
seed used = 141399353

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


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b0700.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 2  	ls = 1411
# site patterns = 271
   12   36    7   16   48   25   18   55   59   53   37   33   19    7    1
    4   27   22    2   48    1   10   44   38    6    4    4    2    7   10
    8    7    1   76   19   16    3    7   49   28   10    2   35   14   29
   15   27    7   32    8   21    6    4    8   21   32    1    5   11    4
    1    1    1    2    2    1    1    3    1    1    1    3    1    8    3
    2    1    1    2    2    1    1    1    1    1    1    1    1    3    1
    2    1    2    1    2    2    3    3    1    1    1    1    1    2    1
    1    3    1    1    1    1    3    1    1    1    3    1    1    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    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    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
    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
    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    1    1    1    1    1    1    1    1    1    1    1    1
    1

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



Codon usage in sequences
--------------------------------------------------------------
Phe TTT 13  9 | Ser TCT  5  1 | Tyr TAT 38 43 | Cys TGT 12  7
    TTC 13 16 |     TCC  8  8 |     TAC 38 39 |     TGC  7  6
Leu TTA 13 14 |     TCA  8  6 | *** TAA  0  0 | *** TGA  0  0
    TTG  3  3 |     TCG  4  5 |     TAG  0  0 | Trp TGG 30 29
--------------------------------------------------------------
Leu CTT  8  7 | Pro CCT  9 12 | His CAT 14 11 | Arg CGT 22 22
    CTC 21 20 |     CCC 11 16 |     CAC 34 35 |     CGC 53 50
    CTA  4  1 |     CCA  7 13 | Gln CAA  7  5 |     CGA  3  2
    CTG 80 82 |     CCG 51 50 |     CAG 55 63 |     CGG 32 33
--------------------------------------------------------------
Ile ATT 12 11 | Thr ACT  6  8 | Asn AAT 17 13 | Ser AGT 21 20
    ATC 30 30 |     ACC 51 47 |     AAC 24 22 |     AGC 40 40
    ATA  9  9 |     ACA 21 23 | Lys AAA 26 28 | Arg AGA  6 11
Met ATG 15 16 |     ACG 40 40 |     AAG  8  9 |     AGG  9 10
--------------------------------------------------------------
Val GTT  4  6 | Ala GCT  6  6 | Asp GAT 37 40 | Gly GGT 29 22
    GTC 10  8 |     GCC 29 29 |     GAC 58 58 |     GGC 63 63
    GTA 10  6 |     GCA 19 25 | Glu GAA 59 54 |     GGA 13 13
    GTG 41 41 |     GCG 28 30 |     GAG 24 24 |     GGG 29 28
--------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13744    C:0.29420    A:0.23980    G:0.32856
position  2:    T:0.20472    C:0.21689    A:0.31424    G:0.26414
position  3:    T:0.18110    C:0.35075    A:0.14674    G:0.32140

#2: O157           
position  1:    T:0.13305    C:0.30186    A:0.24106    G:0.32403
position  2:    T:0.19957    C:0.22818    A:0.31760    G:0.25465
position  3:    T:0.17024    C:0.34835    A:0.15021    G:0.33119

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      22 | Ser S TCT       6 | Tyr Y TAT      81 | Cys C TGT      19
      TTC      29 |       TCC      16 |       TAC      77 |       TGC      13
Leu L TTA      27 |       TCA      14 | *** * TAA       0 | *** * TGA       0
      TTG       6 |       TCG       9 |       TAG       0 | Trp W TGG      59
------------------------------------------------------------------------------
Leu L CTT      15 | Pro P CCT      21 | His H CAT      25 | Arg R CGT      44
      CTC      41 |       CCC      27 |       CAC      69 |       CGC     103
      CTA       5 |       CCA      20 | Gln Q CAA      12 |       CGA       5
      CTG     162 |       CCG     101 |       CAG     118 |       CGG      65
------------------------------------------------------------------------------
Ile I ATT      23 | Thr T ACT      14 | Asn N AAT      30 | Ser S AGT      41
      ATC      60 |       ACC      98 |       AAC      46 |       AGC      80
      ATA      18 |       ACA      44 | Lys K AAA      54 | Arg R AGA      17
Met M ATG      31 |       ACG      80 |       AAG      17 |       AGG      19
------------------------------------------------------------------------------
Val V GTT      10 | Ala A GCT      12 | Asp D GAT      77 | Gly G GGT      51
      GTC      18 |       GCC      58 |       GAC     116 |       GGC     126
      GTA      16 |       GCA      44 | Glu E GAA     113 |       GGA      26
      GTG      82 |       GCG      58 |       GAG      48 |       GGG      57
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.13524    C:0.29803    A:0.24043    G:0.32630
position  2:    T:0.20215    C:0.22254    A:0.31592    G:0.25939
position  3:    T:0.17567    C:0.34955    A:0.14848    G:0.32630

Codon frequencies under model, for use in evolver:
  0.00492824  0.00980629  0.00416542  0.00915388
  0.00542542  0.01079560  0.00458564  0.01007737
  0.00770201  0.01532558  0.00000000  0.00000000
  0.00632385  0.01258329  0.00000000  0.01174613
  0.01086038  0.02161016  0.00917934  0.02017243
  0.01195603  0.02379030  0.01010540  0.02220753
  0.01697294  0.03377305  0.01434577  0.03152612
  0.01393588  0.02772985  0.01177880  0.02588498
  0.00876131  0.01743341  0.00740518  0.01627356
  0.00964520  0.01919218  0.00815225  0.01791532
  0.01369246  0.02724548  0.01157306  0.02543284
  0.01124239  0.02237030  0.00950223  0.02088200
  0.01189035  0.02365962  0.01004989  0.02208554
  0.01308991  0.02604652  0.01106377  0.02431364
  0.01858262  0.03697601  0.01570629  0.03451599
  0.01525753  0.03035969  0.01289588  0.02833986



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                 
O157                 0.6833 (0.0936 0.1370)


TREE #  1:  (1, 2);   MP score: -1
lnL(ntime:  2  np:  7):  -7111.163708     +0.000000
   3..1     3..2  
  1.20893  1.62599  3.14529  0.88074  0.00000  0.06935 162.21639
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   2.83492

(1: 1.208935, 2: 1.625988);

(K12: 1.208935, O157: 1.625988);

Detailed output identifying parameters

kappa (ts/tv) =  3.14529


dN/dS for site classes (K=3)

p:   0.88074  0.00000  0.11926
w:   0.06935  1.00000162.21639

dN & dS for each branch

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

   3..1       1.209   1081.7   3151.3  19.4071   0.5319   0.0274   29.6 1676.2
   3..2       1.626   1081.7   3151.3  19.4071   0.7154   0.0369   39.9 2254.4


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

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

   330 A      0.537         87.133
   336 N      1.000**       162.179
   337 T      0.826         133.955
   364 C      0.644         104.506
   566 V      0.517         83.950
   722 N      0.734         119.094
   757 S      1.000**       162.214
   762 A      0.551         89.481
   763 S      0.611         99.081
   765 H      0.932         151.140
   766 L      0.776         125.938
   774 N      0.999**       162.074
   775 E      0.839         136.055
   814 S      0.908         147.333
   825 E      0.733         118.996
   826 Y      0.782         126.795
   834 E      0.552         89.548
   838 S      0.732         118.774
   863 L      0.776         125.938
   864 S      0.863         139.997
   892 T      0.999**       162.032
   893 T      0.795         128.912
   913 T      0.551         89.481
   931 A      0.551         89.481
   995 A      0.839         136.055
  1088 T      0.982*        159.363
  1171 T      0.768         124.677
  1174 T      0.717         116.393
  1176 A      0.980*        159.027
  1178 Y      0.528         85.693
  1227 R      0.803         130.252
  1250 I      0.941         152.685
  1251 S      1.000**       162.214
  1252 N      0.817         132.607
  1255 P      0.788         127.830
  1256 L      0.996**       161.497
  1258 L      0.692         112.225
  1259 E      0.839         136.055
  1260 T      0.905         146.743
  1261 L      1.000**       162.199
  1262 K      1.000**       162.195
  1263 C      0.996**       161.555
  1264 I      1.000**       162.214
  1265 K      1.000**       162.216
  1266 P      1.000**       162.216
  1267 L      1.000**       162.216
  1268 H      1.000**       162.201
  1269 S      1.000**       162.210
  1270 M      1.000**       162.216
  1272 G      0.982*        159.262
  1274 T      0.980*        158.958
  1275 G      1.000**       162.176
  1276 E      0.552         89.548
  1277 R      1.000**       162.199
  1278 S      1.000**       162.213
  1279 G      1.000**       162.214
  1282 I      1.000**       162.181
  1283 W      1.000**       162.175
  1284 G      1.000**       162.189
  1285 N      1.000**       162.203
  1287 F      1.000**       162.173
  1288 Y      1.000**       162.216
  1289 H      1.000**       162.216
  1290 Q      0.797         129.317
  1291 Y      0.999**       162.135
  1292 L      0.943         153.039
  1293 C      1.000**       162.195
  1294 V      0.994**       161.301
  1296 D      0.820         133.110
  1297 G      1.000**       162.200
  1298 K      0.999**       162.034
  1299 G      0.988*        160.190
  1300 D      0.999**       162.121
  1301 Y      1.000**       162.214
  1302 T      0.845         137.054
  1303 C      0.829         134.532
  1304 G      0.995**       161.337
  1305 G      1.000**       162.212
  1306 Q      1.000**       162.173
  1307 D      0.977*        158.533
  1308 Q      1.000**       162.216
  1309 R      1.000**       162.168
  1310 G      1.000**       162.175
  1311 E      1.000**       162.216
  1312 S      0.995**       161.337
  1313 K      0.554         89.964
  1314 G      0.867         140.620
  1315 D      1.000**       162.216
  1316 G      0.938         152.083
  1317 L      0.989*        160.367
  1318 W      1.000**       162.159
  1319 G      0.988*        160.190
  1320 P      1.000**       162.215
  1321 G      1.000**       162.216
  1322 K      1.000**       162.214
  1323 A      1.000**       162.216
  1324 S      0.985*        159.846
  1325 N      0.999**       162.052
  1326 D      0.999**       161.999
  1327 T      1.000**       162.215
  1328 K      1.000**       162.155
  1329 E      0.552         89.548
  1330 A      0.996**       161.548
  1331 A      1.000**       162.149
  1332 G      1.000**       162.215
  1333 R      1.000**       162.202
  1335 D      1.000**       162.214
  1336 L      0.984*        159.622
  1337 V      1.000**       162.216
  1338 E      0.729         118.235
  1339 T      1.000**       162.204
  1340 D      1.000**       162.212
  1341 N      1.000**       162.155
  1344 S      0.993**       161.128
  1345 C      1.000**       162.216
  1346 V      0.998**       161.914
  1347 E      1.000**       162.209
  1348 N      0.738         119.705
  1349 C      1.000**       162.216
  1350 L      1.000**       162.193
  1351 K      0.999**       162.107
  1352 G      0.993**       161.066
  1353 K      1.000**       162.178
  1354 F      0.991**       160.799
  1355 K      1.000**       162.199
  1356 E      0.764         123.906
  1357 V      0.999**       162.120
  1358 R      0.999**       162.052
  1359 P      0.999**       162.091
  1360 R      0.996**       161.604
  1361 Y      1.000**       162.216
  1362 S      0.885         143.506
  1363 V      1.000**       162.197
  1366 D      1.000**       162.216
  1367 I      1.000**       162.166
  1368 F      0.988*        160.335
  1370 P      1.000**       162.179
  1371 I      0.999**       162.096
  1372 N      0.999**       162.074
  1373 L      1.000**       162.199
  1374 G      1.000**       162.216
  1377 K      1.000**       162.216
  1378 N      0.519         84.144
  1379 C      1.000**       162.215
  1380 Q      1.000**       162.173
  1383 S      1.000**       162.216
  1384 N      1.000**       162.213
  1386 S      1.000**       162.216
  1387 L      0.996**       161.620
  1388 E      0.839         136.055
  1390 C      1.000**       162.216
  1391 K      0.996**       161.564
  1393 K      0.999**       161.999
  1394 C      1.000**       162.207
  1395 S      0.996**       161.491
  1397 N      0.999**       162.074
  1398 N      0.984*        159.562
  1399 I      0.999**       162.025
  1400 G      0.996**       161.586
  1401 R      1.000**       162.214
  1402 F      1.000**       162.188
  1403 I      0.999**       162.034
  1404 R      1.000**       162.161
  1405 F      1.000**       162.216
  1406 V      0.999**       162.120
  1407 F      0.995**       161.435
  1408 T      0.999**       162.009
  1410 V      0.986*        159.914
  1411 M      0.991**       160.772


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

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

   330 A      0.830         8.809 +- 3.737
   336 N      0.990*        10.402 +- 0.963
   337 T      0.904         9.545 +- 2.929
   364 C      0.891         9.418 +- 3.096
   566 V      0.813         8.646 +- 3.876
   722 N      0.825         8.764 +- 3.777
   757 S      0.999**       10.487 +- 0.358
   762 A      0.822         8.730 +- 3.806
   763 S      0.873         9.236 +- 3.311
   765 H      0.855         9.057 +- 3.503
   766 L      0.887         9.383 +- 3.139
   774 N      0.990**       10.409 +- 0.925
   775 E      0.904         9.547 +- 2.925
   814 S      0.923         9.742 +- 2.636
   825 E      0.811         8.626 +- 3.892
   826 Y      0.863         9.137 +- 3.420
   834 E      0.864         9.150 +- 3.406
   838 S      0.836         8.876 +- 3.678
   863 L      0.887         9.383 +- 3.139
   864 S      0.909         9.596 +- 2.857
   892 T      0.990*        10.401 +- 0.968
   893 T      0.886         9.366 +- 3.160
   913 T      0.822         8.730 +- 3.806
   931 A      0.822         8.730 +- 3.806
   995 A      0.904         9.547 +- 2.925
  1088 T      0.855         9.064 +- 3.497
  1171 T      0.858         9.092 +- 3.468
  1174 T      0.903         9.537 +- 2.940
  1176 A      0.899         9.498 +- 2.993
  1178 Y      0.820         8.711 +- 3.822
  1250 I      0.858         9.091 +- 3.469
  1251 S      0.994**       10.447 +- 0.709
  1252 N      0.903         9.540 +- 2.936
  1255 P      0.914         9.644 +- 2.787
  1256 L      0.980*        10.307 +- 1.362
  1259 E      0.904         9.547 +- 2.925
  1260 T      0.926         9.768 +- 2.594
  1261 L      0.995**       10.450 +- 0.688
  1262 K      0.995**       10.448 +- 0.703
  1263 C      0.936         9.863 +- 2.434
  1264 I      0.995**       10.453 +- 0.668
  1265 K      0.998**       10.486 +- 0.371
  1266 P      0.999**       10.491 +- 0.285
  1267 L      0.999**       10.493 +- 0.257
  1268 H      0.992**       10.423 +- 0.852
  1269 S      0.996**       10.462 +- 0.599
  1270 M      1.000**       10.496 +- 0.202
  1272 G      0.898         9.493 +- 2.999
  1274 T      0.893         9.436 +- 3.072
  1275 G      0.989*        10.394 +- 1.001
  1276 E      0.864         9.150 +- 3.406
  1277 R      0.991**       10.414 +- 0.915
  1278 S      0.995**       10.450 +- 0.690
  1279 G      0.997**       10.475 +- 0.483
  1282 I      0.994**       10.447 +- 0.707
  1283 W      0.992**       10.421 +- 0.864
  1284 G      0.991**       10.416 +- 0.894
  1285 N      0.995**       10.455 +- 0.651
  1287 F      0.994**       10.440 +- 0.755
  1288 Y      0.999**       10.494 +- 0.240
  1289 H      0.999**       10.491 +- 0.285
  1290 Q      0.889         9.399 +- 3.119
  1291 Y      0.992**       10.426 +- 0.834
  1292 L      0.860         9.052 +- 3.594
  1293 C      0.994**       10.438 +- 0.764
  1294 V      0.908         9.584 +- 2.877
  1296 D      0.897         9.483 +- 3.012
  1297 G      0.995**       10.455 +- 0.653
  1298 K      0.988*        10.387 +- 1.040
  1299 G      0.964*        10.149 +- 1.821
  1300 D      0.988*        10.383 +- 1.051
  1301 Y      0.995**       10.452 +- 0.677
  1302 T      0.901         9.515 +- 2.969
  1303 C      0.904         9.546 +- 2.926
  1304 G      0.940         9.908 +- 2.352
  1305 G      0.994**       10.447 +- 0.708
  1306 Q      0.993**       10.431 +- 0.808
  1307 D      0.891         9.415 +- 3.100
  1308 Q      0.999**       10.491 +- 0.288
  1309 R      0.990*        10.401 +- 0.976
  1310 G      0.995**       10.450 +- 0.688
  1311 E      0.999**       10.494 +- 0.248
  1312 S      0.973*        10.238 +- 1.587
  1313 K      0.878         9.295 +- 3.245
  1314 G      0.917         9.679 +- 2.734
  1315 D      0.999**       10.494 +- 0.248
  1316 G      0.842         8.932 +- 3.626
  1317 L      0.913         9.634 +- 2.802
  1318 W      0.990*        10.405 +- 0.949
  1319 G      0.964*        10.149 +- 1.821
  1320 P      0.998**       10.480 +- 0.437
  1321 G      0.998**       10.480 +- 0.433
  1322 K      0.996**       10.466 +- 0.571
  1323 A      0.999**       10.491 +- 0.295
  1324 S      0.905         9.557 +- 2.913
  1325 N      0.988*        10.390 +- 1.019
  1326 D      0.987*        10.373 +- 1.093
  1327 T      0.996**       10.464 +- 0.587
  1328 K      0.994**       10.441 +- 0.750
  1329 E      0.864         9.150 +- 3.406
  1330 A      0.912         9.626 +- 2.814
  1331 A      0.993**       10.437 +- 0.774
  1332 G      0.998**       10.476 +- 0.474
  1333 R      0.995**       10.456 +- 0.647
  1335 D      0.998**       10.484 +- 0.390
  1336 L      0.886         9.374 +- 3.151
  1337 V      0.999**       10.487 +- 0.348
  1338 E      0.849         9.005 +- 3.554
  1339 T      0.993**       10.430 +- 0.815
  1340 D      0.994**       10.447 +- 0.712
  1341 N      0.991**       10.414 +- 0.900
  1344 S      0.976*        10.271 +- 1.480
  1345 C      0.999**       10.495 +- 0.226
  1346 V      0.986*        10.361 +- 1.151
  1347 E      0.994**       10.442 +- 0.743
  1348 N      0.783         8.341 +- 4.105
  1349 C      0.999**       10.490 +- 0.302
  1350 L      0.995**       10.453 +- 0.668
  1351 K      0.991**       10.419 +- 0.878
  1352 G      0.978*        10.283 +- 1.435
  1353 K      0.993**       10.429 +- 0.820
  1354 F      0.910         9.609 +- 2.839
  1355 K      0.995**       10.451 +- 0.685
  1356 E      0.833         8.843 +- 3.708
  1357 V      0.994**       10.441 +- 0.747
  1358 R      0.988*        10.390 +- 1.019
  1359 P      0.992**       10.426 +- 0.836
  1360 R      0.946         9.969 +- 2.234
  1361 Y      0.999**       10.492 +- 0.270
  1362 S      0.919         9.697 +- 2.707
  1363 V      0.995**       10.450 +- 0.687
  1366 D      0.999**       10.491 +- 0.297
  1367 I      0.994**       10.446 +- 0.716
  1368 F      0.890         9.411 +- 3.105
  1370 P      0.995**       10.449 +- 0.696
  1371 I      0.993**       10.437 +- 0.770
  1372 N      0.990**       10.409 +- 0.925
  1373 L      0.998**       10.479 +- 0.454
  1374 G      0.999**       10.491 +- 0.297
  1377 K      0.999**       10.493 +- 0.263
  1378 N      0.755         8.061 +- 4.285
  1379 C      0.996**       10.461 +- 0.607
  1380 Q      0.993**       10.431 +- 0.808
  1383 S      0.999**       10.495 +- 0.227
  1384 N      0.995**       10.451 +- 0.681
  1386 S      0.998**       10.479 +- 0.447
  1387 L      0.983*        10.329 +- 1.285
  1388 E      0.904         9.547 +- 2.925
  1390 C      0.998**       10.478 +- 0.454
  1391 K      0.984*        10.352 +- 1.181
  1392 M      0.833         8.838 +- 3.711
  1393 K      0.987*        10.373 +- 1.093
  1394 C      0.993**       10.435 +- 0.783
  1395 S      0.980*        10.300 +- 1.385
  1397 N      0.990**       10.409 +- 0.925
  1398 N      0.896         9.463 +- 3.039
  1399 I      0.986*        10.362 +- 1.156
  1400 G      0.945         9.954 +- 2.265
  1401 R      0.999**       10.491 +- 0.296
  1402 F      0.993**       10.431 +- 0.809
  1403 I      0.988*        10.387 +- 1.040
  1404 R      0.989*        10.391 +- 1.029
  1405 F      0.999**       10.495 +- 0.221
  1406 V      0.994**       10.441 +- 0.747
  1407 F      0.978*        10.287 +- 1.429
  1408 T      0.988*        10.379 +- 1.077
  1410 V      0.979*        10.294 +- 1.404
  1411 M      0.966*        10.169 +- 1.777



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:   0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  1.000

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 0.702 0.297 0.000 0.000

sum of density on p0-p1 =   1.000000
