The following supplement accompanies the article
Mitogenome analysis reveals a complex phylogeographic
relationship within the wild tiger population of Thailand
Waradee Buddhakosai, Worata Klinsawat, Olutolani Smith, Manakorn Sukmak, Nongnid
Kaolim, Somphot Duangchantrasiri, Achara Simcharoen, Boripat Siriaroonrat, Worawidh
Wajjwalku*
*Corresponding author: [email protected]
Endangered Species Research 30: 125–131 (2016)
Supplementary Files:
Table S1 The full details of the primers used in this study.
Table S2 The list of reference sequences used in this study.
Table S3 The components of the WEFCOM and Ti2 (P. t. jacksoni) mitochondrial genome.
Table S4 The variable sites between WEFCOM and Ti2.
Fig. S1 Sites of sample collection
Fig. S2 The alignment of the control region of the WEFCOM and Malayan tigers reported in this study with
previous reports. These sequences contain different lengths of the control region resulting in different sizes of
the complete mitochondrial genome. The different lengths of the control region are a result of the variable
number of tandem repeats in the repetitive sequence box 3 (RS-3). HVS = hypervariable site, RS = repetitive
sequence, CCR = central conserved region, CSB = conserved sequence box.
Fig. S3 The mitogenome map of the tiger (P. tigris) including F2 numt (red curve). Fragment 9 of this study
contained two distinct sequences; 9.1 (blue line) and 9.2 (blue dashed line), where the numt sequence was found
(red box). The grey curve indicates the region containing two highly distinct sequences when compared with
other reported complete mitogenomes.
Fig. S4 The alignment of confounding sequences near the 5’ end of F2 numt (red arrow). The sequences of the
WEFCOM tiger (fragment numbers 8, 9.1, 9.2 and 10) were aligned to HM569215 P27 of Zhang et al. (2011),
JF357971 CORBETTI1 of Kitpipit et al. (2012), cymt DQ151550 and F2 numt (DQ151551) reported by Kim et
al. (2006). The sequences resembling F2 numt are labeled in red. Two distinct sequences contaminated with
numt were found in fragment 9. The start point of the ambiguous sequences is at the last domain of the COX1
gene. The alignment shows that the amplicon 9.1 was initially similar to numt and could not be aligned with the
adjacent fragment (red dashed boxes). There is a turning point at the middle of COX2 (red arrow head) where
the amplicon 9.2 which was initially identical to cymt turned to the numt sequence and amplicon 9.1 turned to
the cymt sequence. After the end of F2 numt at the ATP6 gene, the 9.1 and 9.2 amplicons remain different
(labeled cyan).
1
Table S1. The full details of the primers used in this study.
No.
1
2
3
4
5
6
7
8
9.1
9.2
10
11
12
13
Size of PCR
product
Primer names
Primer sequences (5’-3’)
Gene
wTG3021F
Dloopre
TGDL1F
wTG4940R
wTG4753F
wTG6290R
TG6031F
TG7276R
H2513
wTG8870R
wTG8191F
wTG9920R
TG9711F
TG11294R
wTG11001F
wTG12044R
mtDNA6H
mtDNA6L
CTTATCCATCTTAATCTTAGCCAC
CCTGAAGAAAGAACCAGATGC
GATTTAGAGCAGTTCTTTCATGGAT
TATATTTAAGCTACATTAACCAAGGC
AGACTAAACCCGTATCTAGGCAC
TTCATCCTGTAATAGATTGTTTATCGG
CTTGAGCTAGAGCTAGCCCAACTA
GGGTAACTTGTTCCGTTGATCACGC
GCCTGTTTACCAAAAACATCAC
ACGGTTGATATAATGATGGTGAGG
GAATACATCTGGCTCATCATCGCT
GCTCTTGGTCTAGTTTGACCCT
TAGCCATAACAGCACTACTTAACGTA
CCCAAAGCCCATAGTATAGCGCGA
CCAGAAGTCTATATCTTAATCCTG
AATGTATGATCATGGAAGTGTGAA
GCTCATTTATTTCACTAACAGCAGT
GGGCTACAGCAAATTCAAGGAT
CR
951
Ta
58
Ref.
CR
1,137
58
CR - 12S rRNA
1,563
60
16S rRNA
1,271
60
16S rRNA - ND1
2,027
56
ND1 - ND2
1,729
60
ND2 - COX1
1,618
60
COX1 - COX2
1,049
60
COX2 - ATP6
1,856
58
TG6H
TG6L
mtDNA7H
mtDNA7L
mtDNA8H
mtDNA8L
mtDNA9H
wTG1680R
TND6-1
wTG3170R
ACAACTAATCTCGAATGACTTGAC
TCCTCCGATTAGGTGTATTAATTAA
TTGGCTCACTTTCTACCTCAAGG
GTGGGGATGATGATTTTTAGCATTGTA
CCAAAACAAATGATTTCGACTCA
GGTTCCTAAGACCAATGGATTACTTCT
AAACCATCATTCACACGAGAAAAC
GGTGCGGGTGATTGAGTGGTC
CTATCCTTCCATAATCACCCTG
GCCGATGGCAATAAAGGGGTGT
COX2 - ATP6
1,667
58
ATP6 – ND4L
1,890
60
ND4L – ND4
1,889
60
ND4- ND6
2,270
58
ND5 – CYT B
1,693
58
This study
(Ward et al. 1999)
This study
This study
This study
This study
This study
This study
(Kitano et al. 2007)
This study
This study
This study
This study
This study
This study
This study
(Delisle & Strobeck 2002)
(Delisle & Strobeck 2002)
This study
This study
(Delisle & Strobeck 2002)
(Delisle & Strobeck 2002)
(Delisle & Strobeck 2002)
(Delisle & Strobeck 2002)
(Delisle & Strobeck 2002)
This study
This study
This study
2
Table S2. The list of reference sequences used in this study.
Accession No.
Species/subspecies
Haplotye/ individual
NC_010638
EF551002
DQ257669
KF297576
DQ151550
DQ151551
HM589214
HM589215
JF357967
P. uncia
P. pardus
N. nebulosa
P. t. altaica
P. tigris
P. tigris
P. t. amoyensis
P. t. amoyensis
P. t . tigris
F2 nuclear copy
P25
P27
TIGRIS1
JF357968
P. t. tigris
TIGRIS2
16,976
JF357969
P. t. sumatrae
SUMATRA1
16,998
JF357970
P. t. sumatrae
SUMATRA2
17,001
JF357971
P. t . corbetti
CORBETTI1
16,602
JF357972
P. t. corbetti
CORBETTI2
14,174
JF357973
P. t. altaica
ALTAICA4
16,980
JF357974
P. t. altaica
ALTAICA1
17,015
AY736559–
AY736808
All subspecies of
extant
Panthera tigris
P. tigris
ALT, AMO1-3, COR18,
SUM1-8, TIG1-6
NHM
P. t. sondaica,
P. t. balica
SON, BAL
JN786601- JN786684
KJ686500-KJ686533
Length
(bp)
16,773
16,964
16,884
16,996
12,912
12,559
16,957
17,001
16,637
250 - 593
199 - 482
67 - 223
Reference
Wei et al. 2010
Wei et al. 2011
Wu et al. 2007
Sun et al. 2014
Kim et al. 2006
Kim et al. 2006
Zhang et al. 2011
Zhang et al. 2011
Kitpipit et al.
2012
Kitpipit et al.
2012
Kitpipit et al.
2012
Kitpipit et al.
2012
Kitpipit et al.
2012
Kitpipit et al.
2012
Kitpipit et al.
2012
Kitpipit et al.
2012
Luo et al. 2004
Mondol et al.
2013
Xue et al. 2015
3
Table S3. The components of the WEFCOM and Ti2 (P. t. jacksoni) tiger mitochondrial genome.
Position
Gene
Phe
tRNA12S rRNA
tRNA-Val
16S rRNA
tRNA-Leu
ND1
tRNA-Ile
tRNA-Gln
tRNA-Met
ND2
tRNA-Trp
tRNA-Ala
tNRA-Asn
tNRA-Cys
tNRA-Tyr
COX1
tRNA-Ser
tRNA-Asp
COX2
tRNA-Lys
ATP8
ATP6
COX3
tRNA-Gly
ND3
tRNA-Arg
ND4L
ND4
tRNA-His
tRNA-Ser
tNRA-Leu
WEFCOM
ORF
Ti2 (P. t. jacksoni)
start
stop
start
stop
1
72
1,032
1,100
2,675
2,752
3,708
3,774
3,848
3,917
4,959
5,042
5,112
5,218
5,283
5,351
6,893
6,968
7,037
7,724
7,793
7,954
8,634
9,418
9,487
9,834
9,903
10,193
11,571
11,640
11,699
71
1,031
1,099
2,674
2,749
3,707
3,776
3,847
3,916
4,958
5,026
5,110
5,184
5,282
5,349
6,895
6,961
7,036
7,720
7,791
7,996
8,634
9,417
9,486
9,833
9,902
10,199
11,570
11,638
11,698
11,768
1
72
1,032
1,100
2,675
2,752
3,708
3,774
3,848
3,917
4,959
5,042
5,112
5,217
5,282
5,350
6,892
6,967
7,036
7,723
7,792
7,953
8,633
9,417
9,486
9,833
9,902
10,192
11,570
11,639
11,698
71
1,031
1,099
2,674
2,749
3,707
3,776
3,847
3,916
4,958
5,026
5,110
5,184
5,281
5,348
6,894
6,960
7,035
7,719
7,790
7,995
8,633
9,416
9,485
9,832
9,901
10,198
11,569
11,637
11,697
11,767
start
ND5
ND6
tRNA-Glu
CYT B
tNRA-Thr
tRNA-Pro
CR
WEFCOM
start
stop
11,769
13,573
14,101
14,173
15,313
15,383
15,450
13,589
14,100
14,169
15,312
15,382
15,449
16,954
Ti2 (P. t. jacksoni)
start
stop
11,768
13,572
14,100
14,172
15,312
15,382
15,449
13,588
14,099
14,168
15,311
15,381
15,448
17,008
stop
ATG
TAA
ATC
TAA
ATG
TAA
ATG
TAA
ATG
ATG
ATG
TAA
TAA
TAA
ATA
TAA
ATG
ATG
TAA
TAA
Position
Gene
Strand
ORF
start
H
H
H
H
H
H
H
L
H
H
H
L
L
L
L
H
L
H
H
H
H
H
H
H
H
H
H
H
H
H
H
Strand
stop
ATA
ATG
TAA
TAA
ATG
AGA
H
L
L
H
H
L
H
4
Table S4. The variable sites between the WEFCOM and Malayan (Ti2) haplotype. The variations between HVS-I of CR to first base of tRNA-Phe were excluded. The new
mutation sites comparing to previous reports (Luo et al. 2004, Driscoll et al. 2009, Zhang et al. 2011, Kitppipit et al. 2012, Mondol et al. 2013, Sun et al. 2014, Xue et al.
2015) are indicated by the red marks. The red box indicates the position that was excluded from phylogenetic analysis as it may contain additional numt.
Gene
12S
16S
ND2
COI
COII
COX
III
ATP6
9
3
7
6
9
1
4
4
1
0
0
0
9
9
5
3
8
1
0
4
0
3
ND4
1 1
0 0
5 9
4 7
9 2
1 1
1 1
4 8
1 3
4 7
C
T
C
T
A
G
G
A
T
C
T
C
A
G
T
C
A
G
T
C
C
T
T
C
T
C
G
A
C
T
A
G
C
T
-
-
-
-
-
-
-
G/A
-
-
A/G
A
-
-
-
C
-
A/G
G
C/T
C
-
-
-
-
-
-
-
-
-
-
A/G
A
-
G
-
-
-
C
-
G
G
C/T
T
-
-
A
C
T
C
C
G
G
C
C
G/A
T
G
T
C
C
C
G
T/C
G/A
C
C
G
C
T
C
C
G
G
C
C
G/A
T
G/A
T
C
C
C
G
T/C
G/A
C
C
G
C
T
C
C
G
G
C
C
A
T
A
T
C
C
C
G
C
A
C
Position
on
WEFCOM
sequence
2
4
0
8
0
6
1
3
3
3
1
4
8
0
2
3
4
3
3
9
2
8
4
8
2
5
5
6
0
2
6
0
9
7
7
0
4
9
7
3
1
7
8
2
7
7
8
3
2
6
8
3
7
0
8
4
1
2
8
5
1
1
Position
on
Felis catus
(NC_001700)
1
1
0
4
1
6
7
1
2
1
9
8
2
3
4
5
3
2
0
7
4
7
9
2
5
6
8
9
6
4
6
7
6
9
6
2
7
9
1
4
8
1
8
2
9
1
4
2
9
1
9
1
9
2
3
5
9
2
7
7
WEFCOM
Ti2 (P.t.jacksoni)
Luo et al. 2004
(AY736559-808)
Driscoll et al. 2009
Mondol et al. 2013
(JN786601 –84)
Xue et al. 2015
Zhang et al. 2011
(HM589214-15)
Kitpipit et al. 2012
(JF357967-74)
Sun et al. 2014
(KF297576)
C
T
T
C
C
T
G
A
C
T
T
C
C
T
G
A
T
C
C
T
C
T
G
A
T
C
C
T
-
T/C
-
-
-
-
-
T
-
-
C
-
-
-
-
-
-
-
-
-
-
-
T
-
-
-
-
-
T/C
C/T
C
G/A
T
C/T
T
G
C
T
C
T/C
C/T
C
G
T
T
T
G
C
T
C
T
C
A
T
T
T
G
C
T
ND3
ND5
1
1
2
2
3
7
0
8
8
3
1
1
3
3
1
6
7
4
3
8
ND6
1
3
8
4
6
1
4
7
1
1
Q
1
4
1
3
6
1
5
0
0
1
1
4
4
0
0
1
5
2
6
5
1
4
4
6
3
1
5
3
2
8
1
4
6
9
4
1
5
5
5
9
Cytb
1
4
7
3
7
1
5
6
0
2
1
4
8
9
1
1
5
7
5
6
1
5
1
7
1
1
6
0
3
6
CR
1
5
5
3
4
1
6
4
0
0
5
Fig. S1. Sites of sample collection.
6
Fig. S2. The alignment of the control region of the WEFCOM and Malayan tigers reported in this study with previous
reports. These sequences contain different lengths of the control region resulting in different sizes of the complete
mitochondrial genome. The different lengths of control region are a result of the variable number of tandem repeats in
the repetitive sequence box 3 (RS-3). HVS = hypervariable site, RS = repetitive sequence, CCR = central conserved
region, CSB = conserved sequence box.
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
GAAAAAATCCTCAATCCCCGTTAATACAGAACACACAACACGAAAT-AACCTGTTAACTACCGGACCCCCCCCCCTCCCCCCGTTAATACATTACGTAGG
CG
AG 198
..............................................-...........................-......................... 197
CORBETTI1
..............................................-...........................-......................... 197
ALTAICA4
..............................................-...........................-............C............ 197
ALTAICA1
..............................................-...........................-......................... 197
SUMATRA1
..............................................-...........................-......................... 197
SUMATRA2
..............................................-...........................-......................... 197
TIGRIS1
..............................................-..........T................-.........-.............A. 195
TIGRIS2
..............................................-..........T................-.........-.............A. 195
amoyensis P27 ..............................................-.......C............................................. 198
amoyensis P25 ..............................................-..................................................... 198
P.tigris
..............................................-........................................C............ 198
F2 Numt
.TG............T...A.-..C...-...G.....TGTA...CC.....A...G.....AATA...G.....-----------------------A. 175
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
GCATACTATGGATATCGTGCATTAATCGCCTGTCCCCATGAATATTAAGCATGTACAGTAGTTTATATATATTACATAAGGCATACTATGGATATCGTGC 298
..........T............G..................................................................T......... 297
..........T......G........................................A...............................T......G.. 297
..........T......G........................................................................T......G.. 297
..........T...............................................................................T......... 297
..........T......G.........T..............................................................T......G.. 297
..........T...............................................................................T......... 297
..........T...............................................................................T......... 295
..........T...............................................................................T......... 295
..........T...............................................................................T......... 298
..........T...............................................................................T......... 298
.
A.........T.......................................................................... .....T.........
298
..T......
..CCR
275
A.........T..............CT..T..........C................A......................A.........T.........
RS-2
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
ATTAATCGCTTGTCCCCATGAATATTAAGCATGTACAGTAGTTCATATATATTACATAAGACATAATAGTGCT TAATCGTGCATATTCATGATTTAGAGC
T
398
.................................................................................................... 397
CORBETTI1
...........................................T....................................................A... 397
ALTAICA4
................................................................................................A.A. 397
ALTAICA1
.................................................................................................... 397
SUMATRA1
...........................................T........................................................ 397
SUMATRA2
...........................................T........................................................ 397
TIGRIS1
...........................................T........................................................ 395
TIGRIS2
...........................................T........................................................ 395
amoyensis P27 ...........................................T........................................................ 398
amoyensis P25 .............................................................................................C...... 398
P.tigris
..................................................................................................A. 398
F2 Numt
......T....................................T........................................G.C......C..T.A. 375
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
AGTTCTTTCATGGATCTCAACTATCCGAAAGAGCTTAATCACCTGGCCTCGAGAAACCAACAACCCTTGCTCGAGCGTGTACCTCTT -CTCGCTCCGGGC 497
....................................................................................... -............ 496
CORBETTI1
..................................................A.................................... -............ 496
ALTAICA4
..........................C............................................................T............ 497
ALTAICA1
....................................................................................... -............ 496
SUMATRA1
......................G...A............................................................ -............ 496
SUMATRA2
......................G................................................................ -............ 496
TIGRIS1
....................................................................................... -............ 494
TIGRIS2
....................................................................................... -............ 494
amoyensis P27 ......................G................................................................ -............ 497
amoyensis P25 ........T.............................................................................. -............ 497
P.tigris
....................................................................................... -............ 497
F2 Numt
...C..C.-.....C.......G....................................G..........CT............. ..-...........G 473
CCAATACCAAAAAACAACCCCATGACTTTCATAATTCATATATTGCATATACCCGTACTGTGCTTGCCCAGTATGTCCTCATCC -CCACAAAAAATAAGT
.................................................................................... -T..............
T................................................................................... -...............
.................................................................................... -...............
....C............................................................................... -...............
.................................................................................... -...............
.................................................................................... -...............
.................................................................................... -.........-.....
.................................................................................... -.........-.....
.................................................................................... -...............
T................................................................................... -...............
.................................................................................... -...............
..................................................................................TTT..........AGCAA
..TTT....
....AGCAA
HVS-1
RS-2
99
99
99
99
99
99
99
98
98
99
99
99
100
7
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
CCATTTCAACGTGGGGGTGTCTATAGTGA-AACTATATCTGGCATCTGGTTCTTACTTCAGGGTCATGACATTCTTAAATCCAATCCTTCAACTTTCTCA
.............................-......................................................................
CORBETTI1
.........................AC..-......................................................................
ALTAICA4
.....................C.......-.......C..............................................................
ALTAICA1
.............................-.......C..............................................................
SUMATRA1
.............................-.-....................................................................
SUMATRA2
.............................-......................................................................
TIGRIS1
.............................-...------------------------------------------------------------------TIGRIS2
.............................-......................................................................
amoyensis P27 .............................-.......C..............................................................
amoyensis P25 .............................-.......C..............................................................
P.tigris
.............................-.......C..............................................................
F2 Numt
.........................AC.GG..............................N..G....................................
596
595
595
596
595
594
595
526
593
596
596
596
573
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
AATA-GGACATCTCGATGGGTTAATGACTAATCAGCCCATGATCACACATAACTGTGGTGTCATGCATTTGGTATTTTTAATTTTTAGGGGGTCGAACTT
....-................................................................................. ..............
....-...............................................................................................
....-......................................................................... ......................
....-...............................................................................................
....-................................................................. ..............................
....-...............................................................................................
---------------------------------------------------------------------------------------------------....-...............................................................................................
....-...............................................................................................
....-...............................................................................................
....-...............................................................................................
....A...N.......A................-..................................................................
695
694
694
695
694
693
694
526
692
695
695
695
672
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
GCTATGACTCAGCTATGACCTAAAGGTCCTGACTCAGTCAAATATAATGTAGCTGGACTTATTCTCTATGCGGGGGTTCCACACGTACAACAAACAAGGT
.............................C......................................................................
CORBETTI1
.............................C......................................................................
ALTAICA4
.............................C................................................................ ......
ALTAICA1
.............................C......................................................................
SUMATRA1
.............................C..........................G...........................................
SUMATRA2
.............................C..........................G...........................................
TIGRIS1
---------------------------------------------------------------------------------------------------TIGRIS2
.............................C......................................................................
amoyensis P27 .............................C......................................................................
amoyensis P25 .............................C......................................................................
..
..
P.tigris
.............................C......................................................................
........
.........
F2 Numt
....................C.......................................................
C.......................
CCR
RS-3
795
7 94
794
795
794
793
794
526
792
795
795
795
772
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
GTTATTCAGTCAATGGTCACAGGACATATACTTAAATTCCTATTGTTCCACAGGACACGGCATGCGCGCACCCACGTATACGCGTACACGTATACACGTA
TTCAGTCAATGGTCACAGGACATATA
AC
GT
.........................
.............................................................................................G......
.........................
....................................................................................Y...............
.........................
....................................................................................................
..............G..........
..................G.........................................................................C.......
..............G..........
..................G.........................................................................C.......
..............G..........
..................G.........................................................................C.......
-------------------------------------------------------------------------------------------------G....C...TA........C.......
.........................
....................................................................................................
.........................
............................................................................................C.......
.........................
....................................................................................................
.........................
....................................................................................................
.........................
.............................................C...................................A..........
--------
895
894
894
895
894
893
894
553
892
895
895
895
864
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
TACACGTACACACGTACACACGTACACACGTATAC----------------ACGTACACACGTACACACGTATACACGTATACACGTACAC------ACG
................................C..ACGTATACACGTATAC.....................C.......C.......T..ACGTAT...
................T.......T.......C..--------ACGTATAC.....T..................................------...
C...............................C..--------ACGTATAC.....T.......T.......................T..------...
C..................R.......R....C..GTGTA--CACGTACAC.....................C.......C..R.......GTGTAC...
C..................................ACGTATACGCGTACAC--...................C.......C.......T..ACGTAT...
C...............................C..ACGTACACACGTACAC.....T...............C.......C.... ......ACGTAT..A
C................................------A--CACGTACAC.....................C.......C.......Y..------...
C...............................C------A--CACGTATAC.....T...............C.......C..........------...
C.......................T..........GCGTAC--ACGTACAC.....................C...............T..GCGTAC...
C.......--------------------------------TACACGTACAC.....................C.......C.....-------------C...............................C..--------ACGTATAC.....T...............C.......C.......T..------...
--------------------------------------------------------------- -------------------------------------
973
994
980
981
992
991
994
639
978
993
949
981
864
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
TACACACGTACACACGTACACACGTATACACGTACACACGTA--------------CACACGTACACACGTACACACGTATACGCGTACAC--GTACACCGT.......................C...............--------------........................C..A....T..AC...T..G
..........T...............C...............--------------T.......T.......T..G....C..--......AC........T.......T.......T...............----------------------T.......................C..A.......AC...T............................C...............CACACGTACACGTGT.......................C..A.......AC...... CGT.......................C.......T.......--------------...........................A....T..GC...--.CGT.T..ACGT.T.............C...............--------------........................C..A....T..AC...T....T.......................C...............--------------........T.......T.......C..A.......AC................T...............C...............--------------................T..........A....Y..AC................................C...............--------------T.......................C..A.......AC................................C...............--------------........T.......T..........A.......AC........T.......T.......T...............T.......--------------T.......T...............C..A.......AC...T..----------------------------------------------------------------------------------------------------
1056
1080
1063
1058
1091
1074
1079
724
1063
1078
1034
1066
864
CSB I
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
8
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
WEFCOM
Ti2
JF357971
JF357973
JF357974
JF357969
JF357970
JF357967
JF357968
HM589215
HM589214
DQ151550
DQ151551
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
-----ACGTACACACGTACACACGTATACGCGTACAC--GTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACA
CGTAC.....................C..A.......AC.............................................................
-----.....................C..------..--.............................................................
-----.....T.......T..................--.............................................................
-----.....................C..A.......AC...........................................................T.
-----.....................C..A.......AC............................................. ................
-----G.......--...........C..A.......AC.............................................................
-----................G........N...Y..--...................................................T.......T.
-----........................A....T..--.CGT...............................................T.......T.
-----.............T..................--.............................................................
-----.....T.......T..................--.............................................................
-----.....T..G.......GTAC.C...TAC....--.............................................................
------------------------------------------------------------------------------------------------------
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
CACGTACACACGTACACACGTACACACGTA------------------------TACACGTATACACGTATACACGTATACACATGCAAACTTTTTTGAT
AT
T
......................T.......TACACGTATACACGTATACACGTA..............................................
..............................CACACGTACACACGTATACACGTA.............................G.AT.C.. --------..............................TACACGTATACACGTATACACGTA..............................................
......T.......T.......T.......TACACGTATACACGTATACACGTA..............................................
..............T.......T.......TACGCGTATACACGTATACACGTA..............................................
..............T.......T.......TACACGTATACACGTATACACGTA..............................................
......T.......................CACACGTACACACGTATACACGTA.....................A.GC --------.............
......T.......T...............CACACGTACACACGTATACACGTA.......................CG --------.............
..............................CACACGTACACACGTATACACGTA................................ ..............
......................T.......TACACGTATACACGTATACACGTA..............................................
..............................CACACGTACACACGTACACACGTA......................... .....................
---------------------------------------------------------------- ....................................
1225
1280
1241
1251
1286
1269
1272
909
1248
1271
1227
1259
900
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
TTAGTAAATAATTAGCTTAACCAAACCCCCCTTACCCCCC-GTTAATCTTATTTATTATAGTACGTGTTTATTTCTGTCTTGCCAAACCCCAAAAACAAG
CAAACCCCCCTTACCCCCC
GCCAAACCCCAAAAACA
..................
.................
........................................-....................................C......................
------------------------------------------------------------------------------------------------------------------------------------.................
.................
........................................-...........................................................
.................
.................
........................................-...........................................................
.................
.................
........................................-...........................................................
.................
.................
........................................-...........................................................
.................
................
........................................-...........................................................
.................
................
........................................-...........................................................
.................
.................
........................................-...........................................................
.................
.................
........................................-...........................................................
.................
.................
........................................-...........................................................
.................
.......A........
..........T.........A...................C.....C...........C.A.......C....................A..........
1324
1379
1241
1350
1385
1368
1371
1008
1347
1370
1326
1358
1000
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
ACTAAACCCGTATCTAGGCACAAGGCCTAAGA-TTAACGTTTACAAACTCTACCAACCCCATCATTACCAATTATTAATACTAAATCATAACTTCGTTCG
................................-...................................................................
--------------------------------------..A....C-----------------------------------------------------................................-...................................................................
................................-...................................................................
................................-...................................................................
................................-...................................................................
................................-...................................................................
................................-...................................................................
................................-...................................................................
................................-...................................................................
................................-.................................................................T.
........-.....C.A..GT...........A..........T.....T...........C..............G.................T.....
1423
1478
1249
1449
1484
1467
1470
1107
1446
1469
1425
1457
1099
CORBETTI1
ALTAICA4
ALTAICA1
SUMATRA1
SUMATRA2
TIGRIS1
TIGRIS2
amoyensis P27
amoyensis P25
P.tigris
F2 Numt
CAGTTATCTATAGATACGACAACCCGATCTCTAATTCGTCCCTATCGAACAATATTTACATACCCAACAACCCTATGTCTTG
..................................................................................
---------------------------------------------------------------------------------..................................................................................
..................................................................................
............................................................C.....................
............................................................C.....................
..................................................................................
..................................................................................
..................................................................................
..................................................................................
.............................................................................C....
..................T...............C.........................C.........T.....A.....
HVS-2
RS-3
CSB II
CSB III
1149
1180
1150
1151
1186
1169
1172
817
1156
1171
1127
1159
864
1505
1560
1249
1531
1566
1549
1552
1189
1528
1551
1507
1539
1181
9
Fig. S3. The mitogenome map of the tiger (P. t. tigris) including F2 numt (red curve). Fragment 9 of
this study contained two distinct sequences; 9.1 (blue line) and 9.2 (blue dashed line), where the numt
sequence was found (red box). The grey curve indicates the region containing two highly distinct
sequences when compared with other reported complete mitogenomes. The green curve indicates the
sequence range used to construct the phylogenetic tree in Figure 2.
10
Fig. S4. The alignment of confounding sequences near the 5’ end of F2 numt (red arrow). The sequences of the WEFCOM tiger (fragment numbers 8, 9.1, 9.2 and 10) were
aligned to HM569215 P27 of Zhang et al. (2011), JF357971 CORBETTI1 of Kitpipit et al. (2012, cymt DQ151550 and F2 numt (DQ151551) reported by Kim et al. (2006).
The sequences resembling F2 numt are labeled in red. Two distinct sequences contaminated with numt were found in fragment 9. The start point of the ambiguous sequences
is at the last domain of the COX1 gene. The alignment shows that the amplicon 9.1 was initially similar to numt and could not be aligned with the adjacent fragment (red
dashed boxes). There is a turning point at the middle of COX2 (red arrow head) where the amplicon 9.2 which was initially identical to cymt turned to the numt sequence and
amplicon 9.1 turned to the cymt sequence. After the end of F2 numt at the ATP6 gene, the 9.1 and 9.2 amplicons remain different (labeled cyan).
COX1
HM589215 P27
ATG-TTCATAAACCGCTGAGTATTTTCAACCAATCACAAGGATATTGTAACTCTTTACCTTTTATTTGGCGCCTGGGCTGGTATGGTGGGGACTGCCCTCAGTCTCCTAATTCGAGCCGAACTGGGTCA ACCTGGCACACTACTAGGAGA
JF357971 CORBETTI1
...-...............C...........................G.....................T...............................................T................................
DQ151550
...G.......-.......C....C......................G.....C..............................A.................................................... .............
DQ151551 F2 Numt
TATG...............C...................A...T...G...C.........C................C........A........T....... ..T....C..........................G........G..
HM589215 P27
TGACCAAATTTATAATGTGGTAGTTACTGCCCATGCCTTTGTGATAATCTTTT TTATAGTAATGCCTATTATAATTGGAGGGTTCGGAAACTGGCTAGTTCCGTTAATAATCGGGGCCCCCGATATGGCATTCCCTCGAATGAATAACAT
JF357971 CORBETTI1
..................A..............................................................A...................... ..........A...................................
DQ151550
.................NA..............................................................A...................... ..........A...................................
DQ151551 F2 Numt
C.................A..C..C..C..............A... .....C....................G........A...........AT.G.....A........T..A...........A....................T..
HM589215 P27
AAGCTTCTGACTCCTTCCCCCATCCTTCCTACTTCTGCTCGCATCGTCTATGGTAGAAGCTGGGGCAGGAACTGGGTGGACAGTATACCCACCCCTAGCTGGCA ACCTAGCCCATGCAGGAGCATCCGTGGATCTAACTATTTTTTCACT
JF357971 CORBETTI1
........................................................................................................ ..............................................
DQ151550
......................................................................................................................................................
DQ151551 F2 Numt
G....................G..T.........T..........A...........G.....A.....G.....A.................T.....C.... .......T.................A....................
HM589215 P27
ACACCTAGCAGGCGTCTCCTCAATCTTAGGTGCTATTAATTTTATTACTACTATTATTAATATAAAACCGCCCGCTATGTCCCAATACCAAACACCCCTATTTG TTTGATCGGTTCTAATTACTGCTGTGTTGCTACTTCTATCACTGCC
JF357971 CORBETTI1
...................................................................................................G..................................................
DQ151550
...................................................................................................G.... ..............................................
DQ151551 F2 Numt
............G.N...............N.................C....................C..T.....A........T................ .C.........T....C........A.................A..
HM589215 P27
AGTTTTAGCAGCAGGCATCACCATGCTACTGACAGATCGAAATCTAAATACCACATTTTTTGATCCT-GCTGGGGGAGGAGACCCCATCTTA----TATCAACACCTATTCTGATTCTTCGGTCACCCAGAAGTCTATATCTTAATCCTG
JF357971 CORBETTI1
................................................................... -..C.....................----......................................................
DQ151550
................................................................... -..C.....................----......................................................
DQ151551 F2 Numt
.....................T..A....................G..C..............C..CC..C..A.....G..T..T......CTTA....................T....................C.. T.....TT.A
HM589215 P27
CCCGGGTTTGGAATAATTTCACATATTGTCACCTACTACTCAGGCAAAAAAGAACCTTTTGGCTACATGGGGATAGTCTGAGCCATAATGTCAATTGGCTTTCT GGGCTTTATCGTATGGGCCCATCACATGTTTACTGTAGGGATAGAT
JF357971 CORBETTI1
.............................................................. ........................................................................................
DQ151550
........................................................................................................ ..............................................
DQ151551 F2 Numt
............................CT..............T..........................A.....T.....T.....A.............. ...............A....................G.........
WEFCOM 8
---------------------.................................................................................................................................
HM589215 P27
GTGGATACACGAGCATACTTTACGTCAGCTACTATAATTATCGCTATTCCTACTGGGGTAAAAGTATTTAGCTGATTGGCCACTCTTCACGGGGGTAATATTAA ATGGTCTCCCGCTATACTATGGGCTTTGGGATTCATTTTCCTATTC
JF357971 CORBETTI1
........................................................................................................ ..............................................
DQ151550
......................................................................................................................................................
DQ151551 F2 Numt
.....C.................A.................T........C........................C.............T..A........C.. ......C..T.....G.....A...C................C...
WEFCOM 8
........................................................................................................ ..............................................
HM589215 P27
ACCGTAGGGGGCTTAACAGGAATTGTATTAGCAAACTCCTCATTGGATATTGTCCTTCACGACACATACTACGTAGTAGCCCACTTCCACTACGTCTTGTCAATAGGAGCAGTATTTGCTATCATAGGGGGCTTCGTTCACTGATTCCCC
JF357971 CORBETTI1
........................................................................................................ ..............................................
DQ151550
...........................C............................................................................ ..................T...........................
DQ151551 F2 Numt
........A..................C.......T........A........T......................................T...................................A........C..T.........
WEFCOM 8
........................................................................................................ ..............................................
11
HM589215 P27
TTATTCTCAGGGTATACTCTTGATAATACTTGGGCAAAAGTTCATTTTACGATCATGTTCGTAGGTGTCAATATAACGTTTTTCCCTCAGCATTTCCTAGGCCT GTCTGGGATGCCTCGACGTTATTCTGACTATCCAGACGCGTATACA
JF357971 CORBETTI1
................................................................................................................................................... ...
DQ151550
........................................................................................................ ..............................................
DQ151551 F2 Numt
C...................C..................A.............T.........................................T........ ...C..A............G..........C........A......
WEFCOM 8
........................................................................................................ ..............................................
START
HM589215 P27
ACTTGAAACGCAATCTCCTCAATAGGCTCTTTTATTTCACTAACAGCAGTAATATTAA TAGTCTTTATAATGTGAGAAGCTTTCGCATCAAAGCGAGAAGTAGCCACAGTGGAACTAACCACAACTAATCTCGAATGACTTCACGGATGT
JF357971 CORBETTI1 .........A...........................................................G................................... .............................................
DQ151550
............................................................................................................................. .........................
DQ151551 F2 Numt
.........A.......................................... C..C......T...... G.............T.................G....T........................T.....G..G..T......
WEFCOM 8
.........A...........................................................G....................................................... .........................
WEFCOM 9.1
--------------------------------------------------------------- ......G.............T.................G....T........................T.....G..G..T......
tRNA-Ser
tRNA-Asp
HM589215 P27
CCTCCTCCGTATCACACATTTGAAGAGCCAGCCTACGTGCTGTTAAAATAAGAAAGGAAGGAATCGAACCTCCTTAGACTGGTTTCAAGCCAATACCATAACCA CTATGTCTTTCTCAATTAAGAAGTATTAGTAAAATAATTACATAAC
JF357971 CORBETTI1
........................................................................................................ ..............................................
DQ151550
......................................................................................................................................................
DQ151551 F2 Numt
..C.....A.....................A....T.......G.......................................C.......G............T...............C.... .............C...........
WEFCOM 8
............................................................................................................................. .........................
WEFCOM 9.1
..C.....A.....................A....T.......G.......................................C.......G............T...............C...... ...........C...........
WEFCOM 9.2
--------------...................................................................... ..................................................................
COX2
HM589215 P27
JF357971 CORBETTI1
DQ151550
DQ151551 F2 Numt
WEFCOM 8
WEFCOM 9.1
WEFCOM 9.2
TTTGTCAAAGTTAAATTATAGGTTTAAGCCCTATGTGCTT-CCATGGCATACCCCTTCCAACTAGGTTTTCAAGATGCTACATCCCCCATTATAGAAGAGCTTTCACACTT -CCATGATCATACATTAATAATTGTATTCCTAATTAGCT
........................................-...............................................................T...... -......................................
........................................-......................................................................-......................................
........G.............C.............A...T....................T............................C...........CCT......T.........C... C.........-..............
........................................-..............C................................................ ---------------------------------------------........G.............C.............A...-.................................................C...........CCT......-.........C...C........................
........................................-..............C................................................T...... -......................................
HM589215 P27
JF357971 CORBETTI1
DQ151550
DQ151551 F2 Numt
WEFCOM 9.1
WEFCOM 9.2
CCCTAGTCCTCTACATTATCTCATTAATACTGACAACTAAACTTACGCATACAAGCACAATAGATGCCCAAGAAGTAGAAACTATCTGAACCATTTTACCAGCC ATCATCTTAATTCTCATTGCCCTGCCTTCCTTACGAATTCTCTATA
............................................... ................................G......................................................................
............................................................................................................................. .........................
..........T..T..C......C.......A.....C.....C.....C...........G....................C..T.................T..................... ..A..C...................
..........T..T..C......C.......A.....C.....C.....C...........G....................C....................T.......................A..C.......... .........
............................................................................................... .......................................................
TURNING POINT
HM589215 P27
TAATAGATGAGATTAATAATCCCTCCCTCACTGTAAAGACTATAGGACATCAGTGATACTGAAGTTATGAGTACACCGACTATGAGGACCTAAGCTTCGACTCC TATATAATTCCCACTCAAGAGCTAAAGCCCGGAGAACTCCGACTAT
JF357971 CORBETTI1 ..........................................................................................................C.....C............ T.............G.........C
DQ151550
.................................................................................. ....................................................................
DQ151551 F2 Numt
.......C.C........GC...C.T..T...........C..G........A..G..T.....C.....A.....T........A...........T ...........................T.............G.........C
WEFCOM 9.1
.......C.C........GC...C.T..T...........C..G........A..G..T.....C.....A.....T........A...........T.......................... ..........................
WEFCOM 9.2
..........................................................................................................C.....C............ T.............G.........C
HM589215 P27
JF357971 CORBETTI1
DQ151550
DQ151551 F2 Numt
WEFCOM 9.1
WEFCOM 9.2
TAGAAGTTGATAACCGAGTAGTACTACCAATAGAAGTGACCATTCGCGTGTTAATCTCATCAGAAGACGTACTACACTCAT GAGCCGTCCCATCCCTGGGCCTAAAAACTGATGCTATTCCAGGCCGACTAAACCAAACAACCCTAATGG
......................GT.G..............T......A.....G..........G........G.....G......A.........................C.....C...... .......................A.
............................................................................................................................. .........................
......................GT.G..............T......A.....G..........G........G .....G......A.........................C.....C.............................A.
........................................................................................................ ..............................................
......................GT.G..............T......A.....G..........G........G.....G......A.........................C.....C...... .......................A.
HM589215 P27
JF357971 CORBETTI1
DQ151550
DQ151551 F2 Numt
WEFCOM 9.1
WEFCOM 9.2
GTACACGACCTGGACTGTATTATGGTCGGTGCTCAGAGATCTGCGGCTCAAACCACAGTTTTATGCCCATTGTTCTTGAACTAGTCCCATTATCATATTTTGAA AAATGATCTGCGTCTATACTGTAAATTCATTAAGAAGCTAAACTAG
.C.....G.....G..A..........A.........A..............T......... ...........C..............GC.G........C..............A............T....C............T...
........................................................................................................ ..............................................
.C.....G.....G..A..........A.........A..............T....................C..............GC.G........C..............A .....G......T....C............T...
........................................................................................................ ..............................................
.C.....G.....G..A..........A.........A..............T......... ...........C..............GC.G........C..............A............T....C............T...
tRNA-Lys
12
ATP8
HM589215 P27
JF357971 CORBETTI1
DQ151550
DQ151551 F2 Numt
WEFCOM 9.1
WEFCOM 9.2
CGTTAACCTTTTAAGTTAAAAACTGGGAGTTTAAACCTCCCCTTAATGACATGCCACAGTTAGATACATCAACCTGATTCATCACTATTATTTCAATAATTATA ACACTATTTATTATATTTCAACTAAAAA-TCTCAAAACACCTGTAT
...............................C.............G..................C...........G..T..T.................C..G.....G..CG........... .......-..........T.....C
............................................................................................................................. .......-.................
...............................C.......T.....G............AC...................T... ........A...........C.....GC.C.............C.....A.T........TTCA...
........................................................................................................ ............................-.................
...............................C.............G..................C...........G..T..T.................C..G.....G..CG........... .......-..........T.....C
HM589215 P27
JF357971 CORBETTI1
DQ151550
DQ151551 F2 Numt
WEFCOM 8
WEFCOM 9.1
WEFCOM 9.2
CCATCAAGCCCGGAACCCAAATCTACAGCTGCACTAAAACAGCCTAACCCTGGAGAAAAAAAATGAACGAAAATCTATTCACCTCTTTCACTACCCCAACAATAATAGGATTGCCTGTTGTCGTATTAATTATTATGTTCCCCAGCATTC
TCTTTCACTACCCCAACAATAATAGGATTGCCTGTTGTCGTATTAATTATTATGTTCCCCAGCATTC
...........A.....................T..........G.GT..CT.............................. ......T.....................C..........T..G.....CG..................
...........A.....................T..........G.GT..CT...........C................G.. -----------------------------------------------------------------------------------------------------------------------------------....G..AT..A.....T......G..TTAA.G..G.....A.....T..CT.....G.....C................G.. ----------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------------------------------..................................................................
...................................................T.......... ........................................................................................
...........A.....................T..........G.GT..CT.............................. ......T.....................C..........T..G.....CG.............
.....T.....................C..........T..G.....CG..................
.....
Numt
ATP6
5’end
HM589215 P27
TAGTCCCCTCACCTAACCGACTAATTAATAACCGTTTAGTCTCACTTCGACAGTGATTAGTACAACTAACATCAAAACAAATACTAGCCATTCACAATCACAAA GGACAAACTTGGGCCCTAATACTCATATCTCTCATTTTATTTATTG
JF357971 CORBETTI1
..T.T.....G.......................CC..........C.A... A...C..........T....T...G........GATT.CC......T.............C..............T..G...................
WEFCOM 9.1
........................................................................................................ ..............................................
WEFCOM 9.2
..T.T.....G.......................CC..........C.A...A..............T....T...G........GATT.CC......T..... ........C..............T..G...................
HM589215 P27
GATCAACAAACCTGTTAGGTCTACTGCCTCACTCATTTACTCCAACTACCCAATTATCAATAAACTTAGGAATAGCTATTCCCCTATGAGCCGGTACCGTAATCACCGGGTTTCGCCACAAAACTAAAGCGTCCCTGGCCCACTTTCTAC
JF357971 CORBETTI1
.G........T...C..........A.......................................C....C.....C..C...T.G........C......... ..T..A..C..T..............A...................
WEFCOM 9.1
........................................................................................................ ..............................................
WEFCOM 9.2
.G........T...C..........A.......................................C....C.....C..C...T.G........C...........T..A..C..T..............A...T...............
HM589215 P27
JF357971 CORBETTI1
WEFCOM 9.1
WEFCOM 9.2
WEFCOM 10
CACAAGGAACAGCAATCCCCCTGATCCCTATGCTTGTAATTATTGAAACCATTAGCCTTTTTATCCAGCCCGTGGCTCTGGCCGTACGACTTACAGC
CACAAGGAACAGCAATCCCCCTGATCCCTATGCTTGTAATTATTGAAACCATTAGCCTTTTTATCCAGCCCGTGGCTCTGGCCGTACGACTTACAGCTAACATT
ACTGCAGGCCACCTATTCATACACTTACTTGGAGGAGCTGCTCTGG
...........C..G.....T.A...........C........C.....T..C....................A..C..A...........C....
...........C..G.....T.A...........C........C.....T..C....................A..C..A...........C........T... ...........TT....A......C..A.C............T.A.
.................................................................................................
......................................................................................................................................................
-...........C..G.....T.A.....C.....C........C.....T..C....................A..C..A...........C... -----------------------------------------------------------------------------------.....C........C.....T..C....................A..C..A...........C......
-----------------------------.....C........C.....T..C....................A..C..A...........C........T..............TT....A......C..A.C............T.A.
COX3
HM589215 P27
CCCTAACAAACATCAGTACCTCTATTGCTTTAATCACCTTTATTATCCTCATCCTACTGACAATCCTTGAATTTGCTGTGGCTCTAATCCAAGCCTACGTCTTT ACCCTACTTGTAAGCCTGTATCTACATGACGATACTTAATGACCCA
JF357971 CORBETTI1 ..........T..T...G..C...C.........T........C................... .T........C.....A.................T..T..............G.........T.......TA...............
WEFCOM 9.1
........................................---------------------------------------------------------------------------------------------------------- ---WEFCOM 10
..........T..T...G..C...C.........T........C....................T........C.....A.................T..T... ...........G.........T.......TA...............
13