CODONML (in paml 3.14, March 2005)    test.codon   Model: several dN/dS ratios for branches 
Codon frequencies: F3x4

ns = 2  	ls = 177
# site patterns = 105
    2    1    1    1    1    1    1    1    1    1    4    3    2    1    2
    1    1    4    1    1    2    1    1    1    7    2    3    1    2    1
    2    1    3    1    1    2    2    8    1    1    1    1    1    1    7
    1    1    1    3    1    4    1    1    4    1    1    3    2    1    6
    1    1    1    2    1    1    1    6    2    1    3    1    1    4    1
    1    1    1    1    1    1    1    1    1    1    1    3    1    1    1
    1    1    1    1    1    1    1    1    1    2    2    1    1    1    1


1       
BC070280              CTA AAC TGC ATC GTC GCT GTG TCC CAG AAC ATG GGC ATC GGC AAG AAC GGG GAC CTG CCC CCA CCG CTC AGG AAT GAA TTC CAG AGA ACC ACA ACC TCT TCA GTA GAA GGT AAA CAG CTG GTG ATT ATG GGT AAG ACC TGG TCC ATT CCT GAG CGA CCT TTA GGT AGA GTT CTC AGC GAA CTC CCT CCA CAA GGA GCT CAT TTT CTT TCC AGT CTA GAT GAT GCC CTT ACT CCA GCA GTA ATG CTC TGG ATA GTT GGT TAT GCC GGC CAT CTT GTG AGG CAA GAA ACG ATT TTG CTG CCA TAC GTC CAG GTA GAG 
pseudogene            ... ... ... ..T ... AA. .AT ... ... ..G ... ... ... AT. .G. ..T ... ... ... ... ..T .A. ... .AA ... A.. ... ..A ... ... ... C.. ... ... .C. ..G ... ... G.A T.A ..A T.. T.A AT. ... .A. ... ..G ... A.. ... .A. ... ... TA. .T. ... G.. ..T ... TC. ..A ..G ... A.. C.. .C. ... ... GA. ... ..G .G. ... ... .G. .T. .T. ... CA. G.. T.T .TT .C. ..G ..A ... T.. .A. ... T.. ... T.. ..G C.. ... GG. ..A ..C ... ... ..G G.. ... ..A 

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

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

#1: BC070280       
position  1:    T:0.16384    C:0.20339    A:0.32768    G:0.30508
position  2:    T:0.31638    C:0.16949    A:0.37288    G:0.14124
position  3:    T:0.29944    C:0.21469    A:0.27119    G:0.21469

#2: pseudogene     
position  1:    T:0.20904    C:0.17514    A:0.33333    G:0.28249
position  2:    T:0.31073    C:0.15819    A:0.40678    G:0.12429
position  3:    T:0.32768    C:0.18079    A:0.28814    G:0.20339

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      16 | Ser S TCT       6 | Tyr Y TAT       7 | Cys C TGT       0
      TTC       6 |       TCC       6 |       TAC       4 |       TGC       2
Leu L TTA      11 |       TCA       2 | *** * TAA       0 | *** * TGA       0
      TTG       1 |       TCG       1 |       TAG       0 | Trp W TGG       4
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       8 | His H CAT       3 | Arg R CGT       1
      CTC       7 |       CCC       3 |       CAC       0 |       CGC       0
      CTA       6 |       CCA       9 | Gln Q CAA       9 |       CGA       1
      CTG       5 |       CCG       2 |       CAG       7 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      11 | Thr T ACT       2 | Asn N AAT      16 | Ser S AGT       7
      ATC       6 |       ACC       4 |       AAC       5 |       AGC       1
      ATA       2 |       ACA       5 | Lys K AAA      19 | Arg R AGA       6
Met M ATG      10 |       ACG       2 |       AAG      17 |       AGG       4
------------------------------------------------------------------------------
Val V GTT       7 | Ala A GCT       2 | Asp D GAT      10 | Gly G GGT       9
      GTC       5 |       GCC       3 |       GAC      10 |       GGC       8
      GTA       5 |       GCA       3 | Glu E GAA      19 |       GGA       2
      GTG       7 |       GCG       0 |       GAG      12 |       GGG       2
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.18644    C:0.18927    A:0.33051    G:0.29379
position  2:    T:0.31356    C:0.16384    A:0.38983    G:0.13277
position  3:    T:0.31356    C:0.19774    A:0.27966    G:0.20904


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.)

BC070280            
pseudogene           0.5224 (0.1421 0.2721)

pairwise comparison, codon frequencies: F3x4.


2 (pseudogene) ... 1 (BC070280)
lnL =-1014.258355
  0.52723  1.94064  0.59797

t= 0.5272  S=   129.6  N=   401.4  dN/dS= 0.5980  dN= 0.1510  dS= 0.2525
