
seed used = 141371489

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


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b3482.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 2  	ls = 1426
# site patterns = 257
   13   36    6   19   47   24   22   55    3   53   36   35   58   21    9
    3    4   26   22    1    2   11   44   40    5    4    6    1   11    7
    8   78   18   19    6    6   50   28   12    6   46   35   16   33   14
   25    8   31    9   21    6    3    7   24   33    1    5   14    1    4
    1    1    5    1    1    1    2    1    2    8    2    1    2    1    1
    2    1    1    1    2    1    1    1    1    2    2    1    1    3    1
    1    1    1    1    1    1    1    1    2    1    1    1    3    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    3
    1    1    1    1    2    1    1    1    1    1    1    2    2    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    3    1    1    2
    1    1    1    1    1    1    1    1    2    1    1    1    1    3    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    1    1    1    1    1    1    1
    1    1

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



Codon usage in sequences
--------------------------------------------------------------
Phe TTT 11 11 | Ser TCT  5  3 | Tyr TAT 40 43 | Cys TGT  6  7
    TTC 14 14 |     TCC  8  7 |     TAC 38 38 |     TGC  9  7
Leu TTA 13 11 |     TCA 10  9 | *** TAA  0  0 | *** TGA  0  0
    TTG  4  4 |     TCG  5  4 |     TAG  0  0 | Trp TGG 28 27
--------------------------------------------------------------
Leu CTT  8  7 | Pro CCT 11  8 | His CAT 16 11 | Arg CGT 25 22
    CTC 19 20 |     CCC 13 13 |     CAC 34 36 |     CGC 46 50
    CTA  2  4 |     CCA  5  4 | Gln CAA  5  4 |     CGA  3  3
    CTG 81 79 |     CCG 47 50 |     CAG 55 56 |     CGG 36 33
--------------------------------------------------------------
Ile ATT  9 10 | Thr ACT  8  6 | Asn AAT 16 21 | Ser AGT 20 21
    ATC 31 30 |     ACC 48 48 |     AAC 27 24 |     AGC 42 41
    ATA 14 10 |     ACA 18 18 | Lys AAA 30 32 | Arg AGA  7  6
Met ATG 16 18 |     ACG 39 39 |     AAG  9  9 |     AGG 10  9
--------------------------------------------------------------
Val GTT  5  5 | Ala GCT  7  6 | Asp GAT 40 41 | Gly GGT 33 25
    GTC 10  8 |     GCC 31 28 |     GAC 58 56 |     GGC 61 64
    GTA  6  8 |     GCA 25 21 | Glu GAA 57 59 |     GGA 12 15
    GTG 42 42 |     GCG 28 27 |     GAG 30 26 |     GGG 25 27
--------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13536    C:0.28774    A:0.24380    G:0.33310
position  2:    T:0.20198    C:0.21828    A:0.32247    G:0.25726
position  3:    T:0.18427    C:0.34656    A:0.14670    G:0.32247

#2: O157           
position  1:    T:0.13357    C:0.28881    A:0.24693    G:0.33069
position  2:    T:0.20289    C:0.21011    A:0.32924    G:0.25776
position  3:    T:0.17834    C:0.34946    A:0.14729    G:0.32491

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      22 | Ser S TCT       8 | Tyr Y TAT      83 | Cys C TGT      13
      TTC      28 |       TCC      15 |       TAC      76 |       TGC      16
Leu L TTA      24 |       TCA      19 | *** * TAA       0 | *** * TGA       0
      TTG       8 |       TCG       9 |       TAG       0 | Trp W TGG      55
------------------------------------------------------------------------------
Leu L CTT      15 | Pro P CCT      19 | His H CAT      27 | Arg R CGT      47
      CTC      39 |       CCC      26 |       CAC      70 |       CGC      96
      CTA       6 |       CCA       9 | Gln Q CAA       9 |       CGA       6
      CTG     160 |       CCG      97 |       CAG     111 |       CGG      69
------------------------------------------------------------------------------
Ile I ATT      19 | Thr T ACT      14 | Asn N AAT      37 | Ser S AGT      41
      ATC      61 |       ACC      96 |       AAC      51 |       AGC      83
      ATA      24 |       ACA      36 | Lys K AAA      62 | Arg R AGA      13
Met M ATG      34 |       ACG      78 |       AAG      18 |       AGG      19
------------------------------------------------------------------------------
Val V GTT      10 | Ala A GCT      13 | Asp D GAT      81 | Gly G GGT      58
      GTC      18 |       GCC      59 |       GAC     114 |       GGC     125
      GTA      14 |       GCA      46 | Glu E GAA     116 |       GGA      27
      GTG      84 |       GCG      55 |       GAG      56 |       GGG      52
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.13448    C:0.28827    A:0.24535    G:0.33190
position  2:    T:0.20243    C:0.21423    A:0.32582    G:0.25751
position  3:    T:0.18133    C:0.34800    A:0.14700    G:0.32368

Codon frequencies under model, for use in evolver:
  0.00506657  0.00972342  0.00410722  0.00904388
  0.00536197  0.01029033  0.00434669  0.00957117
  0.00815485  0.01565023  0.00000000  0.00000000
  0.00644511  0.01236901  0.00000000  0.01150458
  0.01086078  0.02084328  0.00880430  0.01938661
  0.01149401  0.02205852  0.00931763  0.02051692
  0.01748087  0.03354811  0.01417089  0.03120353
  0.01381584  0.02651442  0.01119982  0.02466141
  0.00924379  0.01774006  0.00749349  0.01650026
  0.00978274  0.01877438  0.00793039  0.01746229
  0.01487826  0.02855335  0.01206108  0.02655784
  0.01175889  0.02256686  0.00953235  0.02098973
  0.01250472  0.02399822  0.01013697  0.02232106
  0.01323380  0.02539741  0.01072799  0.02362246
  0.02012686  0.03862611  0.01631586  0.03592665
  0.01590707  0.03052777  0.01289508  0.02839428



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                 0.6269 (0.0697 0.1112)


TREE #  1:  (1, 2);   MP score: -1
lnL(ntime:  2  np:  7):  -6925.121667     +0.000000
   3..1     3..2  
  1.73184  0.18924  2.80662  0.74269  0.17979  0.00000 163.48433
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.92108

(1: 1.731842, 2: 0.189242);

(K12: 1.731842, O157: 0.189242);

Detailed output identifying parameters

kappa (ts/tv) =  2.80662


dN/dS for site classes (K=3)

p:   0.74269  0.17979  0.07753
w:   0.00000  1.00000163.48433

dN & dS for each branch

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

   3..1       1.732   1071.7   3206.3  12.8543   0.7507   0.0584   62.6 2407.0
   3..2       0.189   1071.7   3206.3  12.8543   0.0820   0.0064    6.8  263.0


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

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

   491 L      0.963*        157.491
   604 I      0.871         142.573
   812 Y      0.980*        160.276
   864 S      0.554         90.981
   892 T      0.935         152.853
  1176 A      0.923         150.917
  1227 R      0.727         118.857
  1244 G      0.983*        160.750
  1246 Q      0.927         151.610
  1248 N      0.830         135.929
  1250 I      0.886         145.012
  1251 S      1.000**       163.476
  1256 L      0.622         101.789
  1259 S      0.554         90.981
  1260 M      0.997**       163.005
  1261 W      0.990**       161.870
  1262 E      0.834         136.550
  1263 D      1.000**       163.471
  1264 A      0.975*        159.448
  1291 S      0.988*        161.476
  1292 T      0.849         138.939
  1293 A      0.567         93.051
  1294 Y      1.000**       163.473
  1295 D      0.999**       163.368
  1298 N      0.999**       163.398
  1299 K      0.945         154.543
  1300 I      1.000**       163.475
  1302 S      0.938         153.379
  1306 C      0.949         155.242
  1311 F      0.955*        156.095
  1312 A      0.550         90.410
  1318 D      0.926         151.417
  1321 S      1.000**       163.404
  1323 R      0.921         150.665
  1326 S      0.959*        156.754
  1327 T      0.888         145.298
  1328 A      0.999**       163.398
  1331 N      0.838         137.086
  1332 R      0.994**       162.571
  1333 G      0.998**       163.223
  1335 R      0.960*        157.025
  1336 K      0.949         155.212
  1337 G      0.956*        156.377
  1338 S      0.992**       162.123
  1339 Y      0.932         152.433
  1340 P      0.996**       162.837
  1341 F      0.999**       163.399
  1345 S      0.983*        160.697
  1346 P      1.000**       163.458
  1349 N      0.947         154.947
  1351 T      0.988*        161.533
  1355 S      1.000**       163.459
  1356 A      0.518         85.165
  1362 A      1.000**       163.445
  1363 D      0.917         149.994
  1364 S      0.995**       162.593
  1365 H      0.910         148.827
  1369 W      0.999**       163.318
  1370 D      0.929         151.941
  1371 E      0.947         154.947
  1373 F      0.988*        161.512
  1374 S      0.657         107.770
  1375 G      0.998**       163.227
  1379 K      0.949         155.212
  1380 I      0.963*        157.408
  1381 V      0.992**       162.139
  1382 K      0.949         155.212
  1384 K      0.992**       162.157
  1386 N      0.999**       163.399
  1387 N      1.000**       163.476
  1390 S      1.000**       163.471
  1392 Y      1.000**       163.466
  1393 L      1.000**       163.477
  1394 G      0.994**       162.524
  1395 T      1.000**       163.466
  1396 P      0.999**       163.333
  1399 N      0.979*        160.100
  1400 F      1.000**       163.470
  1402 A      0.975*        159.448
  1403 I      0.974*        159.197
  1404 D      0.996**       162.915
  1405 N      0.838         137.086
  1406 H      0.997**       162.922
  1407 G      0.999**       163.281
  1408 K      0.991**       161.987
  1411 T      0.631         103.483
  1413 R      0.947         154.881
  1414 K      0.979*        160.031
  1415 G      1.000**       163.425
  1417 P      1.000**       163.458
  1419 V      0.996**       162.835
  1420 C      0.954*        156.076
  1423 H      0.982*        160.536
  1426 M      0.998**       163.112


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

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

    45 S      0.861         9.098 +- 3.486
   248 W      0.880         9.298 +- 3.264
   400 D      0.759         8.070 +- 4.316
   411 A      0.872         9.217 +- 3.358
   478 N      0.775         8.228 +- 4.215
   491 L      0.991**       10.415 +- 0.905
   498 L      0.896         9.454 +- 3.071
   604 I      0.991**       10.415 +- 0.896
   610 A      0.831         8.795 +- 3.779
   630 V      0.824         8.726 +- 3.839
   631 R      0.896         9.456 +- 3.068
   750 A      0.841         8.902 +- 3.681
   754 R      0.810         8.589 +- 3.952
   812 Y      0.993**       10.430 +- 0.813
   825 E      0.811         8.600 +- 3.944
   826 Y      0.868         9.169 +- 3.411
   834 E      0.867         9.162 +- 3.419
   838 S      0.842         8.908 +- 3.675
   863 L      0.890         9.391 +- 3.151
   864 S      0.913         9.625 +- 2.834
   892 T      0.992**       10.425 +- 0.841
   893 T      0.890         9.399 +- 3.142
  1053 S      0.861         9.099 +- 3.486
  1138 E      0.865         9.139 +- 3.444
  1142 N      0.775         8.228 +- 4.215
  1171 T      0.862         9.110 +- 3.475
  1176 A      0.906         9.552 +- 2.940
  1244 G      0.996**       10.463 +- 0.589
  1246 Q      0.916         9.659 +- 2.785
  1248 N      0.870         9.188 +- 3.392
  1250 I      0.982*        10.325 +- 1.300
  1251 S      0.999**       10.493 +- 0.242
  1252 D      0.778         8.260 +- 4.194
  1253 I      0.805         8.535 +- 3.994
  1259 S      0.913         9.625 +- 2.834
  1260 M      0.997**       10.470 +- 0.532
  1261 W      0.995**       10.452 +- 0.670
  1262 E      0.887         9.365 +- 3.186
  1263 D      0.999**       10.492 +- 0.260
  1264 A      0.995**       10.456 +- 0.644
  1265 K      0.864         9.127 +- 3.456
  1291 S      0.993**       10.430 +- 0.814
  1292 T      0.876         9.255 +- 3.315
  1293 A      0.922         9.716 +- 2.696
  1294 Y      1.000**       10.495 +- 0.211
  1295 D      0.996**       10.465 +- 0.569
  1298 N      0.999**       10.491 +- 0.275
  1299 K      0.963*        10.131 +- 1.885
  1300 I      0.999**       10.494 +- 0.218
  1302 S      0.961*        10.113 +- 1.928
  1303 Q      0.886         9.352 +- 3.199
  1306 C      0.994**       10.438 +- 0.762
  1308 D      0.850         8.990 +- 3.596
  1311 F      0.895         9.441 +- 3.088
  1312 A      0.913         9.627 +- 2.832
  1318 D      0.990*        10.402 +- 0.960
  1321 S      0.999**       10.493 +- 0.237
  1323 R      0.994**       10.444 +- 0.729
  1326 S      0.897         9.467 +- 3.054
  1327 T      0.968*        10.185 +- 1.744
  1328 A      0.999**       10.491 +- 0.275
  1331 N      0.872         9.209 +- 3.369
  1332 R      0.997**       10.468 +- 0.548
  1333 G      0.999**       10.490 +- 0.293
  1334 E      0.850         8.990 +- 3.596
  1335 R      0.994**       10.439 +- 0.758
  1336 K      0.993**       10.431 +- 0.808
  1337 G      0.978*        10.285 +- 1.446
  1338 S      0.997**       10.466 +- 0.562
  1339 Y      0.905         9.545 +- 2.950
  1340 P      0.980*        10.299 +- 1.400
  1341 F      0.997**       10.474 +- 0.494
  1345 S      0.982*        10.318 +- 1.333
  1346 P      0.999**       10.494 +- 0.223
  1349 N      0.993**       10.430 +- 0.813
  1351 T      0.931         9.807 +- 2.546
  1353 K      0.883         9.324 +- 3.234
  1355 S      0.998**       10.477 +- 0.463
  1356 A      0.899         9.484 +- 3.032
  1362 A      0.998**       10.484 +- 0.379
  1363 D      0.904         9.530 +- 2.971
  1364 S      0.997**       10.468 +- 0.546
  1365 H      0.901         9.503 +- 3.009
  1368 Y      0.899         9.488 +- 3.026
  1369 W      0.997**       10.471 +- 0.519
  1370 D      0.968*        10.176 +- 1.767
  1371 E      0.993**       10.430 +- 0.813
  1372 I      0.895         9.446 +- 3.081
  1373 F      0.978*        10.279 +- 1.467
  1374 S      0.931         9.806 +- 2.548
  1375 G      0.999**       10.492 +- 0.273
  1376 K      0.867         9.162 +- 3.419
  1377 D      0.850         8.990 +- 3.596
  1379 K      0.993**       10.431 +- 0.808
  1380 I      0.930         9.801 +- 2.558
  1381 V      0.996**       10.464 +- 0.579
  1382 K      0.993**       10.431 +- 0.808
  1384 K      0.996**       10.462 +- 0.597
  1385 D      0.850         8.990 +- 3.596
  1386 N      0.997**       10.470 +- 0.530
  1387 N      0.999**       10.493 +- 0.242
  1388 I      0.857         9.058 +- 3.529
  1390 S      0.999**       10.492 +- 0.260
  1391 F      0.918         9.676 +- 2.758
  1392 Y      1.000**       10.495 +- 0.202
  1393 L      1.000**       10.496 +- 0.192
  1394 G      0.997**       10.468 +- 0.547
  1395 T      1.000**       10.495 +- 0.202
  1396 P      0.998**       10.485 +- 0.373
  1397 S      0.862         9.109 +- 3.475
  1399 N      0.993**       10.434 +- 0.786
  1400 F      0.999**       10.488 +- 0.336
  1402 A      0.995**       10.456 +- 0.644
  1403 I      0.995**       10.452 +- 0.670
  1404 D      0.995**       10.452 +- 0.669
  1405 N      0.872         9.209 +- 3.369
  1406 H      0.995**       10.452 +- 0.673
  1407 G      0.999**       10.488 +- 0.323
  1408 K      0.996**       10.462 +- 0.599
  1409 E      0.884         9.332 +- 3.224
  1410 I      0.899         9.481 +- 3.036
  1411 T      0.923         9.725 +- 2.682
  1413 R      0.991**       10.417 +- 0.885
  1414 K      0.990*        10.398 +- 0.988
  1415 G      0.999**       10.491 +- 0.278
  1417 P      0.999**       10.494 +- 0.223
  1418 N      0.905         9.547 +- 2.946
  1419 V      0.995**       10.450 +- 0.686
  1420 C      0.994**       10.444 +- 0.728
  1421 R      0.883         9.324 +- 3.234
  1422 V      0.897         9.463 +- 3.060
  1423 H      0.995**       10.447 +- 0.707
  1426 M      0.997**       10.472 +- 0.510



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  0.001  0.999

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 0.999 0.000 0.000

sum of density on p0-p1 =   1.000000
