
seed used = 140021353

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3538.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 559
# site patterns = 93
   13    6   11   16    7   10   11   13    4    4    7    4   18    8    9
   21    8   19   18    8   28   15    5    1   10   15    3    1   20    1
   14    4    1    1    9    8    4   12    7    4   11    1   11    1   11
    8   11    6    5   16    4    1    6    6    1    2    2    3    5    7
    1   10    1    1    1    3   15    5    1    1    1    1    1    1    2
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 16 17 17 16 16 | Ser TCT  4  4  4  4  4 | Tyr TAT  8  8  8  8  8 | Cys TGT  1  1  1  1  1
    TTC 19 18 18 20 19 |     TCC  8  8  8  9  7 |     TAC  8  8  8  8  8 |     TGC  2  2  2  2  2
Leu TTA  5  5  5  4  5 |     TCA  2  2  2  2  3 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG 11 11 11 10 11 |     TCG 11 11 11 11 11 |     TAG  0  0  0  0  0 | Trp TGG 18 18 18 18 18
--------------------------------------------------------------------------------------------------
Leu CTT 11 10 10  9  9 | Pro CCT  4  4  4  4  4 | His CAT  9  8  8  9  9 | Arg CGT  5  6  6  6  5
    CTC  5  4  4  4  4 |     CCC  4  4  4  4  4 |     CAC  4  5  5  4  4 |     CGC 11 10 10 10 11
    CTA  3  3  3  3  3 |     CCA  7  8  8  8  8 | Gln CAA 11 12 12 12 11 |     CGA  0  0  0  0  0
    CTG 28 29 29 31 30 |     CCG 21 20 20 20 20 |     CAG 13 12 12 12 13 |     CGG  1  1  1  1  1
--------------------------------------------------------------------------------------------------
Ile ATT 12 14 14 15 13 | Thr ACT  6  7  7  6  7 | Asn AAT 10 10 10 11 10 | Ser AGT  5  5  5  5  5
    ATC  8  8  8  9  8 |     ACC 15 13 13 12 15 |     AAC 20 20 20 19 20 |     AGC 10  9  9 10  9
    ATA  3  3  3  2  3 |     ACA  6  7  7  8  6 | Lys AAA 15 15 15 15 15 | Arg AGA  1  1  1  1  1
Met ATG 14 14 14 13 14 |     ACG  8  8  8  7  8 |     AAG  5  5  5  5  5 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT 15 15 15 15 15 | Ala GCT  5  4  4  4  5 | Asp GAT 16 17 17 17 16 | Gly GGT  8  8  8 10  8
    GTC  6  6  6  6  6 |     GCC 14 15 15 15 14 |     GAC 12 13 13 12 13 |     GGC 22 22 22 22 23
    GTA  5  5  5  5  5 |     GCA 10 10 10 11 10 | Glu GAA 12 11 11 11 11 |     GGA  4  4  4  4  4
    GTG 14 14 14 14 14 |     GCG 16 16 16 15 16 |     GAG  4  3  3  4  4 |     GGG  8  8  8  6  7
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.20215    C:0.24508    A:0.24687    G:0.30590
position  2:    T:0.31306    C:0.25224    A:0.26297    G:0.17174
position  3:    T:0.24150    C:0.30054    A:0.15027    G:0.30769

#2: S2457T         
position  1:    T:0.20215    C:0.24329    A:0.24866    G:0.30590
position  2:    T:0.31485    C:0.25224    A:0.26297    G:0.16995
position  3:    T:0.24687    C:0.29517    A:0.15385    G:0.30411

#3: Shig4337       
position  1:    T:0.20215    C:0.24329    A:0.24866    G:0.30590
position  2:    T:0.31485    C:0.25224    A:0.26297    G:0.16995
position  3:    T:0.24687    C:0.29517    A:0.15385    G:0.30411

#4: CFT073         
position  1:    T:0.20215    C:0.24508    A:0.24687    G:0.30590
position  2:    T:0.31485    C:0.25045    A:0.26297    G:0.17174
position  3:    T:0.25045    C:0.29696    A:0.15385    G:0.29875

#5: O157           
position  1:    T:0.20215    C:0.24329    A:0.24866    G:0.30590
position  2:    T:0.31306    C:0.25403    A:0.26297    G:0.16995
position  3:    T:0.24150    C:0.29875    A:0.15206    G:0.30769

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      82 | Ser S TCT      20 | Tyr Y TAT      40 | Cys C TGT       5
      TTC      94 |       TCC      40 |       TAC      40 |       TGC      10
Leu L TTA      24 |       TCA      11 | *** * TAA       0 | *** * TGA       0
      TTG      54 |       TCG      55 |       TAG       0 | Trp W TGG      90
------------------------------------------------------------------------------
Leu L CTT      49 | Pro P CCT      20 | His H CAT      43 | Arg R CGT      28
      CTC      21 |       CCC      20 |       CAC      22 |       CGC      52
      CTA      15 |       CCA      39 | Gln Q CAA      58 |       CGA       0
      CTG     147 |       CCG     101 |       CAG      62 |       CGG       5
------------------------------------------------------------------------------
Ile I ATT      68 | Thr T ACT      33 | Asn N AAT      51 | Ser S AGT      25
      ATC      41 |       ACC      68 |       AAC      99 |       AGC      47
      ATA      14 |       ACA      34 | Lys K AAA      75 | Arg R AGA       5
Met M ATG      69 |       ACG      39 |       AAG      25 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      75 | Ala A GCT      22 | Asp D GAT      83 | Gly G GGT      42
      GTC      30 |       GCC      73 |       GAC      63 |       GGC     111
      GTA      25 |       GCA      51 | Glu E GAA      56 |       GGA      20
      GTG      70 |       GCG      79 |       GAG      18 |       GGG      37
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.20215    C:0.24401    A:0.24794    G:0.30590
position  2:    T:0.31413    C:0.25224    A:0.26297    G:0.17066
position  3:    T:0.24544    C:0.29732    A:0.15277    G:0.30447

Codon frequencies under model, for use in evolver:
  0.01606055  0.01945528  0.00999688  0.01992352
  0.01289600  0.01562183  0.00802710  0.01599781
  0.01344477  0.01628659  0.00000000  0.00000000
  0.00872538  0.01056967  0.00000000  0.01082405
  0.01938637  0.02348407  0.01206702  0.02404927
  0.01556650  0.01885680  0.00968935  0.01931063
  0.01622891  0.01965922  0.01010167  0.02013236
  0.01053223  0.01275843  0.00655578  0.01306549
  0.01969905  0.02386284  0.01226165  0.02443716
  0.01581758  0.01916094  0.00984563  0.01962209
  0.01649066  0.01997630  0.01026460  0.02045708
  0.01070210  0.01296421  0.00666151  0.01327623
  0.02430402  0.02944117  0.01512801  0.03014974
  0.01951519  0.02364012  0.01214721  0.02420908
  0.02034562  0.02464608  0.01266411  0.02523925
  0.01320389  0.01599481  0.00821875  0.01637976



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               0.1424 (0.0039 0.0277)
Shig4337             0.1424 (0.0039 0.0277)-1.0000 (0.0000 0.0000)
CFT073               0.0977 (0.0047 0.0484) 0.1082 (0.0055 0.0510) 0.1082 (0.0055 0.0510)
O157                 0.1049 (0.0024 0.0225) 0.0628 (0.0016 0.0251) 0.0628 (0.0016 0.0251) 0.0974 (0.0039 0.0405)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 37
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -2524.095812     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.01479  0.05676  0.06815  0.00000  0.00000  0.00277  0.15044  0.01902  1.95348  0.99821  0.00000  0.10485 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.31194

((1: 0.056762, (2: 0.000004, 3: 0.000004): 0.068153): 0.014790, (4: 0.150437, 5: 0.019016): 0.002775);

((K12: 0.056762, (S2457T: 0.000004, Shig4337: 0.000004): 0.068153): 0.014790, (CFT073: 0.150437, O157: 0.019016): 0.002775);

Detailed output identifying parameters

kappa (ts/tv) =  1.95348


dN/dS for site classes (K=3)

p:   0.99821  0.00000  0.00179
w:   0.10485  1.00000999.00000

dN & dS for each branch

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

   6..7       0.015    448.1   1228.9   1.8941   0.0056   0.0030    1.3    6.9
   7..1       0.057    448.1   1228.9   1.8941   0.0217   0.0114    5.1   26.6
   7..8       0.068    448.1   1228.9   1.8941   0.0260   0.0137    6.1   31.9
   8..2       0.000    448.1   1228.9   1.8941   0.0000   0.0000    0.0    0.0
   8..3       0.000    448.1   1228.9   1.8941   0.0000   0.0000    0.0    0.0
   6..9       0.003    448.1   1228.9   1.8941   0.0011   0.0006    0.3    1.3
   9..4       0.150    448.1   1228.9   1.8941   0.0574   0.0303   13.6   70.5
   9..5       0.019    448.1   1228.9   1.8941   0.0073   0.0038    1.7    8.9


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

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

   344 S      0.997**       996.416


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

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

   344 S      0.770         2.470 +- 1.579



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:   0.944  0.055  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.400  0.276  0.163  0.084  0.041  0.019  0.009  0.005  0.002  0.001

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 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.072
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.009 0.085 0.829

sum of density on p0-p1 =   1.000000
