2 195
seq1 GTT ACC GGT CTT GAC ATG AAC ATC AGC CAA TTT CTA AAA AGC CTT GGC CTT GAA CAC CTT CGG GAT ATC TTT GAA ACA GAA CAG ATT ACA CTA GAT GTG TTG GCT GAT ATG GGT CAT GAA GAG TTG AAA GAA ATA GGC ATC AAT GCA TAT GGG CAC CGC CAC AAA TTA ATC AAA GGA GTA GAA AGA CTT TTA GGT
seq2 GTT GCT GGT CTT GAC ATG AAT ATC AGC CAA TTT CTA AAA AGC CTT GGC CTT GAA CAC CTT CGG GAT ATC TTT GAA ACA GAA CAG ATT ACA CTA GAT GTG TTG GCT GAT ATG GGT CAT GAA GAG TTG AAA GAA ATA GGC ATC AAT GCA TAT GGG CAC CGC CAC AAA TTA ATC AAA GGA GTA GAA AGA CTC TTA GGT
Printing out site pattern counts
2 111 P
seq1 AAA AAC AAT ACA ACC AGA AGC ATA ATC ATG ATT CAA CAC CAG CAT CGC CGG CTA CTT CTT GAA GAC GAG GAT GCA GCT GGA GGC GGG GGT GTA GTG GTT TAT TTA TTG TTT
seq2 ... ..T ... ... G.T ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
4 1 1 2 1 1 2 1 4 2 1 1 3 1 1
1 1 2 1 4 6 1 1 3 1 1 1 2 1 3
1 1 1 1 2 2 2
CODONML (in paml version 4.5, December 2011) /var/folders/pr/wb88nxq93xn7hdhgr2_bjd5w0000gn/T/UIa4SSyGGv/Bw_1hNQpYZ
Model: One dN/dS ratio for branches kappa = 2.000 fixed
Codon frequency model: F3x4
ns = 2 ls = 65
Codon usage in sequences
--------------------------------------------------------------
Phe TTT 2 2 | Ser TCT 0 0 | Tyr TAT 1 1 | Cys TGT 0 0
TTC 0 0 | TCC 0 0 | TAC 0 0 | TGC 0 0
Leu TTA 2 2 | TCA 0 0 | *** TAA 0 0 | *** TGA 0 0
TTG 2 2 | TCG 0 0 | TAG 0 0 | Trp TGG 0 0
--------------------------------------------------------------
Leu CTT 5 4 | Pro CCT 0 0 | His CAT 1 1 | Arg CGT 0 0
CTC 0 1 | CCC 0 0 | CAC 3 3 | CGC 1 1
CTA 2 2 | CCA 0 0 | Gln CAA 1 1 | CGA 0 0
CTG 0 0 | CCG 0 0 | CAG 1 1 | CGG 1 1
--------------------------------------------------------------
Ile ATT 1 1 | Thr ACT 0 0 | Asn AAT 1 2 | Ser AGT 0 0
ATC 4 4 | ACC 1 0 | AAC 1 0 | AGC 2 2
ATA 1 1 | ACA 2 2 | Lys AAA 4 4 | Arg AGA 1 1
Met ATG 2 2 | ACG 0 0 | AAG 0 0 | AGG 0 0
--------------------------------------------------------------
Val GTT 1 1 | Ala GCT 1 2 | Asp GAT 3 3 | Gly GGT 3 3
GTC 0 0 | GCC 0 0 | GAC 1 1 | GGC 2 2
GTA 1 1 | GCA 1 1 | Glu GAA 6 6 | GGA 1 1
GTG 1 1 | GCG 0 0 | GAG 1 1 | GGG 1 1
--------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: seq1
position 1: T:0.10769 C:0.23077 A:0.30769 G:0.35385
position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462
position 3: T:0.29231 C:0.23077 A:0.33846 G:0.13846
Average T:0.25641 C:0.17949 A:0.33846 G:0.22564
#2: seq2
position 1: T:0.10769 C:0.23077 A:0.29231 G:0.36923
position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462
position 3: T:0.30769 C:0.21538 A:0.33846 G:0.13846
Average T:0.26154 C:0.17436 A:0.33333 G:0.23077
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 4 | Ser S TCT 0 | Tyr Y TAT 2 | Cys C TGT 0
TTC 0 | TCC 0 | TAC 0 | TGC 0
Leu L TTA 4 | TCA 0 | *** * TAA 0 | *** * TGA 0
TTG 4 | TCG 0 | TAG 0 | Trp W TGG 0
------------------------------------------------------------------------------
Leu L CTT 9 | Pro P CCT 0 | His H CAT 2 | Arg R CGT 0
CTC 1 | CCC 0 | CAC 6 | CGC 2
CTA 4 | CCA 0 | Gln Q CAA 2 | CGA 0
CTG 0 | CCG 0 | CAG 2 | CGG 2
------------------------------------------------------------------------------
Ile I ATT 2 | Thr T ACT 0 | Asn N AAT 3 | Ser S AGT 0
ATC 8 | ACC 1 | AAC 1 | AGC 4
ATA 2 | ACA 4 | Lys K AAA 8 | Arg R AGA 2
Met M ATG 4 | ACG 0 | AAG 0 | AGG 0
------------------------------------------------------------------------------
Val V GTT 2 | Ala A GCT 3 | Asp D GAT 6 | Gly G GGT 6
GTC 0 | GCC 0 | GAC 2 | GGC 4
GTA 2 | GCA 2 | Glu E GAA 12 | GGA 2
GTG 2 | GCG 0 | GAG 2 | GGG 2
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.10769 C:0.23077 A:0.30000 G:0.36154
position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462
position 3: T:0.30000 C:0.22308 A:0.33846 G:0.13846
Average T:0.25897 C:0.17692 A:0.33590 G:0.22821
Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
0.01224357 0.00910419 0.01381326 0.00565088
0.00255074 0.00189671 0.00287776 0.00117727
0.01224357 0.00910419 0.00000000 0.00000000
0.00612179 0.00455210 0.00000000 0.00282544
0.02623622 0.01950899 0.02959984 0.01210903
0.00546588 0.00406437 0.00616663 0.00252271
0.02623622 0.01950899 0.02959984 0.01210903
0.01311811 0.00975449 0.01479992 0.00605451
0.03410709 0.02536168 0.03847979 0.01574173
0.00710564 0.00528368 0.00801662 0.00327953
0.03410709 0.02536168 0.03847979 0.01574173
0.01705355 0.01268084 0.01923990 0.00787087
0.04110342 0.03056408 0.04637309 0.01897081
0.00856321 0.00636752 0.00966106 0.00395225
0.04110342 0.03056408 0.04637309 0.01897081
0.02055171 0.01528204 0.02318654 0.00948540
Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)
seq1
seq2 0.0913 (0.0066 0.0726)
pairwise comparison, codon frequencies: F3x4.
2 (seq2) ... 1 (seq1)
lnL = -272.706911
0.06846 0.10294
t= 0.0685 S= 51.9 N= 143.1 dN/dS= 0.1029 dN = 0.0069 dS = 0.0668