
seed used = 141410053

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


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b1494.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 646
# site patterns = 158
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1   10    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    2    1    1    1    1    1
    1    5    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    9   21   29    9   29   11    1   14    8   11    4   12    9   14
   12    8   24   13    6    6    5    9    4   24    9   12   16    6    9
   12   13    1   11    1    5    6   21   15    7    5    1   13   17    6
    6    1   10    1    1    1    1    1    2    6    4    2    1    2    1
    1    1    1    7    1    1    1    2    1    1    1    1    6    2    1
    1    1    2    1    1    1    1    1    2    1    1    1    1    1    1
    1    1    1    1    1    1    1    1

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



Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT 13 14 12 13 | Ser TCT  6  7  7  6 | Tyr TAT 11  9 11 11 | Cys TGT  1  1  1  1
    TTC  8  9  9  8 |     TCC  6  7  6  6 |     TAC  2  5  2  2 |     TGC  0  0  0  0
Leu TTA 16 12 15 16 |     TCA  5  7  5  5 | *** TAA  0  0  0  0 | *** TGA  0  0  0  0
    TTG 12 10 13 12 |     TCG  8  8  7  8 |     TAG  0  0  0  0 | Trp TGG 14 14 14 14
--------------------------------------------------------------------------------------
Leu CTT  4  5  5  4 | Pro CCT  6  6  6  6 | His CAT  7  5  6  7 | Arg CGT 10 10  9 10
    CTC 10  6  8 10 |     CCC  2  1  2  2 |     CAC  2  5  2  2 |     CGC 14 15 16 14
    CTA  2  2  3  2 |     CCA  5  8  5  6 | Gln CAA 23 21 24 23 |     CGA  3  2  4  3
    CTG 30 27 29 30 |     CCG  9  7  9  8 |     CAG 23 22 23 23 |     CGG  3  2  2  3
--------------------------------------------------------------------------------------
Ile ATT 18 14 18 18 | Thr ACT  7  8  6  7 | Asn AAT 33 31 31 32 | Ser AGT 11 14 11 11
    ATC 11 11 12 12 |     ACC 14 13 15 14 |     AAC 13 13 15 14 |     AGC 13 16 13 13
    ATA  2  3  2  2 |     ACA  9  9 10  9 | Lys AAA 25 27 26 25 | Arg AGA  2  3  2  2
Met ATG 15 17 15 15 |     ACG  9 10  8  9 |     AAG  9  7  8  9 |     AGG  1  1  1  1
--------------------------------------------------------------------------------------
Val GTT  9  9  8 10 | Ala GCT 12 15 15 14 | Asp GAT 19 17 18 18 | Gly GGT  7  6  8  7
    GTC  8  8  7  6 |     GCC 13 12 13 12 |     GAC 11 10 12 12 |     GGC 16 16 15 16
    GTA 10 11 11 10 |     GCA 20 21 18 20 | Glu GAA 31 30 31 32 |     GGA  1  5  1  1
    GTG  9  8  9  9 |     GCG 19 18 18 17 |     GAG 12 13 12 12 |     GGG  2  0  2  2
--------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.15789    C:0.23684    A:0.29721    G:0.30805
position  2:    T:0.27399    C:0.23220    A:0.34211    G:0.15170
position  3:    T:0.26935    C:0.22136    A:0.23839    G:0.27090

#2: Shig4337       
position  1:    T:0.16019    C:0.22395    A:0.30638    G:0.30949
position  2:    T:0.25816    C:0.24417    A:0.33437    G:0.16330
position  3:    T:0.26594    C:0.22862    A:0.25039    G:0.25505

#3: CFT073         
position  1:    T:0.15789    C:0.23684    A:0.29876    G:0.30650
position  2:    T:0.27245    C:0.23220    A:0.34211    G:0.15325
position  3:    T:0.26625    C:0.22755    A:0.24303    G:0.26316

#4: O157           
position  1:    T:0.15789    C:0.23684    A:0.29876    G:0.30650
position  2:    T:0.27399    C:0.23065    A:0.34365    G:0.15170
position  3:    T:0.27090    C:0.22136    A:0.24149    G:0.26625

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      52 | Ser S TCT      26 | Tyr Y TAT      42 | Cys C TGT       4
      TTC      34 |       TCC      25 |       TAC      11 |       TGC       0
Leu L TTA      59 |       TCA      22 | *** * TAA       0 | *** * TGA       0
      TTG      47 |       TCG      31 |       TAG       0 | Trp W TGG      56
------------------------------------------------------------------------------
Leu L CTT      18 | Pro P CCT      24 | His H CAT      25 | Arg R CGT      39
      CTC      34 |       CCC       7 |       CAC      11 |       CGC      59
      CTA       9 |       CCA      24 | Gln Q CAA      91 |       CGA      12
      CTG     116 |       CCG      33 |       CAG      91 |       CGG      10
------------------------------------------------------------------------------
Ile I ATT      68 | Thr T ACT      28 | Asn N AAT     127 | Ser S AGT      47
      ATC      46 |       ACC      56 |       AAC      55 |       AGC      55
      ATA       9 |       ACA      37 | Lys K AAA     103 | Arg R AGA       9
Met M ATG      62 |       ACG      36 |       AAG      33 |       AGG       4
------------------------------------------------------------------------------
Val V GTT      36 | Ala A GCT      56 | Asp D GAT      72 | Gly G GGT      28
      GTC      29 |       GCC      50 |       GAC      45 |       GGC      63
      GTA      42 |       GCA      79 | Glu E GAA     124 |       GGA       8
      GTG      35 |       GCG      72 |       GAG      49 |       GGG       6
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.15847    C:0.23363    A:0.30027    G:0.30763
position  2:    T:0.26966    C:0.23479    A:0.34057    G:0.15498
position  3:    T:0.26811    C:0.22472    A:0.24332    G:0.26385

Codon frequencies under model, for use in evolver:
  0.01185233  0.00993403  0.01075616  0.01166393
  0.01031970  0.00864946  0.00936528  0.01015566
  0.01496868  0.01254600  0.00000000  0.00000000
  0.00681168  0.00570922  0.00000000  0.00670341
  0.01747422  0.01464602  0.01585811  0.01719645
  0.01521462  0.01275214  0.01380749  0.01497277
  0.02206873  0.01849691  0.02002769  0.02171793
  0.01004265  0.00841725  0.00911385  0.00988302
  0.02245857  0.01882366  0.02038148  0.02210157
  0.01955445  0.01638957  0.01774594  0.01924361
  0.02836363  0.02377298  0.02574040  0.02791276
  0.01290723  0.01081819  0.01171349  0.01270205
  0.02300917  0.01928514  0.02088115  0.02264342
  0.02003385  0.01679137  0.01818100  0.01971539
  0.02905899  0.02435580  0.02637146  0.02859707
  0.01322366  0.01108341  0.01200066  0.01301346



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                 
Shig4337             0.6047 (0.0695 0.1150)
CFT073               0.0365 (0.0020 0.0553) 0.4767 (0.0679 0.1423)
O157                 0.1192 (0.0027 0.0226) 0.6038 (0.0695 0.1151) 0.0364 (0.0020 0.0554)


TREE #  1:  ((1, 2), (3, 4));   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  6  np: 11):  -3411.075606     +0.000000
   5..6     6..1     6..2     5..7     7..3     7..4  
  0.00000  0.00997  0.50399  0.00168  0.03443  0.01164  1.61146  0.91544  0.00000  0.07461 21.52225
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.56170

((1: 0.009970, 2: 0.503989): 0.000000, (3: 0.034429, 4: 0.011635): 0.001681);

((K12: 0.009970, Shig4337: 0.503989): 0.000000, (CFT073: 0.034429, O157: 0.011635): 0.001681);

Detailed output identifying parameters

kappa (ts/tv) =  1.61146


dN/dS for site classes (K=3)

p:   0.91544  0.00000  0.08456
w:   0.07461  1.00000 21.52225

dN & dS for each branch

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

   5..6       0.000    493.3   1444.7   1.8883   0.0000   0.0000    0.0    0.0
   6..1       0.010    493.3   1444.7   1.8883   0.0038   0.0020    1.0    5.5
   6..2       0.504    493.3   1444.7   1.8883   0.1908   0.1011   49.9  275.7
   5..7       0.002    493.3   1444.7   1.8883   0.0006   0.0003    0.2    0.9
   7..3       0.034    493.3   1444.7   1.8883   0.0130   0.0069    3.4   18.8
   7..4       0.012    493.3   1444.7   1.8883   0.0044   0.0023    1.2    6.4


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

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

     1 N      1.000**       21.522
     2 L      0.828         17.838
     5 L      1.000**       21.515
     6 L      0.999**       21.501
     8 L      0.998**       21.489
     9 V      0.701         15.105
    10 A      0.795         17.116
    11 T      0.825         17.763
    12 L      0.997**       21.466
    14 L      0.959*        20.645
    15 P      0.644         13.888
    17 R      0.938         20.196
    18 L      0.999**       21.510
    19 I      0.502         10.835
    21 A      0.644         13.894
    22 A      0.825         17.762
    23 L      0.999**       21.508
    26 D      0.721         15.545
    27 E      1.000**       21.521
    28 K      0.990*        21.301
    29 L      1.000**       21.521
    30 I      1.000**       21.513
    31 T      0.804         17.319
    33 Q      0.997**       21.462
    34 L      0.999**       21.510
    35 D      0.999**       21.504
    38 L      1.000**       21.522
    39 R      0.666         14.355
    40 Y      0.999**       21.505
    41 M      1.000**       21.521
    42 I      0.999**       21.497
    43 Y      0.999**       21.505
    44 P      0.874         18.824
    45 H      0.999**       21.499
    46 A      1.000**       21.518
    47 H      1.000**       21.522
    49 K      1.000**       21.512
    50 D      0.779         16.782
    51 Q      1.000**       21.519
    52 V      0.995**       21.419
    53 N      1.000**       21.519
    54 L      0.659         14.218
    55 W      0.997**       21.463
    56 L      0.985*        21.195
    58 I      0.996**       21.437
    59 H      0.741         15.974
    60 T      0.854         18.389
    70 L      0.630         13.581
   207 R      0.613         13.229
   360 A      0.597         12.876
   460 V      0.576         12.438
   487 V      0.568         12.264
   641 A      0.699         15.066
   642 L      0.520         11.235
   643 K      0.999**       21.508
   644 T      0.787         16.957
   645 L      0.999**       21.494


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

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

     1 N      0.997**       10.312 +- 0.640
     2 L      0.786         8.234 +- 4.044
     5 L      0.993**       10.272 +- 0.882
     6 L      0.985*        10.199 +- 1.203
     7 T      0.568         6.076 +- 4.889
     8 L      0.984*        10.183 +- 1.261
     9 V      0.703         7.413 +- 4.506
    10 A      0.770         8.075 +- 4.152
    11 T      0.797         8.343 +- 3.969
    12 L      0.979*        10.135 +- 1.422
    14 L      0.932         9.675 +- 2.472
    15 P      0.744         7.821 +- 4.298
    17 R      0.873         9.084 +- 3.299
    18 L      0.989*        10.233 +- 1.066
    19 I      0.659         6.976 +- 4.674
    21 A      0.690         7.286 +- 4.559
    22 A      0.755         7.920 +- 4.247
    23 L      0.996**       10.294 +- 0.762
    25 Q      0.568         6.076 +- 4.887
    26 D      0.737         7.750 +- 4.343
    27 E      0.997**       10.308 +- 0.669
    28 K      0.951*        9.879 +- 2.059
    29 L      0.998**       10.315 +- 0.618
    30 I      0.993**       10.267 +- 0.907
    31 T      0.743         7.805 +- 4.312
    33 Q      0.985*        10.196 +- 1.224
    34 L      0.991**       10.249 +- 0.993
    35 D      0.987*        10.211 +- 1.155
    38 L      0.997**       10.314 +- 0.625
    39 R      0.741         7.792 +- 4.315
    40 Y      0.987*        10.215 +- 1.139
    41 M      0.996**       10.301 +- 0.716
    42 I      0.984*        10.187 +- 1.248
    43 Y      0.987*        10.215 +- 1.139
    44 P      0.795         8.321 +- 3.983
    45 H      0.995**       10.285 +- 0.819
    46 A      0.994**       10.284 +- 0.817
    47 H      1.000**       10.333 +- 0.458
    49 K      0.991**       10.252 +- 0.981
    50 D      0.777         8.137 +- 4.112
    51 Q      0.996**       10.298 +- 0.735
    52 V      0.969*        10.043 +- 1.685
    53 N      0.996**       10.298 +- 0.732
    54 L      0.745         7.832 +- 4.292
    55 W      0.976*        10.111 +- 1.494
    56 L      0.966*        10.011 +- 1.792
    58 I      0.972*        10.072 +- 1.605
    59 H      0.749         7.865 +- 4.278
    60 T      0.782         8.193 +- 4.072
    70 L      0.737         7.750 +- 4.337
   207 R      0.732         7.702 +- 4.363
   295 I      0.654         6.930 +- 4.689
   360 A      0.673         7.119 +- 4.625
   460 V      0.697         7.357 +- 4.528
   487 V      0.652         6.906 +- 4.699
   525 R      0.581         6.204 +- 4.867
   641 A      0.704         7.422 +- 4.502
   642 L      0.658         6.966 +- 4.678
   643 K      0.990**       10.245 +- 1.012
   644 T      0.753         7.906 +- 4.252
   645 L      0.983*        10.173 +- 1.298
   646 D      0.660         6.983 +- 4.670



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:   0.991  0.009  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.000  0.000  0.000  0.001  0.015  0.129  0.855

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 0.001 0.014 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.640 0.345 0.000

sum of density on p0-p1 =   1.000000
