
seed used = 140026053

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3904.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 489
# site patterns = 107
    8   15    8   13   17    2    9   16   17    7   15    5    1    6    5
   13   24   12    8    2    7   16    8    1   12    9   13    6   10    1
    1    1    1   10    9    1    1   17    7    1    4    3    9    8   16
    7    3    4    6    1    1    2    3    1    6    1    1    2    1    1
    1    2    5    1    1    8    1    1    1    1    3    1    1    1    1
    1    1    1    2    1    2    3    2    1    1    1    3    2    1    1
    1    1    3    1    4    1    1    1    1    1    1    1    1    1    1
    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  8  8  8  9  8 | Ser TCT  3  3  3  3  3 | Tyr TAT 10 10 10 10 10 | Cys TGT  2  3  3  4  2
    TTC  7  7  7  6  7 |     TCC  2  1  1  1  2 |     TAC  2  2  2  2  2 |     TGC 10  9  9  8 10
Leu TTA  4  4  4  4  4 |     TCA  2  3  3  2  2 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  3  3  3  3  3 |     TCG  4  3  3  4  4 |     TAG  0  0  0  0  0 | Trp TGG  9  9  9  9  9
--------------------------------------------------------------------------------------------------
Leu CTT 10  8  8  8 10 | Pro CCT  5  5  5  4  5 | His CAT  6  6  6  6  6 | Arg CGT  9  8  8  9  9
    CTC  7  8  8  7  7 |     CCC  3  3  3  3  3 |     CAC  5  5  5  5  5 |     CGC 15 15 16 15 15
    CTA  3  3  3  3  3 |     CCA  3  2  2  4  3 | Gln CAA 11 10 10 10 11 |     CGA  2  3  2  2  2
    CTG 26 27 27 27 26 |     CCG  9 11 11  9  9 |     CAG 20 19 19 20 18 |     CGG  3  4  4  4  5
--------------------------------------------------------------------------------------------------
Ile ATT 18 18 18 17 18 | Thr ACT  0  0  0  1  0 | Asn AAT 18 19 19 19 18 | Ser AGT  7  6  6  6  7
    ATC 13 14 14 15 13 |     ACC 16 17 17 15 16 |     AAC 12 11 11 12 12 |     AGC 12 13 13 13 12
    ATA  1  0  0  2  1 |     ACA  3  4  4  4  3 | Lys AAA  3  3  3  3  3 | Arg AGA  0  0  0  0  0
Met ATG  9  9  9  8  9 |     ACG 13 10 10 11 13 |     AAG  3  3  3  3  3 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT  4  4  4  4  4 | Ala GCT  8  6  6  6  8 | Asp GAT 18 18 18 17 18 | Gly GGT  8  9  9 11  9
    GTC  9  9  9  9  9 |     GCC 16 19 19 19 16 |     GAC  9 10 10 10  9 |     GGC 17 16 16 17 16
    GTA  0  0  0  0  0 |     GCA  6  5  5  7  6 | Glu GAA 17 17 17 17 17 |     GGA  2  2  2  1  2
    GTG 13 13 13 13 13 |     GCG 15 15 15 14 15 |     GAG  9  9  9  9  9 |     GGG  7  8  8  5  7
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13497    C:0.28016    A:0.26176    G:0.32311
position  2:    T:0.27607    C:0.22086    A:0.29243    G:0.21063
position  3:    T:0.27403    C:0.31697    A:0.11656    G:0.29243

#2: S2457T         
position  1:    T:0.13292    C:0.28016    A:0.25971    G:0.32720
position  2:    T:0.27607    C:0.21881    A:0.29039    G:0.21472
position  3:    T:0.26789    C:0.32515    A:0.11452    G:0.29243

#3: Shig4337       
position  1:    T:0.13292    C:0.28016    A:0.25971    G:0.32720
position  2:    T:0.27607    C:0.21881    A:0.29039    G:0.21472
position  3:    T:0.26789    C:0.32720    A:0.11247    G:0.29243

#4: CFT073         
position  1:    T:0.13292    C:0.27812    A:0.26380    G:0.32515
position  2:    T:0.27607    C:0.21881    A:0.29243    G:0.21268
position  3:    T:0.27403    C:0.32106    A:0.12065    G:0.28425

#5: O157           
position  1:    T:0.13497    C:0.28016    A:0.26176    G:0.32311
position  2:    T:0.27607    C:0.22086    A:0.28834    G:0.21472
position  3:    T:0.27607    C:0.31493    A:0.11656    G:0.29243

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      41 | Ser S TCT      15 | Tyr Y TAT      50 | Cys C TGT      14
      TTC      34 |       TCC       7 |       TAC      10 |       TGC      46
Leu L TTA      20 |       TCA      12 | *** * TAA       0 | *** * TGA       0
      TTG      15 |       TCG      18 |       TAG       0 | Trp W TGG      45
------------------------------------------------------------------------------
Leu L CTT      44 | Pro P CCT      24 | His H CAT      30 | Arg R CGT      43
      CTC      37 |       CCC      15 |       CAC      25 |       CGC      76
      CTA      15 |       CCA      14 | Gln Q CAA      52 |       CGA      11
      CTG     133 |       CCG      49 |       CAG      96 |       CGG      20
------------------------------------------------------------------------------
Ile I ATT      89 | Thr T ACT       1 | Asn N AAT      93 | Ser S AGT      32
      ATC      69 |       ACC      81 |       AAC      58 |       AGC      63
      ATA       4 |       ACA      18 | Lys K AAA      15 | Arg R AGA       0
Met M ATG      44 |       ACG      57 |       AAG      15 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      20 | Ala A GCT      34 | Asp D GAT      89 | Gly G GGT      46
      GTC      45 |       GCC      89 |       GAC      48 |       GGC      82
      GTA       0 |       GCA      29 | Glu E GAA      85 |       GGA       9
      GTG      65 |       GCG      74 |       GAG      45 |       GGG      35
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.13374    C:0.27975    A:0.26135    G:0.32515
position  2:    T:0.27607    C:0.21963    A:0.29080    G:0.21350
position  3:    T:0.27198    C:0.32106    A:0.11616    G:0.29080

Codon frequencies under model, for use in evolver:
  0.01023838  0.01208591  0.00437248  0.01094660
  0.00814520  0.00961501  0.00347855  0.00870863
  0.01078443  0.01273049  0.00000000  0.00000000
  0.00791768  0.00934644  0.00000000  0.00846537
  0.02141606  0.02528061  0.00914611  0.02289747
  0.01703767  0.02011213  0.00727624  0.01821621
  0.02255825  0.02662891  0.00963390  0.02411867
  0.01656175  0.01955034  0.00707299  0.01770738
  0.02000711  0.02361742  0.00854439  0.02139106
  0.01591677  0.01878897  0.00679754  0.01701778
  0.02107416  0.02487701  0.00900009  0.02253192
  0.01547217  0.01826413  0.00660766  0.01654242
  0.02489148  0.02938317  0.01063034  0.02661329
  0.01980255  0.02337594  0.00845703  0.02117235
  0.02621902  0.03095027  0.01119730  0.02803267
  0.01924941  0.02272298  0.00822080  0.02058095



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               0.0940 (0.0072 0.0770)
Shig4337             0.0979 (0.0072 0.0739) 0.0000 (0.0000 0.0028)
CFT073               0.0779 (0.0072 0.0928) 0.0548 (0.0054 0.0990) 0.0565 (0.0054 0.0958)
O157                 0.6394 (0.0018 0.0028) 0.0983 (0.0072 0.0736) 0.1025 (0.0072 0.0706) 0.0809 (0.0072 0.0894)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 68
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -2330.700210     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00000  0.00434  0.07160  0.00202  0.00000  0.00000  0.08665  0.00199  3.75488  0.92684  0.06845  0.00000 15.25584
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.16661

((1: 0.004336, (2: 0.002019, 3: 0.000004): 0.071604): 0.000000, (4: 0.086650, 5: 0.001993): 0.000000);

((K12: 0.004336, (S2457T: 0.002019, Shig4337: 0.000004): 0.071604): 0.000000, (CFT073: 0.086650, O157: 0.001993): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  3.75488


dN/dS for site classes (K=3)

p:   0.92684  0.06845  0.00471
w:   0.00000  1.00000 15.25584

dN & dS for each branch

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

   6..7       0.000    406.6   1060.4   0.1403   0.0000   0.0000    0.0    0.0
   7..1       0.004    406.6   1060.4   0.1403   0.0005   0.0038    1.6    0.6
   7..8       0.072    406.6   1060.4   0.1403   0.0088   0.0630   25.6    9.4
   8..2       0.002    406.6   1060.4   0.1403   0.0002   0.0018    0.7    0.3
   8..3       0.000    406.6   1060.4   0.1403   0.0000   0.0000    0.0    0.0
   6..9       0.000    406.6   1060.4   0.1403   0.0000   0.0000    0.0    0.0
   9..4       0.087    406.6   1060.4   0.1403   0.0107   0.0763   31.0   11.4
   9..5       0.002    406.6   1060.4   0.1403   0.0002   0.0018    0.7    0.3


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

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

   320 S      0.566         9.068
   344 T      0.993**       15.159


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

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

   320 S      0.865         4.268 +- 2.472
   343 E      0.794         3.944 +- 2.520
   344 T      0.973*        4.590 +- 2.288



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:   0.089  0.183  0.198  0.163  0.121  0.086  0.061  0.044  0.032  0.024

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 0.000 0.001 0.998

sum of density on p0-p1 =   1.000000
