
seed used = 140020729

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3492.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 397
# site patterns = 109
   17   14    1    6   10    4    8    1   17    4    8   13    1    7    9
    3    5   22    3   11    1    2    7    3    4    6    7    8    1    1
    6    1    3   11    9    2    5    6    1    1    5   11    4    6    8
    1    4    8    2    1    6    4    4    1    7    2    1    1    1    1
    6    1    1    2    1    4    1    1    1    1    1    2    1    2    3
    6    1    1    1    1    2    1    1    1    1    1    2    1    1    2
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1

1       
K12                   GTG GAA AGG TTT GAT GCC ATT ATA GGC GCT GGT GCG GCG ATG TTC TGT TCT CTG GCA CAG GCA GGA CGC CGG GTT ATC AAT AAA AAA CCA GGG CTT TGC AAC ACC CTT TAT GTC GAA CCA AGC CCG CAT AAG CTC GCA CGT TGG CAC GGC GAG ACG TTA CAA GAC TCC GTG ACC TTC AGA TTG AGT GAA ACA GAT ACT TGC ATC ACT GGT GGG TCA GGG GCG TCG CAA TTT CGC CCA CTC CCT GGC CAC TTG CAG TCA TAC GGG AGC CTA AAC CAA ACA CTA CGC CAG GTT CGT GCA ACC GTA CCC CTC TTC GTC AGT ATT GCA GCA 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... .T. .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ..A ... ... ... ..T ..T ... ... ... ... ... ... ... ... T.. ... ... ... ... ..T ... ..T ... GCG T.. ATT 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... .T. .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ..A ... ... ... ..T ..T ... ... ... ... ... ... ... ... T.. ... ... ... ... ..T ... ..T ... GCG T.. ATT 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... .G. ..G ... ... ... ... ... ..G ... ... ... ... ... ... ... ..G ... ... ... G.. ... ... ... ..C ..T ... ..A ... ... ..T ..C ... ..A ... ... ..A ... ... ..C ..T ... ..T ... ..T ... ..A ... ..C ... ..T ... ... ..T ... ..G ..G ..G ..A ..C ... A.. ..T ... ... ... ... ... ... G.G ... .A. 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ..T ... ..A ... ..T ... ..C ..C ... ... ..C ... ... ... ... ... ... ... ... ... ..T ... ..A ..C ... ... ..T ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ..T ..T ... ... ... ..G 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ..T ... ..A ... ..T ... ..C ..C ... ... ..C ... ... ... ... ... ... ... ... ... ..T ... ..A ..C ... ... ..T ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ..T ..T ... ... ... ..G 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  7  7  7  6  8  8 | Ser TCT  5  5  5  5  5  5 | Tyr TAT  5  5  5  5  5  5 | Cys TGT  3  4  4  3  4  4
    TTC 11 11 11 12  9  9 |     TCC  2  2  2  3  3  3 |     TAC  2  2  2  2  2  2 |     TGC  4  4  4  4  3  3
Leu TTA  4  5  5  5  4  4 |     TCA  3  4  4  2  2  2 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  7  6  6  6  7  7 |     TCG  3  3  3  3  3  3 |     TAG  0  0  0  0  0  0 | Trp TGG  8  8  8  8  8  8
--------------------------------------------------------------------------------------------------------------
Leu CTT  3  4  4  3  3  3 | Pro CCT  2  2  2  2  2  2 | His CAT  4  4  4  4  5  5 | Arg CGT  5  4  4  6  5  5
    CTC 10  9  9 10 10 10 |     CCC  1  1  1  1  1  1 |     CAC  3  3  3  3  2  2 |     CGC  9  9  9  7  9  9
    CTA  3  4  4  2  3  3 |     CCA  3  2  2  2  2  2 | Gln CAA  8  8  8  8  8  8 |     CGA  0  0  0  0  0  0
    CTG 22 22 22 23 22 22 |     CCG 11 11 11 12 12 12 |     CAG 13 13 13 13 13 13 |     CGG  3  3  3  4  3  3
--------------------------------------------------------------------------------------------------------------
Ile ATT  9  9  9  9  9  9 | Thr ACT  5  4  4  5  4  4 | Asn AAT  7  7  7  8  7  7 | Ser AGT  2  3  3  1  3  3
    ATC  7  7  7  6  7  7 |     ACC 11 12 12 10 12 12 |     AAC 12 12 12 11 12 12 |     AGC  6  5  5  7  5  5
    ATA  1  2  2  1  1  1 |     ACA  3  3  3  3  3  3 | Lys AAA  9  8  8  9  9  9 | Arg AGA  1  1  1  1  1  1
Met ATG  7  7  7  7  7  7 |     ACG  4  4  4  5  4  4 |     AAG  6  6  6  6  6  6 |     AGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------
Val GTT  5  6  6  4  6  6 | Ala GCT  4  4  4  4  4  4 | Asp GAT 11 11 11 11 11 11 | Gly GGT  9 11 11 11  8  8
    GTC  7  6  6  8  7  7 |     GCC  4  4  4  5  4  4 |     GAC  7  7  7  7  7  7 |     GGC 19 18 18 18 21 21
    GTA  1  3  3  1  1  1 |     GCA  8  7  7  8  6  6 | Glu GAA 16 16 16 16 16 16 |     GGA  2  2  2  4  2  2
    GTG 18 17 17 19 18 18 |     GCG 16 15 15 14 18 18 |     GAG  6  6  6  6  6  6 |     GGG  9  8  8  7  8  8
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.16121    C:0.25189    A:0.22922    G:0.35768
position  2:    T:0.30730    C:0.21411    A:0.27456    G:0.20403
position  3:    T:0.21662    C:0.28967    A:0.15617    G:0.33753

#2: S2457T         
position  1:    T:0.16625    C:0.24937    A:0.22922    G:0.35516
position  2:    T:0.31486    C:0.20907    A:0.27204    G:0.20403
position  3:    T:0.22670    C:0.28212    A:0.16373    G:0.32746

#3: Shig4337       
position  1:    T:0.16625    C:0.24937    A:0.22922    G:0.35516
position  2:    T:0.31486    C:0.20907    A:0.27204    G:0.20403
position  3:    T:0.22670    C:0.28212    A:0.16373    G:0.32746

#4: CFT073         
position  1:    T:0.16121    C:0.25189    A:0.22670    G:0.36020
position  2:    T:0.30730    C:0.21159    A:0.27456    G:0.20655
position  3:    T:0.21914    C:0.28715    A:0.15617    G:0.33753

#5: O157           
position  1:    T:0.15869    C:0.25189    A:0.22922    G:0.36020
position  2:    T:0.30730    C:0.21411    A:0.27456    G:0.20403
position  3:    T:0.22418    C:0.28715    A:0.14610    G:0.34257

#6: EDL933         
position  1:    T:0.15869    C:0.25189    A:0.22922    G:0.36020
position  2:    T:0.30730    C:0.21411    A:0.27456    G:0.20403
position  3:    T:0.22418    C:0.28715    A:0.14610    G:0.34257

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      43 | Ser S TCT      30 | Tyr Y TAT      30 | Cys C TGT      22
      TTC      63 |       TCC      15 |       TAC      12 |       TGC      22
Leu L TTA      27 |       TCA      17 | *** * TAA       0 | *** * TGA       0
      TTG      39 |       TCG      18 |       TAG       0 | Trp W TGG      48
------------------------------------------------------------------------------
Leu L CTT      20 | Pro P CCT      12 | His H CAT      26 | Arg R CGT      29
      CTC      58 |       CCC       6 |       CAC      16 |       CGC      52
      CTA      19 |       CCA      13 | Gln Q CAA      48 |       CGA       0
      CTG     133 |       CCG      69 |       CAG      78 |       CGG      19
------------------------------------------------------------------------------
Ile I ATT      54 | Thr T ACT      26 | Asn N AAT      43 | Ser S AGT      15
      ATC      41 |       ACC      69 |       AAC      71 |       AGC      33
      ATA       8 |       ACA      18 | Lys K AAA      52 | Arg R AGA       6
Met M ATG      42 |       ACG      25 |       AAG      36 |       AGG       6
------------------------------------------------------------------------------
Val V GTT      33 | Ala A GCT      24 | Asp D GAT      66 | Gly G GGT      58
      GTC      41 |       GCC      25 |       GAC      42 |       GGC     115
      GTA      10 |       GCA      42 | Glu E GAA      96 |       GGA      14
      GTG     107 |       GCG      96 |       GAG      36 |       GGG      48
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16205    C:0.25105    A:0.22880    G:0.35810
position  2:    T:0.30982    C:0.21201    A:0.27372    G:0.20445
position  3:    T:0.22292    C:0.28589    A:0.15533    G:0.33585

Codon frequencies under model, for use in evolver:
  0.01150192  0.01475105  0.00801452  0.01732869
  0.00787055  0.01009387  0.00548419  0.01185771
  0.01016159  0.01303209  0.00000000  0.00000000
  0.00759002  0.00973409  0.00000000  0.01143506
  0.01781903  0.02285266  0.01241628  0.02684600
  0.01219324  0.01563766  0.00849623  0.01837023
  0.01574256  0.02018961  0.01096939  0.02371760
  0.01175863  0.01508028  0.00819340  0.01771545
  0.01623975  0.02082726  0.01131584  0.02446667
  0.01111257  0.01425171  0.00774322  0.01674210
  0.01434732  0.01840023  0.00999719  0.02161554
  0.01071648  0.01374373  0.00746723  0.01614535
  0.02541745  0.03259752  0.01771084  0.03829371
  0.01739270  0.02230589  0.01211921  0.02620369
  0.02245552  0.02879889  0.01564698  0.03383130
  0.01677276  0.02151083  0.01168724  0.02526970



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               0.2605 (0.0105 0.0404)
Shig4337             0.2605 (0.0105 0.0404)-1.0000 (0.0000 0.0000)
CFT073               0.0926 (0.0084 0.0911) 0.1675 (0.0153 0.0911) 0.1675 (0.0153 0.0911)
O157                 0.0691 (0.0034 0.0487) 0.2222 (0.0143 0.0644) 0.2222 (0.0143 0.0644) 0.0640 (0.0073 0.1142)
EDL933               0.0691 (0.0034 0.0487) 0.2222 (0.0143 0.0644) 0.2222 (0.0143 0.0644) 0.0640 (0.0073 0.1142)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 59
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1941.897095     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.02853  0.19831  0.00000  0.00000  0.07124  0.36529  0.13908  0.00000  0.00000  6.48492  0.99494  0.00000  0.10986 501.50324
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.80247

((1: 0.028532, (2: 0.000004, 3: 0.000004): 0.198307): 0.000000, (4: 0.365295, (5: 0.000004, 6: 0.000004): 0.139080): 0.071242);

((K12: 0.028532, (S2457T: 0.000004, Shig4337: 0.000004): 0.198307): 0.000000, (CFT073: 0.365295, (O157: 0.000004, EDL933: 0.000004): 0.139080): 0.071242);

Detailed output identifying parameters

kappa (ts/tv) =  6.48492


dN/dS for site classes (K=3)

p:   0.99494  0.00000  0.00506
w:   0.10986  1.00000501.50324

dN & dS for each branch

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

   7..8       0.000    360.9    830.1   2.6474   0.0000   0.0000    0.0    0.0
   8..1       0.029    360.9    830.1   2.6474   0.0117   0.0044    1.6    9.7
   8..9       0.198    360.9    830.1   2.6474   0.0815   0.0308   11.1   67.6
   9..2       0.000    360.9    830.1   2.6474   0.0000   0.0000    0.0    0.0
   9..3       0.000    360.9    830.1   2.6474   0.0000   0.0000    0.0    0.0
   7..10      0.071    360.9    830.1   2.6474   0.0293   0.0111    4.0   24.3
  10..4       0.365    360.9    830.1   2.6474   0.1501   0.0567   20.5  124.6
  10..11      0.139    360.9    830.1   2.6474   0.0571   0.0216    7.8   47.4
  11..5       0.000    360.9    830.1   2.6474   0.0000   0.0000    0.0    0.0
  11..6       0.000    360.9    830.1   2.6474   0.0000   0.0000    0.0    0.0


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

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

   395 I      1.000**       501.493
   397 A      1.000**       501.498


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

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

    38 P      0.554         4.309 +- 3.817
   395 I      0.997**       7.356 +- 2.115
   396 A      0.511         3.991 +- 3.799
   397 A      0.990*        7.323 +- 2.169



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:   0.981  0.019  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.002  0.014  0.045  0.088  0.127  0.151  0.158  0.153  0.139  0.123

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 0.028
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005 0.966

sum of density on p0-p1 =   1.000000
