
seed used = 140004861

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2011.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 474
# site patterns = 119
   10    1    8    1    1    1    3    1   12    1    1   14    7   24    7
   19    6    5    5   12    9   12    5   10   11    9   17   14    1   15
    5    3    2    2    1    9    1    1    6    1    4    3   14    1    1
    1   15    9    1   11    3    5    2   19    8    2    1    9    4    7
    6    1    2    2    7    1    2    1    1    2    3    2    4    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       
K12                   ATG AAT GAC GGT AAG CAA CAA TCT ACC TTT TTG TTT CAC GAT TAC GAA GGC ACG CCC GCG TTA CGC CCT GCA CAG TTC GCC ATT AGC AAT GTC ATC TGC AAG GCT TAT CAG CCA GGA GCC GTA GGT CCG GAA GCA CGG AAA AAC GCG CGT TCG CTT TGT CTG GTG ACA ATT TGG AGC CAT GTT TGT ATA CTA GAG GCT ACT GCA AAG CAG CCA CTC TTG GTG TCC GGA CGC GTG GAC GAA AGC ACC AAG GTG GTG CGA CTG CGC GTG ACG TCA GAT AAC AAC AGT GCA CTG CGG AAG CTG CGG GCA GGG CGT CGC TTG GGT TAT GCT GAT GAA TTG GTA CAA CAA GAT GAG GCA ATT 
S2457T                ... .CA ... ACA G.T A.. ... C.. ... ..C C.C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... GA. ... ... ... ... ... ..G ... .G. ..T ... ..A ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ... ... ..G ..A ... ... ... ... .CT ... ..G ..T .C. ... ..G .T. G.. ... ... ..A ... ..A ..T ..A ..A ... ... ..T ..T ... ..C ... ..A ... T.. ... ... ... ..C .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ..C 
Shig4337              ... .CA ... ACA G.T A.. ... C.. ... ..C C.C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... GA. ... ... ... ... ... ..G ... .G. ..T ... ..A ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ... ... ..G ..A ... ... ... ... .CT ... ..G ..T .C. ... ..G .T. G.. ... ... ..A ... ..A ..T ..A ..A ... ... ..T ..T ... ..C ... ..A ... T.. ... ... ... ..C .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ..C 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ..T ... ..A ... ... ... ... ..T ... ... ... ..A ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ... ... ..G ..A ... ... ... ... ..T ... ..G ... ... ... ..G ... G.. ... ... ..A ... ..A ..T ... ... ... ..G ... ..T ... ..C ... ..A ..A ... ..A ..G ... ..C ... ... ..C ..C ... ... ... ... .C. ... ..G ... ... ..G ..C 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... GA. ... ... ... ... ... ..G ... ... ..T ... ..A ... ... ... ... ..T ... ... ... ..A ... ... ... ... ... ... ... G.. ... ... ... ... ..C ... ... ... ... ... ..G ..A ..A ... ... ... ..T ... ..G ... ... ..T ... ... ... ..A ..A ... ... ... ..T ... ... ... ... ... ..T ... ..C ..T ... ... ... ... ... ... ..C ... ..A ..C ... ..A ..A ..G A.T .CG ..G ..G ..C ..A ..G ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 15 14 14 15 15 | Ser TCT  1  0  0  1  1 | Tyr TAT 10 10 10  9 10 | Cys TGT  3  3  3  3  2
    TTC  9 10 10  9  9 |     TCC  1  1  1  1  1 |     TAC  7  7  7  8  7 |     TGC  2  2  2  2  3
Leu TTA  9  9  9  9 10 |     TCA  1  1  1  1  1 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  7  7  7  7  5 |     TCG  3  3  3  3  3 |     TAG  0  0  0  0  0 | Trp TGG  9  9  9  9  9
--------------------------------------------------------------------------------------------------
Leu CTT  5  5  5  5  6 | Pro CCT  5  7  7  6  6 | His CAT  7  7  7  7  7 | Arg CGT 12 13 13 12 12
    CTC  2  3  3  2  2 |     CCC  5  5  5  5  5 |     CAC  7  8  8  7  7 |     CGC 15 13 13 15 15
    CTA  2  3  3  3  2 |     CCA  4  3  3  3  3 | Gln CAA  6  5  5  5  6 |     CGA  1  2  2  3  1
    CTG 22 20 20 21 21 |     CCG 14 14 14 14 14 |     CAG 14 13 13 15 14 |     CGG  3  3  3  1  3
--------------------------------------------------------------------------------------------------
Ile ATT 16 14 14 14 16 | Thr ACT  2  2  2  2  2 | Asn AAT 16 17 17 17 17 | Ser AGT  1  1  1  1  1
    ATC  3  5  5  4  3 |     ACC 13 12 12 12 13 |     AAC 11  9  9 10 10 |     AGC  6  4  4  6  5
    ATA  2  2  2  2  2 |     ACA  2  5  5  2  2 | Lys AAA 15 17 17 17 17 | Arg AGA  0  0  0  0  0
Met ATG 10 10 10 10 10 |     ACG  6  5  5  6  6 |     AAG  6  4  4  4  4 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT  6  7  7  8  8 | Ala GCT  3  3  3  3  2 | Asp GAT 27 28 28 26 27 | Gly GGT  5  4  4  4  4
    GTC  5  5  5  5  5 |     GCC 18 19 19 19 18 |     GAC 10 11 11 10 10 |     GGC  6  6  6  7  7
    GTA  5  7  7  5  5 |     GCA 15 14 14 13 14 | Glu GAA 22 20 20 21 23 |     GGA  7  6  6  6  6
    GTG 13  9  9 11 11 |     GCG 13 16 16 16 16 |     GAG  8 10 10 10  8 |     GGG  1  2  2  2  2
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.16245    C:0.26160    A:0.22996    G:0.34599
position  2:    T:0.27637    C:0.22363    A:0.35021    G:0.14979
position  3:    T:0.28270    C:0.25316    A:0.19198    G:0.27215

#2: S2457T         
position  1:    T:0.16034    C:0.26160    A:0.22574    G:0.35232
position  2:    T:0.27426    C:0.23207    A:0.35021    G:0.14346
position  3:    T:0.28481    C:0.25316    A:0.19831    G:0.26371

#3: Shig4337       
position  1:    T:0.16034    C:0.26160    A:0.22574    G:0.35232
position  2:    T:0.27426    C:0.23207    A:0.35021    G:0.14346
position  3:    T:0.28481    C:0.25316    A:0.19831    G:0.26371

#4: CFT073         
position  1:    T:0.16245    C:0.26160    A:0.22574    G:0.35021
position  2:    T:0.27426    C:0.22574    A:0.35021    G:0.14979
position  3:    T:0.28059    C:0.25738    A:0.18987    G:0.27215

#5: O157           
position  1:    T:0.16034    C:0.26160    A:0.22785    G:0.35021
position  2:    T:0.27426    C:0.22574    A:0.35232    G:0.14768
position  3:    T:0.28692    C:0.25316    A:0.19409    G:0.26582

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      73 | Ser S TCT       3 | Tyr Y TAT      49 | Cys C TGT      14
      TTC      47 |       TCC       5 |       TAC      36 |       TGC      11
Leu L TTA      46 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG      33 |       TCG      15 |       TAG       0 | Trp W TGG      45
------------------------------------------------------------------------------
Leu L CTT      26 | Pro P CCT      31 | His H CAT      35 | Arg R CGT      62
      CTC      12 |       CCC      25 |       CAC      37 |       CGC      71
      CTA      13 |       CCA      16 | Gln Q CAA      27 |       CGA       9
      CTG     104 |       CCG      70 |       CAG      69 |       CGG      13
------------------------------------------------------------------------------
Ile I ATT      74 | Thr T ACT      10 | Asn N AAT      84 | Ser S AGT       5
      ATC      20 |       ACC      62 |       AAC      49 |       AGC      25
      ATA      10 |       ACA      16 | Lys K AAA      83 | Arg R AGA       0
Met M ATG      50 |       ACG      28 |       AAG      22 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      36 | Ala A GCT      14 | Asp D GAT     136 | Gly G GGT      21
      GTC      25 |       GCC      93 |       GAC      52 |       GGC      32
      GTA      29 |       GCA      70 | Glu E GAA     106 |       GGA      31
      GTG      53 |       GCG      77 |       GAG      46 |       GGG       9
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16118    C:0.26160    A:0.22700    G:0.35021
position  2:    T:0.27468    C:0.22785    A:0.35063    G:0.14684
position  3:    T:0.28397    C:0.25401    A:0.19451    G:0.26751

Codon frequencies under model, for use in evolver:
  0.01297069  0.01160231  0.00888482  0.01221904
  0.01075910  0.00962403  0.00736990  0.01013561
  0.01655705  0.01481032  0.00000000  0.00000000
  0.00693364  0.00620216  0.00000000  0.00653184
  0.02105190  0.01883097  0.01442040  0.01983195
  0.01746241  0.01562016  0.01196162  0.01645047
  0.02687270  0.02403769  0.01840760  0.02531544
  0.01125355  0.01006633  0.00770860  0.01060141
  0.01826762  0.01634042  0.01251318  0.01720902
  0.01515286  0.01355427  0.01037960  0.01427476
  0.02331857  0.02085851  0.01597305  0.02196727
  0.00976518  0.00873497  0.00668907  0.00919929
  0.02818238  0.02520920  0.01930472  0.02654923
  0.02337709  0.02091086  0.01601313  0.02202240
  0.03597475  0.03217949  0.02464243  0.03389003
  0.01506524  0.01347589  0.01031958  0.01419221



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               0.2026 (0.0164 0.0808)
Shig4337             0.2026 (0.0164 0.0808)-1.0000 (0.0000 0.0000)
CFT073               0.0461 (0.0037 0.0798) 0.2846 (0.0164 0.0575) 0.2846 (0.0164 0.0575)
O157                 0.0642 (0.0064 0.1003) 0.1549 (0.0173 0.1117) 0.1549 (0.0173 0.1117) 0.0843 (0.0064 0.0764)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 72
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -2347.944646     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00065  0.03783  0.06368  0.00000  0.00000  0.01188  0.01589  0.05480  4.28311  0.90216  0.07387  0.00000  6.52461
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.18474

((1: 0.037831, (2: 0.000004, 3: 0.000004): 0.063682): 0.000649, (4: 0.015886, 5: 0.054800): 0.011879);

((K12: 0.037831, (S2457T: 0.000004, Shig4337: 0.000004): 0.063682): 0.000649, (CFT073: 0.015886, O157: 0.054800): 0.011879);

Detailed output identifying parameters

kappa (ts/tv) =  4.28311


dN/dS for site classes (K=3)

p:   0.90216  0.07387  0.02397
w:   0.00000  1.00000  6.52461

dN & dS for each branch

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

   6..7       0.001    437.2    984.8   0.2303   0.0001   0.0005    0.2    0.1
   7..1       0.038    437.2    984.8   0.2303   0.0062   0.0270   11.8    6.1
   7..8       0.064    437.2    984.8   0.2303   0.0105   0.0455   19.9   10.3
   8..2       0.000    437.2    984.8   0.2303   0.0000   0.0000    0.0    0.0
   8..3       0.000    437.2    984.8   0.2303   0.0000   0.0000    0.0    0.0
   6..9       0.012    437.2    984.8   0.2303   0.0020   0.0085    3.7    1.9
   9..4       0.016    437.2    984.8   0.2303   0.0026   0.0113    5.0    2.6
   9..5       0.055    437.2    984.8   0.2303   0.0090   0.0391   17.1    8.9


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

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

     2 N      0.613         4.387
     4 G      0.871         5.814
     5 K      0.703         4.885
    37 S      0.992**       6.483
   287 T      0.780         5.310
   446 L      0.853         5.710
   450 V      0.526         3.904


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

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

     2 N      0.693         4.599 +- 3.156
     4 G      0.936         6.068 +- 2.313
     5 K      0.853         5.580 +- 2.639
    37 S      0.994**       6.341 +- 1.992
   287 T      0.894         5.826 +- 2.497
   446 L      0.928         6.019 +- 2.355
   450 V      0.557         3.767 +- 3.321



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:   0.995  0.005  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.003  0.023  0.084  0.158  0.193  0.181  0.144  0.102  0.068  0.043

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 0.017
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008 0.975

sum of density on p0-p1 =   1.000000
