
seed used = 139996357

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1076.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 402
# site patterns = 110
    7   14   12    5    9    8    9    9    3    3   27    4   20    4   12
    6   13   13    9    6    5    9    1   10   12    5    6   18    7    3
    1    4   15    5    1    4    4    1    1    2    6    1    1    1    1
    6    1    1    1    5    1    1    1    1    1    1    1    1    1    1
    3    2    4    1    1    1    1    2    5    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 GCC TTT TCT CAA GCG GTT AGC GGA TTA AAC GCT ACC CTC GAT ATT GGC AAT ATC TCC TAC AAA TCA ACG GGT TCG GTG CTG GGG GTA GCC ACT CAG GAC CGA TTC CGT GAC GTG AAG GAA AAC GTG ATG GGT CCG GCA ACC AAT GCA GCA AGT CCG CTT CCT ACT ACG CCA TTC AGC TAT GAC AGT CAT GTC TAC AAC TGG GTC CCA AAC AGC ATT GCG AAG ACA GCG ACA ACA GAA GCT ACA TTA GTG GAT GGT GCG ATG GCG AAT AAT ATC GCA GGT GAA CCC AGT AAT AAC TAT TCT GCG TTG ACA GGA ACC CTG CAG CTG CGC 
S2457T                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. .C. ... ... .T. ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..T A.. ... ... ... ... ... ..T ... A.. .G. ... 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. .C. ... ... .T. ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..T A.. ... ... ... ... ... ..T ... A.. .G. ... 
CFT073                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ..T ... ... ... ..A ... ... ... ... ... ..G ... ... ... ... ... ..G ... T.. ... ..C T.. .AC G.. ..T GAT ... ..T ... ... ..G ... ..G ... ... ... .CA G.T .CA ..T G.. C.T ..A .TG ..G .TG ..C GTT C.G ACC TCA .A. C.A .CA AA. G.. --- ..T A.C ..C ..T ... ..C ..C ... ... ..C ..T ... ... ..C ..A ... ... ... ... 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ..T ... ... ... ..T ... ... ... ... ... ..T ..C ... ..G ..C ... ... ..C T.. .AC G.. ..T GAT ... ... ... ... ... ... ... ... ... ... .CA G.T .CA ..C G.. C.T ..A .TG .AG .TG ..C GTT C.G ACC TCA AA. C.A .CA .A. ... --- ..T A.C ..C ... ... ..C ..C ..T ... ... ... ... ... ..C ... T.. ... ... ... 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ..T ... ... ... ..T ... ... ... ... ... ..T ..C ... ..G ..C ... ... ..C T.. .AC G.. ..T GAT ... ... ... ... ... ... ... ... ... ... .CA G.T .CA ..C G.. C.T ..A .TG .AG .TG ..C GTT C.G ACC TCA AA. C.A .CA .A. ... --- ..T A.C ..C ... ... ..C ..C ..T ... ... ... ... ... ..C ... T.. ... ... ... 



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

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

#1: K12            
position  1:    T:0.12935    C:0.16915    A:0.36318    G:0.33831
position  2:    T:0.24876    C:0.28109    A:0.31095    G:0.15920
position  3:    T:0.26368    C:0.34577    A:0.13433    G:0.25622

#2: S2457T         
position  1:    T:0.12935    C:0.16667    A:0.36816    G:0.33582
position  2:    T:0.24627    C:0.28109    A:0.31095    G:0.16169
position  3:    T:0.26866    C:0.34080    A:0.13184    G:0.25871

#3: Shig4337       
position  1:    T:0.12935    C:0.16667    A:0.36816    G:0.33582
position  2:    T:0.24627    C:0.28109    A:0.31095    G:0.16169
position  3:    T:0.26866    C:0.34080    A:0.13184    G:0.25871

#4: CFT073         
position  1:    T:0.13466    C:0.17207    A:0.35162    G:0.34165
position  2:    T:0.24938    C:0.28429    A:0.31172    G:0.15461
position  3:    T:0.27182    C:0.34414    A:0.12718    G:0.25686

#5: O157           
position  1:    T:0.13466    C:0.17207    A:0.35411    G:0.33915
position  2:    T:0.24938    C:0.28180    A:0.31421    G:0.15461
position  3:    T:0.26683    C:0.35411    A:0.12469    G:0.25436

#6: EDL933         
position  1:    T:0.13466    C:0.17207    A:0.35411    G:0.33915
position  2:    T:0.24938    C:0.28180    A:0.31421    G:0.15461
position  3:    T:0.26683    C:0.35411    A:0.12469    G:0.25436

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      75 | Ser S TCT      38 | Tyr Y TAT      24 | Cys C TGT       0
      TTC      27 |       TCC      37 |       TAC      34 |       TGC       0
Leu L TTA      21 |       TCA       9 | *** * TAA       0 | *** * TGA       0
      TTG      10 |       TCG      31 |       TAG       0 | Trp W TGG      12
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       6 | His H CAT       6 | Arg R CGT      27
      CTC      24 |       CCC       9 |       CAC       0 |       CGC       6
      CTA       0 |       CCA      12 | Gln Q CAA      54 |       CGA       3
      CTG     119 |       CCG      41 |       CAG      94 |       CGG       2
------------------------------------------------------------------------------
Ile I ATT      42 | Thr T ACT      31 | Asn N AAT     101 | Ser S AGT      31
      ATC      57 |       ACC     133 |       AAC     186 |       AGC      65
      ATA       0 |       ACA      28 | Lys K AAA      54 | Arg R AGA       0
Met M ATG      52 |       ACG      66 |       AAG      21 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      57 | Ala A GCT      30 | Asp D GAT      85 | Gly G GGT      86
      GTC      35 |       GCC      94 |       GAC      44 |       GGC      84
      GTA      21 |       GCA      44 | Glu E GAA      44 |       GGA      21
      GTG      52 |       GCG      70 |       GAG       5 |       GGG      43
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.13200    C:0.16978    A:0.35990    G:0.33831
position  2:    T:0.24824    C:0.28186    A:0.31216    G:0.15774
position  3:    T:0.26775    C:0.34662    A:0.12910    G:0.25654

Codon frequencies under model, for use in evolver:
  0.00893969  0.01157308  0.00431045  0.00856547
  0.01015058  0.01314068  0.00489431  0.00972567
  0.01124188  0.01455344  0.00000000  0.00000000
  0.00568074  0.00735413  0.00000000  0.00544294
  0.01149790  0.01488488  0.00554395  0.01101659
  0.01305531  0.01690106  0.00629488  0.01250881
  0.01445890  0.01871811  0.00697165  0.01385364
  0.00730636  0.00945862  0.00352291  0.00700051
  0.02437330  0.03155303  0.01175209  0.02335302
  0.02767470  0.03582694  0.01334392  0.02651622
  0.03065004  0.03967873  0.01477854  0.02936701
  0.01548805  0.02005042  0.00746788  0.01483971
  0.02291146  0.02966058  0.01104723  0.02195238
  0.02601486  0.03367815  0.01254360  0.02492586
  0.02881174  0.03729892  0.01389217  0.02760567
  0.01455912  0.01884786  0.00701998  0.01394967



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

K12                 
S2457T               0.3810 (0.0066 0.0173)
Shig4337             0.3810 (0.0066 0.0173)-1.0000 (0.0000 0.0000)
CFT073               0.2571 (0.0342 0.1329) 0.3097 (0.0411 0.1327) 0.3097 (0.0411 0.1327)
O157                 0.2456 (0.0307 0.1250) 0.3111 (0.0376 0.1209) 0.3111 (0.0376 0.1209) 0.1276 (0.0077 0.0605)
EDL933               0.2456 (0.0307 0.1250) 0.3111 (0.0376 0.1209) 0.3111 (0.0376 0.1209) 0.1276 (0.0077 0.0605)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -2053.686518     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00667  0.00467  0.02458  0.00000  0.00000  0.15156  0.04264  0.02335  0.00000  0.00000  2.63279  0.87766  0.00000  0.00000  3.10229
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.25349

((1: 0.004672, (2: 0.000004, 3: 0.000004): 0.024576): 0.006675, (4: 0.042642, (5: 0.000004, 6: 0.000004): 0.023348): 0.151564);

((K12: 0.004672, (S2457T: 0.000004, Shig4337: 0.000004): 0.024576): 0.006675, (CFT073: 0.042642, (O157: 0.000004, EDL933: 0.000004): 0.023348): 0.151564);

Detailed output identifying parameters

kappa (ts/tv) =  2.63279


dN/dS for site classes (K=3)

p:   0.87766  0.00000  0.12234
w:   0.00000  1.00000  3.10229

dN & dS for each branch

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

   7..8       0.007    318.2    887.8   0.3795   0.0016   0.0041    1.3    1.4
   8..1       0.005    318.2    887.8   0.3795   0.0011   0.0029    0.9    1.0
   8..9       0.025    318.2    887.8   0.3795   0.0057   0.0151    4.8    5.1
   9..2       0.000    318.2    887.8   0.3795   0.0000   0.0000    0.0    0.0
   9..3       0.000    318.2    887.8   0.3795   0.0000   0.0000    0.0    0.0
   7..10      0.152    318.2    887.8   0.3795   0.0353   0.0930   29.6   31.3
  10..4       0.043    318.2    887.8   0.3795   0.0099   0.0262    8.3    8.8
  10..11      0.023    318.2    887.8   0.3795   0.0054   0.0143    4.6    4.8
  11..5       0.000    318.2    887.8   0.3795   0.0000   0.0000    0.0    0.0
  11..6       0.000    318.2    887.8   0.3795   0.0000   0.0000    0.0    0.0


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

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

   109 V      1.000**       3.102
   111 M      1.000**       3.102
   121 A      1.000**       3.102
   163 P      1.000**       3.102
   166 T      1.000**       3.102
   168 T      1.000**       3.102
   169 P      1.000**       3.102
   171 S      1.000**       3.102
   207 N      1.000**       3.102
   219 N      1.000**       3.102
   220 S      1.000**       3.102
   221 I      1.000**       3.102
   223 K      1.000**       3.102
   224 T      1.000**       3.102
   226 T      1.000**       3.102
   227 T      1.000**       3.102
   229 E      1.000**       3.102
   235 T      1.000**       3.102
   237 V      1.000**       3.102
   238 D      1.000**       3.102
   239 G      1.000**       3.102
   240 A      1.000**       3.102
   241 M      1.000**       3.102
   242 A      1.000**       3.102
   243 N      1.000**       3.102
   246 A      1.000**       3.102
   254 E      1.000**       3.102
   303 Y      1.000**       3.102
   382 Q      1.000**       3.102
   398 L      1.000**       3.102


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

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

   168 T      0.562         3.311 +- 2.804
   169 P      0.503         3.018 +- 2.822
   171 S      0.730         4.240 +- 2.701
   219 N      0.577         3.418 +- 2.864
   226 T      0.512         3.027 +- 2.762
   235 T      0.816         4.721 +- 2.634
   237 V      0.812         4.685 +- 2.629
   238 D      0.915         5.228 +- 2.419
   239 G      0.806         4.649 +- 2.636
   241 M      0.552         3.264 +- 2.821
   242 A      0.796         4.603 +- 2.652



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:   0.865  0.132  0.003  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.027  0.085  0.149  0.186  0.172  0.136  0.099  0.069  0.046  0.030

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 0.001 0.037
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.035 0.329
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.050 0.383 0.157

sum of density on p0-p1 =   1.000000
