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CODONML (in paml 3.15, November 2005) /tmp/I7ZhE4PgvE/V8dSv7iz0l Model: One dN/dS ratio
Codon frequencies: F3x4
ns = 4 ls = 573
Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT 4 4 5 3 | Ser TCT 16 15 11 15 | Tyr TAT 11 11 14 14 | Cys TGT 2 1 2 1
TTC 7 7 8 8 | TCC 12 8 16 8 | TAC 14 14 10 11 | TGC 1 2 1 2
Leu TTA 1 1 1 2 | TCA 5 7 3 6 | *** TAA 0 0 0 0 | *** TGA 0 0 0 0
TTG 5 5 8 7 | TCG 5 5 8 6 | TAG 0 0 0 0 | Trp TGG 6 6 6 6
--------------------------------------------------------------------------------------
Leu CTT 7 7 10 8 | Pro CCT 22 21 18 17 | His CAT 5 3 3 5 | Arg CGT 3 2 2 2
CTC 14 15 13 17 | CCC 11 13 12 16 | CAC 4 3 5 5 | CGC 4 5 5 4
CTA 1 1 0 2 | CCA 12 13 14 11 | Gln CAA 38 38 40 38 | CGA 4 3 4 2
CTG 7 7 4 4 | CCG 14 13 12 13 | CAG 33 34 28 31 | CGG 2 3 4 5
--------------------------------------------------------------------------------------
Ile ATT 3 4 4 3 | Thr ACT 6 8 4 5 | Asn AAT 9 10 9 6 | Ser AGT 3 3 5 3
ATC 11 11 9 10 | ACC 5 4 7 7 | AAC 14 13 12 15 | AGC 4 4 5 6
ATA 1 2 2 2 | ACA 4 3 9 8 | Lys AAA 6 7 5 4 | Arg AGA 6 7 7 7
Met ATG 9 9 11 8 | ACG 10 9 5 5 | AAG 16 15 17 19 | AGG 7 7 4 5
--------------------------------------------------------------------------------------
Val GTT 3 4 5 5 | Ala GCT 16 16 16 18 | Asp GAT 14 14 15 18 | Gly GGT 17 16 17 18
GTC 8 8 8 8 | GCC 19 18 15 18 | GAC 13 15 13 10 | GGC 8 9 10 9
GTA 7 6 7 6 | GCA 16 17 11 14 | Glu GAA 16 17 19 15 | GGA 7 7 4 6
GTG 5 7 6 7 | GCG 10 8 18 10 | GAG 24 22 21 23 | GGG 6 6 6 6
--------------------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: R265
position 1: T:0.15532 C:0.31588 A:0.19895 G:0.32984
position 2: T:0.16230 C:0.31937 A:0.37871 G:0.13962
position 3: T:0.24607 C:0.26003 A:0.21640 G:0.27749
#2: WM276
position 1: T:0.15009 C:0.31588 A:0.20244 G:0.33159
position 2: T:0.17103 C:0.31065 A:0.37696 G:0.14136
position 3: T:0.24258 C:0.26003 A:0.22513 G:0.27225
#3: H99
position 1: T:0.16230 C:0.30366 A:0.20070 G:0.33333
position 2: T:0.17627 C:0.31239 A:0.36824 G:0.14311
position 3: T:0.24433 C:0.26003 A:0.21990 G:0.27574
#4: JEC21
position 1: T:0.15532 C:0.31414 A:0.19721 G:0.33333
position 2: T:0.17452 C:0.30890 A:0.37347 G:0.14311
position 3: T:0.24607 C:0.26876 A:0.21466 G:0.27051
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 16 | Ser S TCT 57 | Tyr Y TAT 50 | Cys C TGT 6
TTC 30 | TCC 44 | TAC 49 | TGC 6
Leu L TTA 5 | TCA 21 | *** * TAA 0 | *** * TGA 0
TTG 25 | TCG 24 | TAG 0 | Trp W TGG 24
------------------------------------------------------------------------------
Leu L CTT 32 | Pro P CCT 78 | His H CAT 16 | Arg R CGT 9
CTC 59 | CCC 52 | CAC 17 | CGC 18
CTA 4 | CCA 50 | Gln Q CAA 154 | CGA 13
CTG 22 | CCG 52 | CAG 126 | CGG 14
------------------------------------------------------------------------------
Ile I ATT 14 | Thr T ACT 23 | Asn N AAT 34 | Ser S AGT 14
ATC 41 | ACC 23 | AAC 54 | AGC 19
ATA 7 | ACA 24 | Lys K AAA 22 | Arg R AGA 27
Met M ATG 37 | ACG 29 | AAG 67 | AGG 23
------------------------------------------------------------------------------
Val V GTT 17 | Ala A GCT 66 | Asp D GAT 61 | Gly G GGT 68
GTC 32 | GCC 70 | GAC 51 | GGC 36
GTA 26 | GCA 58 | Glu E GAA 67 | GGA 24
GTG 25 | GCG 46 | GAG 90 | GGG 24
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.15576 C:0.31239 A:0.19983 G:0.33202
position 2: T:0.17103 C:0.31283 A:0.37435 G:0.14180
position 3: T:0.24476 C:0.26222 A:0.21902 G:0.27400
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.)
R265
WM276 0.2264 (0.0186 0.0821)
H99 0.1481 (0.0586 0.3959) 0.1481 (0.0611 0.4126)
JEC21 0.1112 (0.0421 0.3787) 0.1173 (0.0466 0.3970) 0.1419 (0.0380 0.2679)
pairwise comparison, codon frequencies: F3x4.
2 (WM276) ... 1 (R265)
lnL =-2569.912690
0.10404 3.29148 0.32693
t= 0.1040 S= 541.4 N= 1177.6 dN/dS= 0.3269 dN= 0.0210 dS= 0.0644
3 (H99) ... 1 (R265)
lnL =-3019.970151
0.43604 3.31017 0.20554
t= 0.4360 S= 540.2 N= 1178.8 dN/dS= 0.2055 dN= 0.0656 dS= 0.3193
3 (H99) ... 2 (WM276)
lnL =-3036.174074
0.45547 3.63495 0.20989
t= 0.4555 S= 547.4 N= 1171.6 dN/dS= 0.2099 dN= 0.0691 dS= 0.3290
4 (JEC21) ... 1 (R265)
lnL =-2937.357570
0.38462 2.95077 0.15134
t= 0.3846 S= 530.2 N= 1188.8 dN/dS= 0.1513 dN= 0.0470 dS= 0.3104
4 (JEC21) ... 2 (WM276)
lnL =-2966.384266
0.41002 3.25414 0.16413
t= 0.4100 S= 538.1 N= 1180.9 dN/dS= 0.1641 dN= 0.0527 dS= 0.3210
4 (JEC21) ... 3 (H99)
lnL =-2844.283241
0.29120 4.67661 0.21504
t= 0.2912 S= 566.5 N= 1152.5 dN/dS= 0.2150 dN= 0.0441 dS= 0.2049
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