 |       AGC      24
      ATA       0 |       ACA      17 | Lys K AAA      90 | Arg R AGA       5
Met M ATG      83 |       ACG      14 |       AAG      16 |       AGG       1
------------------------------------------------------------------------------
Val V GTT      50 | Ala A GCT      56 | Asp D GAT     106 | Gly G GGT      81
      GTC      61 |       GCC     155 |       GAC      75 |       GGC      82
      GTA      22 |       GCA      66 | Glu E GAA     108 |       GGA      18
      GTG      39 |       GCG      86 |       GAG      55 |       GGG      20
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.13599    C:0.22871    A:0.26442    G:0.37088
position  2:    T:0.27679    C:0.27266    A:0.29293    G:0.15762
position  3:    T:0.23386    C:0.36332    A:0.16312    G:0.23970

Codon frequencies under model, for use in evolver:
  0.00897789  0.01394803  0.00626211  0.00920201
  0.00884423  0.01374037  0.00616888  0.00906501
  0.00950142  0.01476138  0.00000000  0.00000000
  0.00511272  0.00794311  0.00000000  0.00524035
  0.01509918  0.02345806  0.01053174  0.01547611
  0.01487438  0.02310881  0.01037494  0.01524570
  0.01597966  0.02482596  0.01114587  0.01637856
  0.00859867  0.01335887  0.00599760  0.00881332
  0.01745702  0.02712118  0.01217633  0.01789280
  0.01719711  0.02671739  0.01199505  0.01762641
  0.01847498  0.02870269  0.01288637  0.01893618
  0.00994140  0.01544494  0.00693416  0.01018957
  0.02448516  0.03804009  0.01707849  0.02509639
  0.02412062  0.03747374  0.01682422  0.02472275
  0.02591296  0.04025831  0.01807438  0.02655983
  0.01394378  0.02166303  0.00972584  0.01429187



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               0.1419 (0.0026 0.0183)
Shig4337             0.1419 (0.0026 0.0183)-1.0000 (0.0000 0.0000)
CFT073               0.3396 (0.0776 0.2284) 0.3414 (0.0761 0.2230) 0.3414 (0.0761 0.2230)
O157                 0.2495 (0.0026 0.0104) 0.1892 (0.0035 0.0183) 0.1892 (0.0035 0.0183) 0.3457 (0.0790 0.2285)
EDL933               0.2495 (0.0026 0.0104) 0.1892 (0.0035 0.0183) 0.1892 (0.0035 0.0183) 0.3457 (0.0790 0.2285)-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):  -2584.860538     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00013  0.00608  0.01427  0.00000  0.00000  0.00209  0.73699  0.00576  0.00000  0.00000  2.36722  0.84623  0.09391  0.07245 17.95768
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.76533

((1: 0.006078, (2: 0.000004, 3: 0.000004): 0.014266): 0.000133, (4: 0.736987, (5: 0.000004, 6: 0.000004): 0.005763): 0.002090);

((K12: 0.006078, (S2457T: 0.000004, Shig4337: 0.000004): 0.014266): 0.000133, (CFT073: 0.736987, (O157: 0.000004, EDL933: 0.000004): 0.005763): 0.002090);

Detailed output identifying parameters

kappa (ts/tv) =  2.36722


dN/dS for site classes (K=3)

p:   0.84623  0.09391  0.05986
w:   0.07245  1.00000 17.95768

dN & dS for each branch

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

   7..8       0.000    422.3   1122.7   1.2302   0.0000   0.0000    0.0    0.1
   8..1       0.006    422.3   1122.7   1.2302   0.0021   0.0017    0.7    2.4
   8..9       0.014    422.3   1122.7   1.2302   0.0050   0.0041    1.7    5.6
   9..2       0.000    422.3   1122.7   1.2302   0.0000   0.0000    0.0    0.0
   9..3       0.000    422.3   1122.7   1.2302   0.0000   0.0000    0.0    0.0
   7..10      0.002    422.3   1122.7   1.2302   0.0007   0.0006    0.3    0.8
  10..4       0.737    422.3   1122.7   1.2302   0.2589   0.2105   88.9  290.7
  10..11      0.006    422.3   1122.7   1.2302   0.0020   0.0016    0.7    2.3
  11..5       0.000    422.3   1122.7   1.2302   0.0000   0.0000    0.0    0.0
  11..6       0.000    422.3   1122.7   1.2302   0.0000   0.0000    0.0    0.0


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

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

   373 R      0.915         16.514
   374 T      0.966*        17.375
   379 A      0.954*        17.172
   380 G      0.521         9.630
   381 S      0.933         16.820
   418 K      0.846         15.338
   420 M      0.992**       17.816
   421 I      0.641         11.761
   423 E      0.639         11.806
   426 A      0.585         10.743
   427 R      0.701         12.755
   446 K      0.846         15.338
   447 L      0.748         13.606
   494 A      0.951*        17.125
   495 Q      0.785         14.297
   496 H      0.987*        17.741
   498 E      0.982*        17.653
   501 L      0.748         13.606
   504 A      0.664         12.125
   505 V      0.961*        17.294
   513 T      0.511         9.527


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

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

   373 R      0.868         7.881 +- 3.102
   374 T      0.943         8.494 +- 2.427
   379 A      0.929         8.382 +- 2.573
   381 S      0.908         8.211 +- 2.775
   418 K      0.857         7.784 +- 3.170
   420 M      0.985*        8.835 +- 1.858
   421 I      0.640         5.932 +- 4.146
   423 E      0.719         6.628 +- 3.833
   426 A      0.560         5.242 +- 4.300
   427 R      0.623         5.798 +- 4.249
   446 K      0.857         7.784 +- 3.170
   447 L      0.728         6.681 +- 3.895
   494 A      0.919         8.304 +- 2.671
   495 Q      0.797         7.280 +- 3.527
   496 H      0.973*        8.741 +- 2.049
   498 E      0.974*        8.743 +- 2.030
   501 L      0.728         6.681 +- 3.895
   504 A      0.635         5.878 +- 4.203
   505 V      0.932         8.410 +- 2.540
   513 T      0.565         5.292 +- 4.213



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:   0.822  0.176  0.003  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.001  0.006  0.019  0.037  0.067  0.112  0.174  0.250  0.334

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.009 0.027
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.283 0.038
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.102 0.518 0.014

sum of density on p0-p1 =   1.000000
