
seed used = 140027981

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4036.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 445
# site patterns = 82
   15    7    7   11    6   11    2    2    5    8    9    6   10   19    1
    7   10   16   12   14    3    7   11    7   22    1   19    2    7    1
   18    6    2   14    2   14   23    4    1    6    3    8   19    1    4
    1    4    1   12    2    1    3    2    1    1    1    1    4    2    4
    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 ATT ACT CTG CGC AAA CTT CCT GCG GTT GCC GTC GCA GGC GTA TCT GCT CAG GAT TTC CAC TAT CGT TCC GGT GGT TGG ACA AGC GGT GAA CAA TGT ACC AGT TAC AAC TTA TTG GTG GAG AAG GAC GCA AAT GAT CCG GGT ATC CCA GGC CAT CTC GCT TTC ATC TTG TCG GGC TTT GGG GTT GCA AAC GTC ACG CTC TCA TAC ACC GGT AAC GCT GAT AAC GCG AAC TTC AAA GCC GTT CCT 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ..A ... ... ..T ... ... ... ..T ... C.. ... ... ... ..T ..C ..G ... ..T ... ... ... ... .A. ..C G.T AGC A.G GTT C.. ... .A. ... ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ..A ... ... ..T ... ... ... ..T ... C.. ... ... ... ..T ..C ..G ... ..T ... ... ... ... .A. ..C G.T AGC A.G GTT C.. ... .A. ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ..G ... ... C.. ... ..T ... ..T ..C ..G ..T ... ... ..T ... ..T ... ... .G. T.. TCA .C. C.A T.. .A. ..G ..T ..G T.G 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ..C ... ... ... ... ... ... ... ..A ... G.. C.. ... ... ... ..T ... ... ... ... ... ... ... ... .A. ..C G.T AGC A.G GTT C.. ... .A. ... ... ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ..C ... ... ... ... ... ... ... ..A ... G.. C.. ... ... ... ..T ... ... ... ... ... ... ... ... .A. ..C G.T AGC A.G GTT C.. ... .A. ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.19775    C:0.15730    A:0.26966    G:0.37528
position  2:    T:0.22697    C:0.20899    A:0.34831    G:0.21573
position  3:    T:0.27191    C:0.38202    A:0.13034    G:0.21573

#2: S2457T         
position  1:    T:0.19551    C:0.16180    A:0.26966    G:0.37303
position  2:    T:0.22697    C:0.20449    A:0.35056    G:0.21798
position  3:    T:0.27191    C:0.37978    A:0.12809    G:0.22022

#3: Shig4337       
position  1:    T:0.19551    C:0.16180    A:0.26966    G:0.37303
position  2:    T:0.22697    C:0.20449    A:0.35056    G:0.21798
position  3:    T:0.27191    C:0.37978    A:0.12809    G:0.22022

#4: CFT073         
position  1:    T:0.20449    C:0.15955    A:0.26742    G:0.36854
position  2:    T:0.22472    C:0.21348    A:0.34382    G:0.21798
position  3:    T:0.27191    C:0.37528    A:0.12809    G:0.22472

#5: O157           
position  1:    T:0.19551    C:0.16180    A:0.26742    G:0.37528
position  2:    T:0.22697    C:0.20449    A:0.35056    G:0.21798
position  3:    T:0.26517    C:0.38652    A:0.13034    G:0.21798

#6: EDL933         
position  1:    T:0.19551    C:0.16180    A:0.26742    G:0.37528
position  2:    T:0.22697    C:0.20449    A:0.35056    G:0.21798
position  3:    T:0.26517    C:0.38652    A:0.13034    G:0.21798

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      26 | Ser S TCT      43 | Tyr Y TAT      43 | Cys C TGT      12
      TTC      89 |       TCC      42 |       TAC      95 |       TGC       0
Leu L TTA      24 |       TCA       7 | *** * TAA       0 | *** * TGA       0
      TTG       7 |       TCG      25 |       TAG       0 | Trp W TGG     114
------------------------------------------------------------------------------
Leu L CTT      13 | Pro P CCT      17 | His H CAT      18 | Arg R CGT      66
      CTC      17 |       CCC       0 |       CAC      18 |       CGC      36
      CTA       0 |       CCA      13 | Gln Q CAA      36 |       CGA       0
      CTG      71 |       CCG      28 |       CAG      96 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      42 | Thr T ACT      42 | Asn N AAT      25 | Ser S AGT      12
      ATC      76 |       ACC      87 |       AAC     154 |       AGC      47
      ATA       0 |       ACA      12 | Lys K AAA      71 | Arg R AGA       0
Met M ATG      90 |       ACG       6 |       AAG      53 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      62 | Ala A GCT      65 | Asp D GAT      81 | Gly G GGT     153
      GTC      45 |       GCC      59 |       GAC     116 |       GGC     138
      GTA       6 |       GCA      66 | Glu E GAA     108 |       GGA       2
      GTG      37 |       GCG      40 |       GAG      18 |       GGG       1
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.19738    C:0.16067    A:0.26854    G:0.37341
position  2:    T:0.22659    C:0.20674    A:0.34906    G:0.21760
position  3:    T:0.26966    C:0.38165    A:0.12921    G:0.21948

Codon frequencies under model, for use in evolver:
  0.01242802  0.01758911  0.00595509  0.01011503
  0.01133929  0.01604824  0.00543341  0.00922892
  0.01914532  0.02709595  0.00000000  0.00000000
  0.01193501  0.01689136  0.00000000  0.00971377
  0.01011693  0.01431827  0.00484770  0.00823406
  0.00923065  0.01306394  0.00442302  0.00751273
  0.01558509  0.02205723  0.00746786  0.01268453
  0.00971560  0.01375027  0.00465539  0.00790742
  0.01690872  0.02393053  0.00810209  0.01376182
  0.01542746  0.02183414  0.00739232  0.01255624
  0.02604781  0.03686488  0.01248124  0.02120002
  0.01623796  0.02298122  0.00778069  0.01321589
  0.02351184  0.03327579  0.01126609  0.01913603
  0.02145213  0.03036072  0.01027914  0.01745965
  0.03621989  0.05126121  0.01735537  0.02947897
  0.02257914  0.03195575  0.01081917  0.01837691



Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
S2457T               0.1966 (0.0097 0.0492)
Shig4337             0.1966 (0.0097 0.0492)-1.0000 (0.0000 0.0000)
CFT073               0.1349 (0.0089 0.0664) 0.1426 (0.0107 0.0747) 0.1426 (0.0107 0.0747)
O157                 0.3060 (0.0106 0.0348) 0.0347 (0.0010 0.0277) 0.0347 (0.0010 0.0277) 0.1640 (0.0116 0.0709)
EDL933               0.3060 (0.0106 0.0348) 0.0347 (0.0010 0.0277) 0.0347 (0.0010 0.0277) 0.1640 (0.0116 0.0709)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 42
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -2048.194646     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.29173  0.18162  0.00000  0.00000  0.00000  0.60134  0.11045  0.00000  0.00000  1.88939  0.92178  0.06913  0.00000 545.21917
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.18516

((1: 0.291731, (2: 0.000004, 3: 0.000004): 0.181620): 0.000000, (4: 0.601344, (5: 0.000004, 6: 0.000004): 0.110452): 0.000000);

((K12: 0.291731, (S2457T: 0.000004, Shig4337: 0.000004): 0.181620): 0.000000, (CFT073: 0.601344, (O157: 0.000004, EDL933: 0.000004): 0.110452): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  1.88939


dN/dS for site classes (K=3)

p:   0.92178  0.06913  0.00909
w:   0.00000  1.00000545.21917

dN & dS for each branch

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

   7..8       0.000    315.8   1019.2   5.0236   0.0000   0.0000    0.0    0.0
   8..1       0.292    315.8   1019.2   5.0236   0.1200   0.0239    7.5  122.3
   8..9       0.182    315.8   1019.2   5.0236   0.0747   0.0149    4.7   76.1
   9..2       0.000    315.8   1019.2   5.0236   0.0000   0.0000    0.0    0.0
   9..3       0.000    315.8   1019.2   5.0236   0.0000   0.0000    0.0    0.0
   7..10      0.000    315.8   1019.2   5.0236   0.0000   0.0000    0.0    0.0
  10..4       0.601    315.8   1019.2   5.0236   0.2473   0.0492   15.5  252.1
  10..11      0.110    315.8   1019.2   5.0236   0.0454   0.0090    2.9   46.3
  11..5       0.000    315.8   1019.2   5.0236   0.0000   0.0000    0.0    0.0
  11..6       0.000    315.8   1019.2   5.0236   0.0000   0.0000    0.0    0.0


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

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

   407 N      0.995**       542.428
   408 A      1.000**       545.217
   409 D      1.000**       545.193
   410 N      1.000**       545.199


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

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

   405 T      0.913         8.784 +- 2.667
   407 N      0.993**       9.470 +- 1.366
   408 A      1.000**       9.524 +- 1.182
   409 D      1.000**       9.525 +- 1.180
   410 N      0.999**       9.523 +- 1.189
   412 A      0.621         6.082 +- 4.524
   419 P      0.579         5.693 +- 4.595



The grid (see ternary graph for p0-p1)

w0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
w2:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

w0:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.002  0.009  0.029  0.073  0.151  0.276  0.460

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 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.997

sum of density on p0-p1 =   1.000000
