
seed used = 139997197

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1197.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 485
# site patterns = 111
   13   11   15   13    9    8    5   18    2   15    7    7    6    6   11
   14   22   13   25    1   15    9    9    5    1    1    3   17    5   10
    4   16    4    9    7    2    4    1    1    3    7    1    1   13    1
   14    1    4    3    1   13    1    4    1    1    2    3    3    2    1
    1    1    2    1    1    1    1    2    1    2    1    1    1    1    4
    1    1    1    3    1    1    3    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 CAG CAA AAC AGC GGA TTT GAT CTG CGC CAT TTC GTT GTC AAT ACC CTG CCG AAA GAA GGC GAG TAT CCA GGG CAG TCA GAA ATT GAC CTT TGG GTA TTA ACG CGT TCT CCG GAA CCT GTG CCG CGC TAC AGT GCC AGC GGT CAC GTC GCG GTG GCT ATA GAC ACT CCC AGT TCG CAA GAT GCG TTG AAG GTC GGT CTC CGA ACC GCC TCG AAC CAG TTA ATC TTT CTC GCC GCA ACG GCA GGG CCG AAC ACA GGG AAT TTA ACA CGG AAG ACC ACG TGC TGT CGT CCG ACC GTT AAG GCA ACG ACG CAA CCC TCA ACC GCA CAA CCC ACA 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... .A. ... ..T ... ... A.. ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ..A A.. ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... .A. ... ..T ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ..A A.. ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..A A.. ... ... ..C ..T ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ..G ..C ... ... ..A ..A ... ... ... ..T ... ..A ..T ... ... ... ... ... ... ... ... ..G ... ... .G. ... ..A ..C ..G ... ... ... G.. ..A ... ... ... ..A CT. AG. G.. A.. ..A CA. .CG GTA AA. CAA ..G G.. ..T ..G 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ..A ... ... ..A ... ... ... ... ..T ... ..T ..A C.. ... ..C ..T ... ... ..A ... ... ..A ... ..T ... ... ... ... ... ... ... ... ... ... ... ..A CT. AG. G.A A.. ..A CA. .CG GTA AA. CAA ..G G.. ..T ..G 

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  6  6  6  6  5 | Ser TCT  4  4  4  4  4 | Tyr TAT  9  9  9  9  9 | Cys TGT  1  1  1  1  1
    TTC  7  7  7  7  8 |     TCC  0  0  0  0  0 |     TAC 13 13 13 13 13 |     TGC  1  1  1  1  1
Leu TTA 11 11 11 10 10 |     TCA  4  4  4  4  3 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  2  2  2  3  2 |     TCG  3  3  3  2  3 |     TAG  0  0  0  0  0 | Trp TGG 16 16 16 16 16
--------------------------------------------------------------------------------------------------
Leu CTT  4  4  4  4  5 | Pro CCT  3  3  3  4  4 | His CAT  7  8  8  7  7 | Arg CGT  3  3  3  4  4
    CTC  2  2  2  3  2 |     CCC  5  5  5  4  3 |     CAC  3  3  3  3  3 |     CGC 16 15 15 15 15
    CTA  0  0  0  2  1 |     CCA  5  5  5  7  8 | Gln CAA 18 18 18 17 17 |     CGA  2  2  2  2  2
    CTG 24 24 24 22 24 |     CCG 17 17 17 15 15 |     CAG 13 13 13 14 14 |     CGG  1  1  1  1  1
--------------------------------------------------------------------------------------------------
Ile ATT  5  5  5  5  5 | Thr ACT  2  2  2  3  3 | Asn AAT 12 13 13 12 13 | Ser AGT  4  5  5  5  5
    ATC  4  5  4  4  4 |     ACC 18 18 18 14 16 |     AAC 15 16 16 14 14 |     AGC 10  9  9 11 10
    ATA  1  1  1  1  1 |     ACA  3  3  3  5  4 | Lys AAA 25 25 25 28 26 | Arg AGA  0  0  0  0  0
Met ATG 13 13 13 13 13 |     ACG 11 11 11  9  9 |     AAG  3  3  3  1  2 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT  7  7  7  6  6 | Ala GCT  4  4  4  4  6 | Asp GAT 19 19 19 18 19 | Gly GGT  5  4  4  5  5
    GTC  8  6  7  7  7 |     GCC 17 16 16 18 15 |     GAC 11 10 10 12 11 |     GGC 15 15 15 15 15
    GTA  4  5  5  7  6 |     GCA  6  6  6  3  5 | Glu GAA 19 19 19 18 20 |     GGA  8  8  8  9  9
    GTG  8  8  8  7  8 |     GCG 14 15 15 16 14 |     GAG  9  9  9 11 10 |     GGG  5  5  5  4  4
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.15876    C:0.25361    A:0.25979    G:0.32784
position  2:    T:0.21856    C:0.23918    A:0.36289    G:0.17938
position  3:    T:0.19588    C:0.29897    A:0.21856    G:0.28660

#2: S2457T         
position  1:    T:0.15876    C:0.25361    A:0.26598    G:0.32165
position  2:    T:0.21856    C:0.23918    A:0.36701    G:0.17526
position  3:    T:0.20000    C:0.29072    A:0.22062    G:0.28866

#3: Shig4337       
position  1:    T:0.15876    C:0.25361    A:0.26392    G:0.32371
position  2:    T:0.21856    C:0.23918    A:0.36701    G:0.17526
position  3:    T:0.20000    C:0.29072    A:0.22062    G:0.28866

#4: CFT073         
position  1:    T:0.15670    C:0.25567    A:0.25773    G:0.32990
position  2:    T:0.22062    C:0.23093    A:0.36495    G:0.18351
position  3:    T:0.20000    C:0.29072    A:0.23299    G:0.27629

#5: EDL933         
position  1:    T:0.15464    C:0.25773    A:0.25773    G:0.32990
position  2:    T:0.22062    C:0.23093    A:0.36701    G:0.18144
position  3:    T:0.20825    C:0.28247    A:0.23093    G:0.27835

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      29 | Ser S TCT      20 | Tyr Y TAT      45 | Cys C TGT       5
      TTC      36 |       TCC       0 |       TAC      65 |       TGC       5
Leu L TTA      53 |       TCA      19 | *** * TAA       0 | *** * TGA       0
      TTG      11 |       TCG      14 |       TAG       0 | Trp W TGG      80
------------------------------------------------------------------------------
Leu L CTT      21 | Pro P CCT      17 | His H CAT      37 | Arg R CGT      17
      CTC      11 |       CCC      22 |       CAC      15 |       CGC      76
      CTA       3 |       CCA      30 | Gln Q CAA      88 |       CGA      10
      CTG     118 |       CCG      81 |       CAG      67 |       CGG       5
------------------------------------------------------------------------------
Ile I ATT      25 | Thr T ACT      12 | Asn N AAT      63 | Ser S AGT      24
      ATC      21 |       ACC      84 |       AAC      75 |       AGC      49
      ATA       5 |       ACA      18 | Lys K AAA     129 | Arg R AGA       0
Met M ATG      65 |       ACG      51 |       AAG      12 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      33 | Ala A GCT      22 | Asp D GAT      94 | Gly G GGT      23
      GTC      35 |       GCC      82 |       GAC      54 |       GGC      75
      GTA      27 |       GCA      26 | Glu E GAA      95 |       GGA      42
      GTG      39 |       GCG      74 |       GAG      48 |       GGG      23
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15753    C:0.25485    A:0.26103    G:0.32660
position  2:    T:0.21938    C:0.23588    A:0.36577    G:0.17897
position  3:    T:0.20082    C:0.29072    A:0.22474    G:0.28371

Codon frequencies under model, for use in evolver:
  0.00719658  0.01041805  0.00805367  0.01016683
  0.00773768  0.01120136  0.00865921  0.01093125
  0.01199881  0.01736994  0.00000000  0.00000000
  0.00587089  0.00849893  0.00000000  0.00829399
  0.01164263  0.01685433  0.01302923  0.01644791
  0.01251802  0.01812157  0.01400887  0.01768459
  0.01941168  0.02810110  0.02172355  0.02742349
  0.00949794  0.01374958  0.01062911  0.01341803
  0.01192522  0.01726341  0.01334547  0.01684713
  0.01282186  0.01856141  0.01434889  0.01811383
  0.01988284  0.02878317  0.02225082  0.02808911
  0.00972847  0.01408331  0.01088710  0.01374371
  0.01492066  0.02159972  0.01669766  0.02107887
  0.01604251  0.02322376  0.01795312  0.02266375
  0.02487711  0.03601307  0.02783989  0.03514467
  0.01217211  0.01762082  0.01362177  0.01719592



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               0.2982 (0.0045 0.0150)
Shig4337             0.2386 (0.0036 0.0150)-1.0000 (0.0009 0.0000)
CFT073               0.2033 (0.0176 0.0867) 0.2656 (0.0222 0.0836) 0.2547 (0.0213 0.0836)
EDL933               0.1862 (0.0149 0.0800) 0.2329 (0.0195 0.0835) 0.2221 (0.0185 0.0835) 0.0315 (0.0027 0.0852)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 59
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -2348.924685     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.04618  0.00482  0.01493  0.00212  0.00000  0.02528  0.04245  0.02989  4.90199  0.97875  0.00000  0.08970 11.61167
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.16568

((1: 0.004821, (2: 0.002123, 3: 0.000004): 0.014930): 0.046179, (4: 0.042448, 5: 0.029888): 0.025285);

((K12: 0.004821, (S2457T: 0.002123, Shig4337: 0.000004): 0.014930): 0.046179, (CFT073: 0.042448, EDL933: 0.029888): 0.025285);

Detailed output identifying parameters

kappa (ts/tv) =  4.90199


dN/dS for site classes (K=3)

p:   0.97875  0.00000  0.02125
w:   0.08970  1.00000 11.61167

dN & dS for each branch

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

   6..7       0.046    433.2   1021.8   0.3345   0.0097   0.0289   12.5    9.9
   7..1       0.005    433.2   1021.8   0.3345   0.0010   0.0030    1.3    1.0
   7..8       0.015    433.2   1021.8   0.3345   0.0031   0.0093    4.0    3.2
   8..2       0.002    433.2   1021.8   0.3345   0.0004   0.0013    0.6    0.5
   8..3       0.000    433.2   1021.8   0.3345   0.0000   0.0000    0.0    0.0
   6..9       0.025    433.2   1021.8   0.3345   0.0053   0.0158    6.9    5.4
   9..4       0.042    433.2   1021.8   0.3345   0.0089   0.0266   11.5    9.1
   9..5       0.030    433.2   1021.8   0.3345   0.0063   0.0187    8.1    6.4


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

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

   468 T      0.984*        11.428
   469 V      0.987*        11.464
   474 T      0.987*        11.463
   476 P      0.987*        11.467
   477 S      0.990**       11.497
   478 T      0.999**       11.606


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

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

   466 R      0.511         4.147 +- 3.888
   468 T      0.935         7.285 +- 2.499
   469 V      0.942         7.336 +- 2.444
   474 T      0.941         7.330 +- 2.452
   475 Q      0.520         4.224 +- 3.900
   476 P      0.941         7.328 +- 2.456
   477 S      0.948         7.378 +- 2.398
   478 T      0.988*        7.623 +- 2.053



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:   0.961  0.039  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.001  0.007  0.024  0.063  0.112  0.154  0.174  0.173  0.157  0.135

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.066
 0.000 0.000 0.000 0.000 0.000 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 0.913

sum of density on p0-p1 =   1.000000
