File: COII_Apes.nex

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#NEXUS
[File generated by DnaSP Ver. 4.00.3, from file: COII_Apes.nex     mar 25, 2004]
[data from: Ruvolo, Zehr and Von Dornum, 1993. Mitochondrial COII Sequences and Modern Human Origins. MBE 10: 1115-1135]
[data from: Horai, Satta, Hayasaka, Kondo, Inoue, Ishida, Hayashi and Takahata. 1992. Man's place in hominoidea revealed by mitochondrial DNA genealogy. JME 35: 32-42]

[

###############################################################################
## POLYMORPHISM

Number of sequences: 24    Number of sequences used: 24
 Selected region: 1-684   Number of sites: 684
 Total number of sites (excluding sites with gaps / missing data): 684

 Number of variable sites, S: 183
 Total number of mutations, Eta: 197

 ===================== G+C content =====================
 G+C content at noncoding positions, G+Cn: 0.153    (3.00 sites)
 G+C content at coding positions, G+Cc: 0.456    (681.00 sites)
 G+C content -Total-, G+C: 0.454    (684.00 sites)

 ============ Haplotype/Nucleotide Diversity ============
 Number of Haplotypes, h: 22
 Haplotype (gene) diversity, Hd: 0.989
    Variance of Haplotype diversity: 0.00030
       Standard Deviation of Haplotype diversity: 0.017

 Nucleotide diversity (per site), Pi: 0.09174
    Sampling variance of Pi: 0.0000492
       Standard deviation of Pi: 0.00701
 Average number of nucleotide differences, k: 62.75000
 Theta (per sequence) from S, Theta-W: 49.00528
 Theta (per site) from S, Theta-W: 0.07165

 ================== Neutrality Tests ==================
 Tajima's D: 1.12467
     Statistical significance: Not significant, P > 0.10
 Fu and Li's D* test statistic: 0.84479
     Statistical significance: Not significant, P > 0.10
 Fu and Li's F* test statistic: 1.09759
     Statistical significance: Not significant, P > 0.10
 Fu's Fs statistic: -0.923
 Strobeck's S statistic: 0.894
    (Probability that NHap <= 22)
 Probability that [NHap = 22]: 0.179

 Calculated using the total number of segregating sites

###############################################################################
## POLYMORPHISM / DIVERGENCE

 Selected region: 1-684   Number of sites: 684
 Total number of sites (excluding sites with gaps / missing data): 684
 Intraspecific Data: Human
    Number of sequences: 6
 Interspecific Data: Chimp
    Number of sequences: 5
       Sequence used to polarize mutations: Ptr1

 Number of variable sites, S: 7
 Total number of mutations, Eta: 7

 ===================== G+C content =====================
 G+C content at noncoding positions, G+Cn: 0.333    (3.00 sites)
 G+C content at coding positions, G+Cc: 0.462    (681.00 sites)
 G+C content -Total-, G+C: 0.462    (684.00 sites)

 ============ Haplotype/Nucleotide Diversity ============
 Number of Haplotypes, h: 4
 Haplotype (gene) diversity, Hd: 0.800
    Variance of Haplotype diversity: 0.02963
       Standard Deviation of Haplotype diversity: 0.172

 Nucleotide diversity (per site), Pi: 0.00341
    Sampling variance of Pi: 0.0000014
       Standard deviation of Pi: 0.00117
 Average number of nucleotide differences, k: 2.33333
 Theta (per sequence) from S, Theta-W: 3.06569
 Theta (per site) from S, Theta-W: 0.00448

 ================== Neutrality Tests ==================
 Tajima's D: -1.39031
     Statistical significance: Not significant, P > 0.10
 Fu and Li's D* test statistic: -1.42394
     Statistical significance: Not significant, P > 0.10
 Fu and Li's F* test statistic: -1.52011
     Statistical significance: Not significant, P > 0.10
 Fu's Fs statistic: -0.219
 Strobeck's S statistic: 0.856
    (Probability that NHap <= 4)
 Probability that [NHap = 4]: 0.302

 Fu and Li's D test statistic, FL-D: -0.5143
     Statistical significance: Not significant, P > 0.10
 Fu and Li's F test statistic, FL-F: -0.8463
     Statistical significance: Not significant, P > 0.10
 Fay and Wu's H test statistic, FW-H: -2.9333

 ================ Divergence ===============
 Nucleotide divergence with Jukes and Cantor, K(JC): 0.10105

 Calculated using the total number of segregating sites

###############################################################################
## GENE FLOW / GENETIC DIFFERENTIATION

 Number of Populations Included: 5
 Selected region: 1-684     Number of sites: 684
 Sites with alignment gaps are: Excluded
 Total sites (excluding alignment gaps): 684

 Population 1: Human
   Number of sequences: 6
   Number of segregating sites, S: 7
   Number of haplotypes, h: 4
   Haplotype diversity, Hd: 0.80000
   Average number of differences, K: 2.33333
   Nucleotide diversity, Pi: 0.00341
   Nucleotide diversity with JC, PiJC: 0.00342

 Population 2: Chimp
   Number of sequences: 5
   Number of segregating sites, S: 16
   Number of haplotypes, h: 5
   Haplotype diversity, Hd: 1.00000
   Average number of differences, K: 7.00000
   Nucleotide diversity, Pi: 0.01023
   Nucleotide diversity with JC, PiJC: 0.01031

 Population 3: PygmyChimp
   Number of sequences: 4
   Number of segregating sites, S: 7
   Number of haplotypes, h: 4
   Haplotype diversity, Hd: 1.00000
   Average number of differences, K: 3.83333
   Nucleotide diversity, Pi: 0.00560
   Nucleotide diversity with JC, PiJC: 0.00563

 Population 4: Gorilla
   Number of sequences: 6
   Number of segregating sites, S: 30
   Number of haplotypes, h: 6
   Haplotype diversity, Hd: 1.00000
   Average number of differences, K: 14.53333
   Nucleotide diversity, Pi: 0.02125
   Nucleotide diversity with JC, PiJC: 0.02166

 Population 5: Orangutan
   Number of sequences: 3
   Number of segregating sites, S: 38
   Number of haplotypes, h: 3
   Haplotype diversity, Hd: 1.00000
   Average number of differences, K: 25.33333
   Nucleotide diversity, Pi: 0.03704
   Nucleotide diversity with JC, PiJC: 0.03830

 Total Data Estimates
   Number of sequences: 24
   Number of segregating sites, S: 183
   Number of haplotypes, h: 22
   Haplotype diversity, Hd: 0.98913
   Average number of nucleotide differences, Kt: 62.75000
   Nucleotide diversity, PiT: 0.09174

 =========== Genetic Differentiation Estimates ==========
  Chi-square (table), Chi2: 96.000   P-value of Chi2: 0.1746 ns;   (df = 84)
    ns, not significant;  *, 0.01<P<0.05;  **, 0.001<P<0.01;  ***, P<0.001

  HBK 1992, Hs: 0.94286   Hst: 0.04678
  HBK 1992, Ks: 9.48056   Kst: 0.84892
  HBK 1992, Ks*: 1.88566   Kst*: 0.50822
  HBK 1992, Z: 27.67619   Z*: 3.04149
  Hudson 2000, Snn: 1.00000

 =========== Gene Flow Estimates ===========
  Genome: Haploid

  Haplotype Data Information
     Nei 1973
        Gst: 0.04074    Nm: 11.77
  Sequence Data Information
     Nei 1982
        DeltaSt: 0.07729    GammaSt: 0.87909    Nm: 0.07
     Lynch and Crease 1990  (with Jukes and Cantor correction)
        Nst: 0.86942    Nm: 0.08
     Hudson, Slatkin and Maddison 1992
        Fst: 0.86070    Nm: 0.08

###############################################################################
## Fu and Li's and Other Tests

Number of sequences: 24    Number of sequences used: 24
 Selected region: 1-684   Number of sites: 684
 Total number of sites (excluding sites with gaps / missing data): 684

 Number of polymorphic (segregating) sites, S: 183
 Total number of mutations, Eta: 197
 Total number of singleton segregating sites, Eta(s): 28

 Average number of pairwise nucleotide differences, k: 62.750
 Nucleotide diversity, Pi: 0.09174

 Theta estimated from k: 62.750
 Theta estimated from Eta(s): 26.833
 Theta estimated from S: 49.005

 Fu and Li's D* test statistic: 0.84479
     Statistical significance: Not significant, P > 0.10
 Fu and Li's F* test statistic: 1.09759
     Statistical significance: Not significant, P > 0.10

 Calculated using the total number of segregating sites

 Number of Haplotypes, h: 22
 Haplotype (gene) diversity, Hd: 0.989
    Variance of Haplotype diversity: 0.00030

 Fu's Fs statistic: -0.923
 Strobeck's S statistic: 0.894
    (Probability that NHap <= 22)
 Probability that [NHap = 22]: 0.179

###############################################################################
## Tajima's D

 Number of sequences: 24    Number of sequences used: 24
 Selected region: 1-684   Number of sites: 684
 Total number of sites (excluding sites with gaps / missing data): 684

 Number of polymorphic (segregating) sites, S: 183
 Total number of mutations, Eta: 197

 Average number of nucleotide differences, k: 62.75000
    Nucleotide diversity, Pi: 0.09174
 Theta (per sequence) from S, Theta-W: 49.00528
    Theta (per site) from S, Theta-W: 0.07165

 Tajima's D: 1.12467     Statistical significance: Not significant, P > 0.10


 ============ Synonymous and NonSynonymous Substitutions ============

 Total number of sites in coding regions: 681
    Total number of sites excluding complex codons or codons with gaps: 675
    Total number of sites in other codons (complex codons) no analyzed: 6
 Total number of sites in noncoding regions: 3

 Coding region: Tajima's D: 1.08776     Not significant, P > 0.10
     Total number of polymorphic sites: 178 (Changes: 191)
 Synonymous sites: Tajima's D(Syn): 1.35960     Not significant, P > 0.10
     Total number of polymorphic sites: 153 (Changes: 166; Syn. Changes: 165)
 NonSynonymous sites: Tajima's D(NonSyn): -0.54877     Not significant, P > 0.10
     Total number of polymorphic sites: 26 (Changes: 27; NonSyn. Changes: 26)
 Silent sites: Tajima's D(Sil): 1.37519     Not significant, P > 0.10
     Total number of polymorphic sites: 154 (Changes: 167; Sil. Changes: 166)

 Tajima's D (NonSyn/Syn) ratio: -0.40362


 Some codons with multiple evolutionary paths were detected.
    The number of synonymous and nonsynonymous mutations were estimated
    using the DnaSP conservative criteria (see the help file).
      Sites affected:  58 60 552

 Calculated using the total number of segregating sites

]


BEGIN TAXA;
DIMENSIONS NTAX=24;

TAXLABELS
Hsa1
Hsa2
Hsa3
Hsa4
Hsa5
Hsa6
Ptr1
Ptr2
Ptr3
Ptr4
Ptr5
Ppa1
Ppa2
Ppa3
Ppa4
Ggo1
Ggo2
Ggo3
Ggo4
Ggo5
Ggo6
Ppy1
Ppy2
Ppy3;
END;

BEGIN CHARACTERS;
DIMENSIONS NCHAR=684;
FORMAT DATATYPE=DNA  MISSING=? GAP=- MATCHCHAR=. INTERLEAVE ;
MATRIX
[             10        20        30        40        50        60]
[              *         *         *         *         *         *]
Hsa1  ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ............................................................
Hsa6  ............................................................
Ptr1  .......................C................................A...
Ptr2  ................................T.......................A...
Ptr3  ........................................................A...
Ptr4  ................................T.......................A...
Ptr5  ........................................................A...
Ppa1  ...................................C....................A...
Ppa2  ...................................C....................A...
Ppa3  ...................................C....................A...
Ppa4  ...................................C....................A...
Ggo1  .........................................T..............A..A
Ggo2  .........................................T..............A..A
Ggo3  .........................................T..............A..A
Ggo4  .........................................T..............A..A
Ggo5  ..............A..........................T..............A..A
Ggo6  ..............A..........................T..............A..A
Ppy1  .....G..C.....A..G....................C..T..............AT.G
Ppy2  .....G..CCG...A..G....................C..T..............AT.G
Ppy3  .....G..C.....A..G......T.............C..T..............AT.G

[             70        80        90       100       110       120]
[              *         *         *         *         *         *]
Hsa1  ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ...........................G................................
Hsa6  ............................................................
Ptr1  ..T.T.........C..T...........T..C..T..C.................A..C
Ptr2  ..T.T......C..C..T...........T..C..T..C........T........A..C
Ptr3  ..T.T.........C..T...........T..C..T..C.................A..C
Ptr4  ..T.T......C..C..T...........T..C..T..C........T........A..C
Ptr5  ..T.T.........C..T...........T..C..T..C.................A..C
Ppa1  ..T.T.........C..T...........T..C..T..C....................C
Ppa2  ..T.T.........C..T...........T..C..T..C....................C
Ppa3  ..T.T.........C..T...........T..C..T..C....................C
Ppa4  ..T.T.........C..T...........T..C..T..C....................C
Ggo1  .................T..T..............T..C.........T..........C
Ggo2  ....T............T.................T..C.........T..........C
Ggo3  .................T..T..............T..C.........T..........C
Ggo4  ....T............T.................T..C.........T..........C
Ggo5  ..T.TT...........T.................T..C.........T..........C
Ggo6  ..T.TT...........T.................T..C.........T..........C
Ppy1  G...T......C..C.................C.....A....................C
Ppy2  G...T......C..C.................C.....A....................C
Ppy3  G...T......C..C.......................A....................C

[            130       140       150       160       170       180]
[              *         *         *         *         *         *]
Hsa1  GCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAA
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ............................................................
Hsa6  ............................................................
Ptr1  ........................................GT..T........C......
Ptr2  ........................................GT..T........C......
Ptr3  ........................................GT..T........C......
Ptr4  ........................................GT..T........C......
Ptr5  ........................................GT..T........C......
Ppa1  ........................................GT..T........C......
Ppa2  ........................................GT..T........C......
Ppa3  ........................................GT..T........C......
Ppa4  ........................................GT..T........C......
Ggo1  ..........................G.......GC..C..............C..A...
Ggo2  ..........................G........C.AC..............C..A...
Ggo3  ..........................G.......GC..C..............C..A...
Ggo4  ..........................G........C..C..............C..A...
Ggo5  ..........................G.......GC..C..............C..A...
Ggo6  ..........................G.......GC..C..............C..A...
Ppy1  .......................G.....C..C..C..............T..C..A..G
Ppy2  .......................G.....C..C..C..............T..C..A..G
Ppy3  .............................C..C..C..C.G............C..A...

[            190       200       210       220       230       240]
[              *         *         *         *         *         *]
Hsa1  ATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCC
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ............................................................
Hsa6  ............................................................
Ptr1  .....G.................A....................T..T.....A......
Ptr2  ............................................T..T.....A......
Ptr3  ............................................T..T.....A......
Ptr4  ............................................T..T.....A......
Ptr5  ............................................T..T.....A......
Ppa1  ............................................T..T.....T.....T
Ppa2  ............................................T..T.....T.....T
Ppa3  ............................................T..T.....T.....T
Ppa4  ............................................T..T.....T.....T
Ggo1  .....G...A.......C.....A.....T..T...T.......G..............T
Ggo2  .....G...A.......C...........T..T...T.......G..............T
Ggo3  .....G...A.......C.....A.....T..T...T.......G..............T
Ggo4  .....G...A.......C...........T..T...T.......G..............T
Ggo5  .....G...........C.....A..A..T..T...T.......G...............
Ggo6  .....G...........C.....A..A..T..T...T.......G...............
Ppy1  ........TA.T...........A..A............A.T..A..............T
Ppy2  ........TA.T.......C...A..A............A.T..A..............T
Ppy3  ..G..G..TA.T...........A..G............A.T..A..............T

[            250       260       270       280       290       300]
[              *         *         *         *         *         *]
Hsa1  CTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT
Hsa2  ..G.........................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ............................................................
Hsa6  ............................................................
Ptr1  ..G..T.............................C......T....T..T........C
Ptr2  ..G..T.............................C......T....T..T........C
Ptr3  ..G..T.............................C......T....T..T........C
Ptr4  ..G..T.............................C......T....T..T........C
Ptr5  ..C..T.............................C......T....T..T........C
Ppa1  .....T........T....................C......T....T..T........C
Ppa2  .....T........T....................C......T....T..T........C
Ppa3  .....T........T....................C......T....T..T........C
Ppa4  .....T........T....................C......T....T..T........C
Ggo1  .....A.....C..T..G.....T..AA....T..C......T.C..T...........C
Ggo2  .....A.....C..T..G.....T..AA....T..C......T.C..T...........C
Ggo3  .....A.....C..T..G.....T..AA....T..C......T.C..T...........C
Ggo4  .....A.....C..T..G.....T..AA....T..C......T.C..T...........C
Ggo5  .....A.....C..T..G.....T..AA..............T....T...........C
Ggo6  .....A.....C..T..G.....T..AA.......C......T....T...........C
Ppy1  ...........C...T..........AA.......C..T...T.C.....T........C
Ppy2  ...........C...T..........AA.......C..T...T.C.....T........C
Ppy3  ...........C...T...........A.......C..T...T.C..............C

[            310       320       330       340       350       360]
[              *         *         *         *         *         *]
Hsa1  GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCC
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ............................................................
Hsa6  ............................................................
Ptr1  .....T.....A..T...........A.................G...............
Ptr2  .....T.....A..T...........A.................G...............
Ptr3  .....T.....A..T...........A.................G...............
Ptr4  .....T.....A..T...........A.................G...............
Ptr5  .....T.....A..T...........A.................G...............
Ppa1  .....T.....A..T...........A.................................
Ppa2  .....T.....A..T...........A.................................
Ppa3  .....T.....A..T...........A.................................
Ppa4  .....T.....A..T...........A.................................
Ggo1  ..T........A..............A...........T..T...T.G.....T......
Ggo2  ..T........A..............A...........T..T...T.G.....T......
Ggo3  ..T........A..............A...........T..T...T.G.....T......
Ggo4  ..T........A..............A...........T..T...T.G.....T......
Ggo5  ..T........A..............A...........T..T...T.GG....T.....T
Ggo6  ..T........A..............A...........T..T...T.G.....T.....T
Ppy1  .....T.......................T..T.....T......T.G...........T
Ppy2  .....T.......................T..T.....T......T.G...........T
Ppy3  ..T..T.....A....................T........T...T.G...........T

[            370       380       390       400       410       420]
[              *         *         *         *         *         *]
Hsa1  TACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAAT
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ..............G.............................................
Hsa6  ............................................................
Ptr1  ........C...........T...........T..T..A.................T..C
Ptr2  ........C...........T...........T..T..A.................T..C
Ptr3  ........C...........T...........T..T..A.................T..C
Ptr4  ........C...........T...........T..T..A.................T..C
Ptr5  ........C...........T...........T..T..A.................T..C
Ppa1  ........C...........T.................A.................T..C
Ppa2  ........C...........T.................A.................T..C
Ppa3  ........C...........T.................A.................T..C
Ppa4  ........C...........T.................A.................T..C
Ggo1  ..T.....C.......................T.....A..............C.....C
Ggo2  ..T.....C.......................T.....A..............C.....C
Ggo3  ..T.....C.......................T.....A..............C.....C
Ggo4  ..T.....C.......................T.....A..............C.....C
Ggo5  ........C..T....................T.....A..............C.....C
Ggo6  ........C..T....................T.....A..............C.....C
Ppy1  .....G..C..A...C......................T........A.....C......
Ppy2  .....G..C..A...C......................T........A.....C......
Ppy3  .....G..C..A...C......................T........C.....C.....C

[            430       440       450       460       470       480]
[              *         *         *         *         *         *]
Hsa1  CGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTG
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  .....................A......................................
Hsa6  ............................................................
Ptr1  .....G..C..T..AG...........G.........................T..TC.A
Ptr2  .....G..C.....AG...........G.........................T..TC.A
Ptr3  ...C.G..C.....AG...........G.........................T..TC.A
Ptr4  .....G..C.....AG...........G.........................T..TC.A
Ptr5  .....G..C.....AG...........G.........................T..TC.A
Ppa1  ..G..G..C.....AG...........G.........................T..TC.A
Ppa2  ..G..G..C.....AG...........G.........................T..TC.A
Ppa3  ..G..G..C.....AG...........G.........................T..TC.A
Ppa4  ..G..G........AG...........G.........................T..TC.A
Ggo1  ........C..T..AG...........G.C.................C.....T.....A
Ggo2  ........C..T..AG...........G.C.................C.....T.....A
Ggo3  ........C..T..AG...........G.C.................C.....T.....A
Ggo4  ........C..T..AG...........G.C.................C.....T.....A
Ggo5  ........C..T..AG...........G.C.................C.....T.....A
Ggo6  ........C..T..AG...........G.C.................C.....T.....A
Ppy1  ........C.....AG.C.........G....C........C.....C............
Ppy2  ........C.....AG.C.........G....C........C.....C............
Ppy3  ........C.....AG.C.....T...G....C........C.....C...........A

[            490       500       510       520       530       540]
[              *         *         *         *         *         *]
Hsa1  CACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAAC
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ............................................................
Hsa6  ...............................................A............
Ptr1  ........G.....T............C..........C..............C......
Ptr2  ..............T............C..........C..............C......
Ptr3  ..............T............C..........C.....................
Ptr4  ..............T............C..........C..............C......
Ptr5  ..............T...........TC..........C..............C......
Ppa1  ............A..............C..........C..............C......
Ppa2  ...........................C..........C..............C......
Ppa3  ..............T............C..........C..............C......
Ppa4  ...........................C..........C..............C......
Ggo1  ..............T............C..........C.....C........C..G...
Ggo2  ..............T............C..........C.....C.....G..C..G...
Ggo3  ..............T............C..........C.....C........C..G...
Ggo4  ..............T............C........C.C.....C........C..G...
Ggo5  ..............T............C..........C.....C.....G..C..G...
Ggo6  ..............T............C..........C.....C.....G..C..G...
Ppy1  .........A.C......T..C.....C.G........C.....C........C......
Ppy2  .........A.C......T..C.....C.G........C.....C........C......
Ppy3  .........A....A...T..C.....C.......G..C.....C........C......

[            550       560       570       580       590       600]
[              *         *         *         *         *         *]
Hsa1  CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ............................................................
Hsa6  ..........................A.................................
Ptr1  .................C........A..A...........C........A.........
Ptr2  .................C........A..A...........C........A.........
Ptr3  .................C........A..A...........C........A.........
Ptr4  .................C........A..A...........C........A.........
Ptr5  .................C........A..A...........C........A.........
Ppa1  .................C........A..A........T..C........A.........
Ppa2  .................C........A..A........T..C........A.........
Ppa3  .................C........A..A...........C........A.........
Ppa4  .................C........A..A...........C........A.........
Ggo1  ........A........C........A..A...........C..G.....A.........
Ggo2  ........A........C........A..A...........C..G.....A.........
Ggo3  ........A........C........A..A...........C..G.....A.........
Ggo4  ........A........C........A..A...........C..G.....A.........
Ggo5  ........A..T.....C........A..............C..G.....A.........
Ggo6  ........A..T.....C........A...C..........C..G.....A.........
Ppy1  ........A.....T..C........A..A.....T..T..C........A.........
Ppy2  ........A.....T..C........A..A.....T..T..C........A.........
Ppy3  ........A..G..T..C..G.....A..A..G.....T..C........A.........

[            610       620       630       640       650       660]
[              *         *         *         *         *         *]
Hsa1  GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAA
Hsa2  ............................................................
Hsa3  ............................................................
Hsa4  ............................................................
Hsa5  ............................................................
Hsa6  ............................................................
Ptr1  .................T..A....................C..T...............
Ptr2  .................T..A..................C....T...............
Ptr3  .................T..A....................C..T...............
Ptr4  .................T..A....................C..T...............
Ptr5  .................T..A....................C..T...............
Ppa1  .................T..A..............G.....C..................
Ppa2  .................T..A..............G...C....................
Ppa3  .................T..A..............G.....C..................
Ppa4  .................T..A..............G.....C..................
Ggo1  .....C...........T........T..T.....GC....C..................
Ggo2  .....C...........T........T..T.....GC..C....................
Ggo3  .....C...........T........T..T.....GC....C..................
Ggo4  .....C...........T........T..T.....GC....C..................
Ggo5  .....C...........T........T.........C....C..................
Ggo6  .....C...........T........T........GC....C..................
Ppy1  .....T........C..T.....T............C..C................C...
Ppy2  .....T........C..T.....T............C....C..............C...
Ppy3  .....C........C..T.....T.................C..............C...

[            670       680    ]
[              *         *    ]
Hsa1  ATAGGGCCCGTATTTACCCTATAG
Hsa2  ........................
Hsa3  ........................
Hsa4  ........................
Hsa5  ........................
Hsa6  .....A..................
Ptr1  .....A......C.C..T......
Ptr2  .....A........C..T......
Ptr3  .....A........C..T......
Ptr4  .....A........C..T......
Ptr5  ..............C..T......
Ppa1  .....A........C..T.....A
Ppa2  .....A........C..T.....A
Ppa3  .....A........CG.T.....A
Ppa4  .....A........CG.T.....A
Ggo1  ..............CG.......A
Ggo2  .....A........CG.......A
Ggo3  ..G...........CG.......A
Ggo4  .....A........CG.......A
Ggo5  ..G...........C........A
Ggo6  ..G...........C........A
Ppy1  .....A........CG.TT....A
Ppy2  .....A........CG.TT....A
Ppy3  ..............C..TT....A
;
END;

BEGIN SETS;
   TaxSet Human = 1-6;
   TaxSet Chimp = 7-11;
   TaxSet PygmyChimp = 12-15;
   TaxSet Gorilla = 16-21;
   TaxSet Orangutan = 22-24;
END;

BEGIN CODONS;
   CODONPOSSET * UNTITLED =
      N: 682-684,
      1: 1-679\3,
      2: 2-680\3,
      3: 3-681\3;
   CODESET * UNTITLED = mtDNA.Mam: all;
END;

BEGIN CODONUSAGE;
END;

BEGIN DnaSP;
   Genome= Haploid;
   ChromosomalLocation= Mitochondrial;
   DnaSPversion= Ver. 4.00.3;
END;