
seed used = 140000681

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1609.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 433
# site patterns = 96
   14   11    1   15   12    8    6   32    8    8    4    2    3    8    6
    3    1    6    1    4   10   15   11    1    9    5   21    6    3    6
   11    1    8    3    6    1    6    6    7    1    1    7    8    1    8
   10    3    6    1    5    1    1    1    1    7    7    6    3    1    1
    6    3    1    7    5    1    1    1    1    1    1    2    1    1    1
    1    1    3    6    2    2    2    1    1    1    1    1    1    1    1
    1    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 16 16 16 15 17 16 | Ser TCT  4  3  3  4  4  4 | Tyr TAT  7  6  6  6  7  7 | Cys TGT  1  1  1  2  1  1
    TTC  3  3  3  4  3  3 |     TCC  3  3  3  3  3  3 |     TAC  6  7  7  7  6  6 |     TGC  3  3  3  2  3  3
Leu TTA  9  9  9  8  8  8 |     TCA  3  4  4  3  3  3 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  9 10 10 10 10 11 |     TCG  5  5  5  5  5  5 |     TAG  0  0  0  0  0  0 | Trp TGG  6  6  6  6  6  6
--------------------------------------------------------------------------------------------------------------
Leu CTT  8  8  8  8  8  8 | Pro CCT  3  3  3  3  3  3 | His CAT  9  9  9  8 10 10 | Arg CGT  8  7  7  7  7  7
    CTC  8  8  8  8  8  8 |     CCC  3  3  3  3  3  3 |     CAC  7  7  7  8  6  6 |     CGC 11 12 12 13 12 12
    CTA  1  1  1  1  1  1 |     CCA  6  6  6  6  6  6 | Gln CAA  5  6  6  6  5  5 |     CGA  7  8  8  6  7  7
    CTG 34 33 33 34 33 33 |     CCG  7  7  7  7  7  7 |     CAG 10  9  9  9 10 10 |     CGG  3  2  2  3  3  3
--------------------------------------------------------------------------------------------------------------
Ile ATT 11 11 11 10 11 11 | Thr ACT  2  1  1  2  2  2 | Asn AAT  8  8  8  8  9  9 | Ser AGT  3  3  3  4  3  3
    ATC 12 14 14 13 13 13 |     ACC  5  4  4  5  5  5 |     AAC  8  8  8  7  7  7 |     AGC 11 11 11 11 11 11
    ATA  2  2  2  2  2  2 |     ACA  2  3  3  2  2  2 | Lys AAA 12 11 11 11 11 11 | Arg AGA  1  1  1  1  1  1
Met ATG 14 15 15 14 15 15 |     ACG  7  8  8  7  7  7 |     AAG  0  1  1  1  1  1 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  7  7  7  6  7  7 | Ala GCT  4  5  5  4  5  5 | Asp GAT 22 22 22 21 22 22 | Gly GGT  7  8  8  7  8  8
    GTC  5  4  4  6  4  4 |     GCC 13 12 12 13 12 12 |     GAC  6  6  6  7  6  6 |     GGC 10  9  9 10  9  9
    GTA  2  2  2  2  2  2 |     GCA  8  7  7  9  8  8 | Glu GAA 16 16 16 16 16 16 |     GGA  0  0  0  0  0  0
    GTG  7  6  6  6  6  6 |     GCG  8  8  8  8  8  8 |     GAG  9  9  9  9  9  9 |     GGG  6  6  6  6  6  6
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.17321    C:0.30023    A:0.22633    G:0.30023
position  2:    T:0.34180    C:0.19169    A:0.28868    G:0.17783
position  3:    T:0.27714    C:0.26328    A:0.17090    G:0.28868

#2: S2457T         
position  1:    T:0.17552    C:0.29792    A:0.23326    G:0.29330
position  2:    T:0.34411    C:0.18938    A:0.28868    G:0.17783
position  3:    T:0.27252    C:0.26328    A:0.17552    G:0.28868

#3: Shig4337       
position  1:    T:0.17552    C:0.29792    A:0.23326    G:0.29330
position  2:    T:0.34411    C:0.18938    A:0.28868    G:0.17783
position  3:    T:0.27252    C:0.26328    A:0.17552    G:0.28868

#4: CFT073         
position  1:    T:0.17321    C:0.30023    A:0.22633    G:0.30023
position  2:    T:0.33949    C:0.19400    A:0.28637    G:0.18014
position  3:    T:0.26559    C:0.27714    A:0.16859    G:0.28868

#5: O157           
position  1:    T:0.17552    C:0.29792    A:0.23095    G:0.29561
position  2:    T:0.34180    C:0.19169    A:0.28868    G:0.17783
position  3:    T:0.28637    C:0.25635    A:0.16628    G:0.29099

#6: EDL933         
position  1:    T:0.17552    C:0.29792    A:0.23095    G:0.29561
position  2:    T:0.34180    C:0.19169    A:0.28868    G:0.17783
position  3:    T:0.28406    C:0.25635    A:0.16628    G:0.29330

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      96 | Ser S TCT      22 | Tyr Y TAT      39 | Cys C TGT       7
      TTC      19 |       TCC      18 |       TAC      39 |       TGC      17
Leu L TTA      51 |       TCA      20 | *** * TAA       0 | *** * TGA       0
      TTG      60 |       TCG      30 |       TAG       0 | Trp W TGG      36
------------------------------------------------------------------------------
Leu L CTT      48 | Pro P CCT      18 | His H CAT      55 | Arg R CGT      43
      CTC      48 |       CCC      18 |       CAC      41 |       CGC      72
      CTA       6 |       CCA      36 | Gln Q CAA      33 |       CGA      43
      CTG     200 |       CCG      42 |       CAG      57 |       CGG      16
------------------------------------------------------------------------------
Ile I ATT      65 | Thr T ACT      10 | Asn N AAT      50 | Ser S AGT      19
      ATC      79 |       ACC      28 |       AAC      45 |       AGC      66
      ATA      12 |       ACA      14 | Lys K AAA      67 | Arg R AGA       6
Met M ATG      88 |       ACG      44 |       AAG       5 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      41 | Ala A GCT      28 | Asp D GAT     131 | Gly G GGT      46
      GTC      27 |       GCC      74 |       GAC      37 |       GGC      56
      GTA      12 |       GCA      47 | Glu E GAA      96 |       GGA       0
      GTG      37 |       GCG      48 |       GAG      54 |       GGG      36
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.17475    C:0.29869    A:0.23018    G:0.29638
position  2:    T:0.34219    C:0.19130    A:0.28830    G:0.17821
position  3:    T:0.27637    C:0.26328    A:0.17052    G:0.28984

Codon frequencies under model, for use in evolver:
  0.01701074  0.01620522  0.01049548  0.01783995
  0.00950994  0.00905961  0.00586755  0.00997352
  0.01433188  0.01365321  0.00000000  0.00000000
  0.00885936  0.00843984  0.00000000  0.00929122
  0.02907562  0.02769878  0.01793942  0.03049296
  0.01625488  0.01548515  0.01002912  0.01704725
  0.02449679  0.02333677  0.01511431  0.02569092
  0.01514287  0.01442580  0.00934303  0.01588104
  0.02240622  0.02134520  0.01382445  0.02349844
  0.01252631  0.01193314  0.00772863  0.01313692
  0.01887768  0.01798375  0.01164737  0.01979790
  0.01166938  0.01111679  0.00719991  0.01223822
  0.02885081  0.02748462  0.01780071  0.03025719
  0.01612919  0.01536542  0.00995158  0.01691544
  0.02430738  0.02315633  0.01499745  0.02549228
  0.01502579  0.01431426  0.00927079  0.01575824



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               0.1260 (0.0041 0.0324)
Shig4337             0.1260 (0.0041 0.0324)-1.0000 (0.0000 0.0000)
CFT073               0.0293 (0.0020 0.0695) 0.0798 (0.0061 0.0767) 0.0798 (0.0061 0.0767)
O157                 0.0783 (0.0031 0.0390) 0.0665 (0.0031 0.0459) 0.0665 (0.0031 0.0459) 0.0731 (0.0051 0.0698)
EDL933               0.0522 (0.0020 0.0390) 0.0444 (0.0020 0.0459) 0.0444 (0.0020 0.0459) 0.0585 (0.0041 0.0697)-1.0000 (0.0010 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 42
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -2003.121457     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00546  0.01185  0.02139  0.00000  0.00000  0.00186  0.04613  0.01499  0.00229  0.00000  6.69130  0.97751  0.00000  0.00000  6.43379
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.10399

((1: 0.011846, (2: 0.000004, 3: 0.000004): 0.021390): 0.005457, (4: 0.046134, (5: 0.002293, 6: 0.000004): 0.014995): 0.001858);

((K12: 0.011846, (S2457T: 0.000004, Shig4337: 0.000004): 0.021390): 0.005457, (CFT073: 0.046134, (O157: 0.002293, EDL933: 0.000004): 0.014995): 0.001858);

Detailed output identifying parameters

kappa (ts/tv) =  6.69130


dN/dS for site classes (K=3)

p:   0.97751  0.00000  0.02249
w:   0.00000  1.00000  6.43379

dN & dS for each branch

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

   7..8       0.005    424.5    874.5   0.1447   0.0006   0.0043    1.8    0.5
   8..1       0.012    424.5    874.5   0.1447   0.0013   0.0093    4.0    1.2
   8..9       0.021    424.5    874.5   0.1447   0.0024   0.0168    7.1    2.1
   9..2       0.000    424.5    874.5   0.1447   0.0000   0.0000    0.0    0.0
   9..3       0.000    424.5    874.5   0.1447   0.0000   0.0000    0.0    0.0
   7..10      0.002    424.5    874.5   0.1447   0.0002   0.0015    0.6    0.2
  10..4       0.046    424.5    874.5   0.1447   0.0052   0.0363   15.4    4.6
  10..11      0.015    424.5    874.5   0.1447   0.0017   0.0118    5.0    1.5
  11..5       0.002    424.5    874.5   0.1447   0.0003   0.0018    0.8    0.2
  11..6       0.000    424.5    874.5   0.1447   0.0000   0.0000    0.0    0.0


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

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

   110 L      1.000**       6.434
   180 N      1.000**       6.434
   196 V      1.000**       6.434
   308 V      1.000**       6.434
   400 A      1.000**       6.434
   409 T      1.000**       6.434


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

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

   110 L      0.541         2.953 +- 2.883
   196 V      0.874         4.453 +- 2.518
   308 V      0.946         4.690 +- 2.382
   400 A      0.518         2.824 +- 2.851



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:   0.990  0.010  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.092  0.157  0.181  0.164  0.130  0.096  0.069  0.049  0.035  0.025

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 0.019
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.019 0.960

sum of density on p0-p1 =   1.000000
