Since
the black bear is the only known extant bear in California, the S26 sequence
was compared to the black bear, Ursus
americanus, in the Nucleotide Database.
There are only six hits, and none coincide with the longer sequence
ranges of the best matches by score in Table 1. However, five of the six
hits are perfect matches (Table 3). Out of 232,065 total Ursidae entries there are 184,051 panda entries, 38,952 polar bear
entries, and only 1583 black bear entries in the Nucleotide Database (as of
June, 2013), explaining why the black bear did not make the hit list as an Ursidae in Table 1: its limited entries in the Nucleotide Database do not match all
of the more extensive sequencing of the panda and the polar bear. We also searched these six specific hit
sequence ranges for other possible matches, and we found four other bears
(polar bear-Ursus maritimus, Asiatic
black bear-Selenarctos thibetanus, brown bear-Ursus arctos, and the giant panda- Ailuropoda melanoleuca) at the top of
the hit lists. Human was way down the
hit lists (Table 3).
Table 3. S26 vs. black bear (Ursus
americanus)
|
|||||||||
S26 vs.
|
Match
|
% ID
|
LEN
|
MIS
|
GAP
|
Start
|
End
|
SCORE
|
|
black bear
|
DQ240386.1
|
100
|
291
|
0
|
0
|
542355
|
542645
|
538
|
|
Asiatic black bear
|
DQ093584.1
|
100
|
291
|
0
|
0
|
542355
|
542645
|
538
|
|
brown bear
|
AY011500.1
|
100
|
291
|
0
|
0
|
542355
|
542645
|
538
|
|
brown bear
|
AF002239.1
|
100
|
291
|
0
|
0
|
542355
|
542645
|
538
|
|
human(348th)
|
HM763820.1
|
94.08
|
287
|
17
|
0
|
542355
|
542641
|
436
|
|
black bear
|
DQ240717.1
|
100
|
173
|
0
|
0
|
814867
|
815039
|
320
|
|
giant panda
|
XM_002926498.1
|
97.11
|
173
|
5
|
0
|
814867
|
815039
|
292
|
|
giant panda
|
DQ240718.1
|
97.11
|
173
|
5
|
0
|
814867
|
815039
|
292
|
|
Pacific walrus
|
XM_004409327.1
|
94.80
|
173
|
9
|
0
|
814867
|
815039
|
270
|
|
human
|
Not among 33 best hits
|
||||||||
black bear
|
DQ240717.1
|
100
|
97
|
0
|
0
|
815040
|
815136
|
180
|
|
giant panda
|
JN414914.1
|
100
|
97
|
0
|
0
|
815040
|
815136
|
180
|
|
giant panda
|
XM_002926498.1
|
100
|
97
|
0
|
0
|
815040
|
815136
|
180
|
|
giant panda
|
DQ240718.1
|
100
|
97
|
0
|
0
|
815040
|
815136
|
180
|
|
human
|
Not among 92 best hits
|
||||||||
black bear
|
DQ914964.1
|
93.67
|
79
|
5
|
0
|
1696406
|
1696484
|
119
|
|
Pacific walrus
|
XR_186719.1
|
96.20
|
79
|
2
|
1
|
1696406
|
1696484
|
128
|
|
S. American sea lion
|
AB714146.1
|
94.94
|
79
|
4
|
0
|
1696406
|
1696484
|
124
|
|
S. American sea lion
|
AB714145.1
|
94.94
|
79
|
4
|
0
|
1696406
|
1696484
|
124
|
|
human(133rd)
|
XM_003846557.1
|
91.14
|
79
|
7
|
0
|
1696406
|
1696484
|
108
|
|
black bear
|
DQ240386.1
|
100
|
53
|
0
|
0
|
542302
|
542354
|
99
|
|
polar bear
|
GAJD01025142.1
|
100
|
53
|
0
|
0
|
542302
|
542354
|
99
|
|
Pacific walrus
|
XM_004408656.1
|
100
|
53
|
0
|
0
|
542302
|
542354
|
99
|
|
giant panda
|
GU931015.2
|
100
|
53
|
0
|
0
|
542302
|
542354
|
99
|
|
human
|
Not among 279 best
hits
|
||||||||
black bear
|
EU031728.1
|
100
|
36
|
0
|
0
|
1964424
|
1964459
|
67.6
|
|
No Other Matches
|
S26 1964424-1964459 vs. nucleotide
|
||||||||
Table 3. The first entry in each group is the black bear match to S26. Following are the top three other hits in that sequence range. Finally, the best human match over the same sequence range with rank in parentheses. column headings same as in Table 1.
Sample 31
We did a S31 preliminary search of the
entire Nucleotide Database which yielded a long list of fungi and bacteria, so
the search was narrowed. Next, we searched S31 against the Nucleotide Database
separately limited to human, to other primates (OP), to Canis, and to all other (AO) species not previously included. “No matches” were filled in by searching the
Reference Genomic Sequence (RS) database, to produce the results in Table 4.
Human was the best match over 12 of 15 unique sequence ranges (fungi and
bacteria excluded). Human tied other
primates three times. Most of the
matches to human are so good, often 100% identity, that the possibility of
another extant hominin is not likely. No
evidence of the human-primate mosaic mentioned in the Ketchum conclusion (2),
above, was found. Specifically, that
would have resulted in some sequence ranges matching human best and other different ranges matching other primates
best. The best match (by score) over a
single range is a fungus, which may have grown on the bait food. The second highest score was questionable with
low %ID matches to the Nucleotide Database.
By searching that specific sequence range over the RS database, we found
a better partial match (shorter sequence) to the pygmy chimpanzee. When the complete nucleotide hit list is
sorted by %ID, then LEN, then SCORE, the human hits surpass all other groups’ hits
in all three parameters, especially over the 99-100% ID ranges. A summary of
Table 4 is found in Table 2.
Human followed by other primates greatly out matches dog and all other
in all four criteria.
Table 4. S31 top 15 human hits and top 15 other
primate hits by score.
|
||||||||
S31 vs.
|
Match
|
%ID
|
LEN
|
MIS
|
GAP
|
Start
|
End
|
SCORE
|
human-N(1)
|
3J3F_5
|
95.21
|
313
|
13
|
2
|
292664
|
292975
|
494
|
OP-N(1): chimpanzee
|
AC194985.3
|
94.25
|
313
|
16
|
2
|
292664
|
292975
|
477
|
Canis-N(1): dog
|
2ZKR_0
|
95.21
|
313
|
13
|
2
|
292664
|
292975
|
494
|
AO-N: fungus
|
JQ689076.1
|
99.67
|
299
|
1
|
0
|
292677
|
292975
|
547
|
human-N, G+T(2)
|
AC126398.5
|
84.08
|
490
|
32
|
14
|
197482
|
197953
|
431
|
OP-N: chimpanzee
|
AC148930.3
|
80.41
|
490
|
52
|
14
|
197482
|
197953
|
333
|
OP-RS: pygmy
chimpanzee
|
NW_003862227.1
|
99.43
|
176
|
0
|
1
|
197482
|
197657(a)
|
318
|
Dog-N,RS
|
No Match
|
|||||||
AO-N: turquoise
killifish
|
GAIB01046747.1
|
79.96
|
484
|
51
|
13
|
197490
|
197953
|
315
|
human-N(3)
|
NG_021375.1
|
100
|
230
|
0
|
0
|
319943
|
320172
|
425
|
OP-RS(2): chimpanzee
|
NC_006478.3
|
99.57
|
230
|
1
|
0
|
319943
|
320172
|
420
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N(4)
|
3J3F_5
|
100
|
218
|
0
|
0
|
323943
|
324160
|
403
|
OP-RS(3): n. white-cheeked gibbon
|
NC_019821.1
|
100
|
218
|
0
|
0
|
323943
|
324160
|
403
|
Canis-N: dog
|
2ZKR_0
|
100
|
214
|
0
|
0
|
323943
|
324156
|
396
|
AO-N: ribbon worm(2)
|
HQ856869.1
|
88.89
|
216
|
19
|
5
|
323938
|
324151
|
261
|
human-N(5)
|
AL109624.11
|
100
|
216
|
0
|
0
|
126039
|
126254
|
399
|
OP-RS(4): gorilla
|
NC_018435.1
|
98.15
|
216
|
4
|
0
|
126039
|
126254
|
377
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N(6)
|
NG_017040.1
|
99.05
|
211
|
1
|
1
|
251897
|
252106
|
377
|
OP-N(9): chimpanzee
|
AC183808.3
|
97.20
|
214
|
5
|
1
|
251897
|
252109
|
361
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N(7)
|
AP001024.6
|
100
|
201
|
0
|
0
|
396912
|
397112
|
372
|
OP-RS(7): chimpanzee
|
NC_006478.3
|
99.50
|
201
|
1
|
0
|
396912
|
397112
|
366
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N(8)
|
AP001788.5
|
100
|
200
|
0
|
0
|
254454
|
254653
|
370
|
OP-N(5): chimpanzee
|
NW_003870591.1
|
100
|
200
|
0
|
0
|
254454
|
254653
|
370
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N(9)
|
AL133399.1
|
99.51
|
203
|
0
|
1
|
131309
|
131510
|
368
|
OP-RS(8): gorilla
|
NC_018435.1
|
99.01
|
203
|
1
|
1
|
131309
|
131510
|
363
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N(10)
|
AC104042.5
|
100
|
199
|
0
|
0
|
143355
|
143553
|
368
|
OP-N(11): chimpanzee
|
NC_006478.3
|
98.99
|
199
|
1
|
1
|
143355
|
143553
|
355
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N(11)
|
AP003097.2
|
100
|
199
|
0
|
0
|
326842
|
327040
|
368
|
OP-RS(6): chimpanzee
|
NC_006478.3
|
100
|
199
|
0
|
0
|
326842
|
327040
|
368
|
Dog-N,RS
|
No Match
|
|||||||
AO: false killer whale
|
AP011079.1
|
80.79
|
151
|
24
|
4
|
326893
|
327040
|
113
|
human-N(12)
|
AP000763.5
|
100
|
198
|
0
|
0
|
276637
|
276834
|
366
|
OP-RS(9): chimpanzee
|
NC_006478.3
|
99.49
|
198
|
1
|
0
|
276637
|
276834
|
361
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N(13)
|
NM_002556.2
|
100
|
197
|
0
|
0
|
217275
|
217471
|
364
|
OP-N(13): pygmy
chimpanzee
|
XM_003826362.1
|
98.48
|
197
|
3
|
0
|
217275
|
217471
|
348
|
Dog-N,RS
|
No Match
|
|||||||
AO-N: rabbit
|
NM_001082233.1
|
87.31
|
197
|
21
|
2
|
217276
|
217471
|
222
|
human-N(13)
|
EF445021.1
|
100
|
197
|
0
|
0
|
414777
|
414973
|
364
|
OP-N(12): pygmy
chimpanzee
|
NW_003870010.1
|
98.98
|
197
|
2
|
0
|
414777
|
414973
|
353
|
Dog-N,RS
|
No Match
|
|||||||
AO-N: stealth virus
|
AF065698.1
|
84.26
|
108
|
17
|
0
|
414778
|
414885
|
106
|
human-N(15)
|
AL136126.34
|
99.01
|
203
|
0
|
1
|
129971
|
130171
|
363
|
OP-RS: orangutan
|
NC_012602.1
|
93.63
|
204
|
7
|
4
|
129971
|
130171
|
300
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N
|
AP003440.2
|
100
|
195
|
0
|
0
|
430331
|
430525
|
361
|
OP-N(14): rhesus
monkey
|
AC211797.4
|
97.44
|
195
|
5
|
0
|
430331
|
430525
|
333
|
Dog-N,RS
|
No Match
|
|||||||
AO-N:
|
No Match
|
|||||||
human-N
|
AP003531.2
|
100
|
180
|
0
|
0
|
278035
|
278214
|
333
|
OP-N(15): gorilla
|
XM_004051797.1
|
99.44
|
180
|
1
|
0
|
278035
|
278214
|
327
|
Dog-N
|
XM_534014.3
|
92.86
|
112
|
7
|
1
|
278107
|
278218
|
161
|
AO-N: giant panda
|
XM_002915314.1
|
95.54
|
112
|
4
|
1
|
278107
|
278218
|
178
|
Table 4. (a) Shorter sequence, best match. Format and abbreviations same as Tables 1 and 5.
A preliminary S140 search of the Nucleotide
Database revealed that human was the best match by highest total score. However, the dog (Canis lupus familiaris) had higher maximum %ID, once again demonstrating
the need for examining the downloaded list of individual hits. Results of S140 searches against both the
nucleotide and the human G+T databases are found in Table 4. The top 15 Canis (dog) hits and the top 15 human
hits by score are listed. Over all 17 of
these sequence ranges Canis Slupus
familiaris (the domestic dog) is the best match, better than human, other
primates, and all other species in the database. Further, when sorted by %ID, then LEN, then
SCORE, the complete Nucleotide Database hit list is dominated by Canis hits, especially over the 99-100%
ID ranges. A final effort was made to
find better mammalian matches for S140 by separately limiting hits to the order
Carnivora, the families, Canidae (dogs, wolves, coyotes, foxes), Felisidae (cats), Mustelidae (weasels), Ursidae
(bears), Mephitidae (skunks), Gilires (rabbits and rodents), Sciurini (squirrels), the genus Vulpes (foxes), the species Mus musculus (the mouse), the northern raccoon (Procyon lotor), and the opossum (Monodelphis
domestica). No matches were as good
as Canis lupus familiaris. Table 2, a summary of Table 5, shows that the dog out matches all
other groups in all four criteria.
Table 5. S140 top 15 Canis and top 15 human hits
by score.
|
|||||||||
S140 vs.
|
Match
|
% ID
|
LEN
|
MIS
|
GAP
|
Start
|
End
|
SCORE
|
|
Canis(1): dog
|
XM_533992.4
|
97.81
|
1645
|
12
|
12
|
1249239
|
1250864
|
2817
|
|
human-N(3)
|
NM_015885.3
|
93.30
|
1642
|
86
|
12
|
1249239
|
1250861
|
2401
|
|
OP: Bolivian squirrel
monkey
|
XM_003935094.1
|
92.94
|
1642
|
89
|
13
|
1249239
|
1250861
|
2364
|
|
AO: giant panda
|
XM_002925391.1
|
95.80
|
1642
|
45
|
12
|
1249239
|
1250861
|
2628
|
|
Canis(1): dog
|
XM_540535.3
|
98.61
|
1578
|
18
|
2
|
655259
|
656836
|
2789
|
|
human-N(1)
|
NR_047674.1
|
94.99
|
1578
|
78
|
1
|
655259
|
656836
|
2475
|
|
OP: chimpanzee
|
XM_001155521.3
|
95.12
|
1578
|
75
|
2
|
655259
|
656836
|
2486
|
|
AO: Pacific walrus
|
XM_004404764.1
|
96.58
|
1578
|
50
|
3
|
655259
|
656836
|
2612
|
|
Canis(3): dog
|
XM_847190.2
|
99.46
|
1470
|
6
|
1
|
1016493
|
1017960
|
2669
|
|
human-N(2)
|
NM_006328.3
|
96.39
|
1470
|
51
|
2
|
1016493
|
1017960
|
2420
|
|
OP: Bolivian squirrel
monkey
|
XM_003941220.1
|
96.53
|
1470
|
49
|
2
|
1016493
|
1017960
|
2431
|
|
AO: giant panda
|
XM_002927796.1
|
98.37
|
1470
|
22
|
1
|
1016493
|
1017960
|
2580
|
|
Canis(4): dog
|
XM_855390.2
|
97.72
|
1488
|
15
|
2
|
802547
|
804034
|
2542
|
|
human-N(4)
|
NR_024222.1
|
92.09
|
1492
|
91
|
7
|
802547
|
804034
|
2076
|
|
OP: gorilla
|
XM_004051066.1
|
92.16
|
1492
|
90
|
7
|
802547
|
804034
|
2082
|
|
AO: Pacific walrus
|
XM_004399514.1
|
95.77
|
1488
|
44
|
2
|
802547
|
804034
|
2381
|
|
Canis(5): dog
|
NC_006603.3
|
99.35
|
1237
|
7
|
1
|
382120
|
383356
|
2239
|
|
human-G+T(5)
|
NW_004078070.1
|
94.76
|
1240
|
60
|
4
|
382120
|
383356
|
1925
|
|
OP: orangutan
|
AC220940.4
|
95.00
|
1240
|
57
|
5
|
382120
|
383356
|
1941
|
|
AO: house mouse
|
AC124775.4
|
89.01
|
1247
|
109
|
20
|
382124
|
383354
|
1519
|
|
Canis(6): dog
|
XM_845613.2
|
98.67
|
1207
|
5
|
7
|
723260
|
724455
|
2130
|
|
human-N(6)
|
BC028235.1
|
93.37
|
1207
|
69
|
4
|
723260
|
724455
|
1775
|
|
OP: gorilla
|
XM_004050991.1
|
93.29
|
1207
|
70
|
4
|
723260
|
724455
|
1770
|
|
AO: cat
|
XM_003993197.1
|
95.69
|
1207
|
41
|
5
|
723260
|
724455
|
1932
|
|
Canis(7): dog
|
XM_540754.2
|
99.62
|
1041
|
0
|
2
|
759403
|
760439
|
1897
|
|
human-N(7)
|
AK000301.1
|
94.62
|
1040
|
52
|
2
|
759404
|
760439
|
1607
|
|
OP: chimpanzee
|
XM_508396.4
|
94.72
|
1041
|
51
|
2
|
759403
|
760439
|
1615
|
|
AO:giant panda
|
XM_002921620.1
|
97.60
|
1041
|
21
|
2
|
759403
|
760439
|
1781
|
|
Canis(8): dog
|
XM_540888.2
|
96.78
|
1150
|
5
|
10
|
939919
|
941036
|
1890
|
|
human-N(11)
|
AB384864.1
|
90.27
|
1151
|
80
|
9
|
939918
|
941036
|
1476
|
|
OP: Rhesus monkey
|
XM_001115424.2
|
90.69
|
1149
|
75
|
9
|
939920
|
941036
|
1500
|
|
AO: giant panda
|
XM_002916673.1
|
92.17
|
1150
|
58
|
9
|
939919
|
941036
|
1596
|
|
Canis(9): dog
|
XM_850778.2
|
98.67
|
981
|
3
|
4
|
2001821
|
2002791
|
1731
|
|
human-N(15)
|
AB528444.1
|
93.39
|
984
|
55
|
4
|
2001818
|
2002791
|
1448
|
|
OP: white-cheeked
gibbon
|
XM_003253412.2
|
93.50
|
984
|
54
|
4
|
2001818
|
2002791
|
1454
|
|
AO: horse
|
XM_001505107.3
|
94.61
|
984
|
43
|
3
|
2001818
|
2002791
|
1515
|
|
Canis(10): dog
|
XM_533158.3
|
99.68
|
939
|
3
|
0
|
586655
|
587593
|
1718
|
|
human-N(8)
|
NM_001278163.1
|
96.06
|
939
|
37
|
0
|
586655
|
587593
|
1530
|
|
OP: gorilla
|
XM_004050910.1
|
96.38
|
939
|
34
|
0
|
586655
|
587593
|
1546
|
|
AO: Pacific walrus
|
XM_004406102.1
|
97.44
|
939
|
24
|
0
|
586655
|
587593
|
1602
|
|
Canis(11): dog
|
XM_540554.3
|
98.86
|
965
|
0
|
1
|
578923
|
579876
|
1711
|
|
human-N(12)
|
NM_001076786.1
|
94.21
|
968
|
39
|
3
|
578923
|
579876
|
1461
|
|
OP: white-cheeked
gibbon
|
XM_003254379.2
|
94.32
|
968
|
38
|
4
|
578923
|
579876
|
1467
|
|
AO: Pacific walrus
|
XM_004406106.1
|
96.38
|
968
|
21
|
4
|
578923
|
579876
|
1581
|
|
Canis(12): dog
|
XM_843660.2
|
99.89
|
898
|
0
|
1
|
1295384
|
1296280
|
1652
|
|
human-N
|
NM_012193.3
|
94.22
|
899
|
51
|
1
|
1295383
|
1296280
|
1371
|
|
OP: pygmy chimpanzee
|
XM_003832981.1
|
94.22
|
899
|
51
|
1
|
1295383
|
1296280
|
1371
|
|
AO: Pacific walrus
|
XM_004414080.1
|
96.88
|
898
|
27
|
1
|
1295384
|
1296280
|
1502
|
|
Canis(13): dog
|
XM_860009.2
|
97.65
|
938
|
1
|
7
|
1034498
|
1035414
|
1591
|
|
human-N(10)
|
JQ710744.1
|
95.52
|
938
|
21
|
7
|
1034498
|
1035414
|
1480
|
|
OP: chimpanzee
|
XM_003951945.1
|
95.74
|
938
|
19
|
7
|
1034498
|
1035414
|
1491
|
|
AO: giant panda
|
XM_002921298.1
|
96.48
|
938
|
12
|
7
|
1034498
|
1035414
|
1530
|
|
Canis(14): dog
|
XM_861143.2
|
96.46
|
961
|
16
|
9
|
992249
|
993192
|
1570
|
|
human-G+T
|
NM_005507.2
|
92.00
|
963
|
56
|
12
|
992249
|
993192
|
1332
|
|
OP: chimpanzee
|
XM_003951935.1
|
92.21
|
963
|
54
|
12
|
992249
|
993192
|
1343
|
|
AO: Pacific walrus
|
XM_004393924.1
|
94.91
|
963
|
29
|
10
|
992249
|
993192
|
1489
|
|
Canis(15): dog
|
XM_003639786.1
|
96.67
|
932
|
12
|
6
|
154301
|
155232
|
1531
|
|
human-N(9)
|
NM_001172705.1
|
95.71
|
933
|
20
|
7
|
154301
|
155232
|
1483
|
|
OP: white cheeked
gibbon
|
XM_003254938.2
|
95.82
|
934
|
17
|
9
|
154301
|
155232
|
1489
|
|
AO: giant panda
|
XM_002925273.1
|
96.24
|
932
|
17
|
5
|
154301
|
155232
|
1511
|
|
Canis: dog
|
NC_006587.3
|
99.53
|
853
|
4
|
0
|
1581864
|
1582716
|
1554
|
|
human-N(13)
|
AK131376.1
|
97.54
|
853
|
20
|
1
|
1581864
|
1582716
|
1458
|
|
OP: Rhesus monkey
|
AC202613.6
|
97.30
|
853
|
22
|
1
|
1581864
|
1582716
|
1447
|
|
AO: house mouse
|
AC183268.4
|
93.10
|
855
|
38
|
8
|
1581864
|
1582716
|
1232
|
|
Canis: dog
|
NC_006603.3
|
99.22
|
900
|
6
|
1
|
113521
|
114420
|
1622
|
|
human-N(14)
|
AC091053.11
|
95.90
|
903
|
30
|
4
|
113521
|
114422
|
1456
|
|
OP: pygmy chimpanzee
|
NW_003870482.1
|
96.34
|
901
|
27
|
5
|
113521
|
114420
|
1476
|
|
AO: house mouse
|
JN950559.1
|
91.58
|
903
|
70
|
5
|
113524
|
114420
|
1242
|
|
Table 5. Format and abbreviations same as Tables 1 and 4.
Whole Genome Searches
and Graphic Displays
In the previous sections we compared hits
with the highest scores in each candidate group. We also thought it important to compare all
hits across the respective whole genomes at some level, ≥ 95% ID. We accomplished this by searching each
sequence against the most relevant genomes in the Reference Genomic Sequence
Database (RS): panda, human and dog. Panda
is the only bear in this database. After
removing duplicates and overlaps, we limited the results to ≥200 bp for S26, ≥150
bp for S31 and ≥100 bp for S140, reflecting the different query sequence
lengths. Results are shown in Table 6 for each sample sequence.
Table
6. Statistics of Reference Genomic
Sequence Matches
RefSeq
|
M1j(a)
|
M2j(b)
|
Ave. %ID(c)
|
Nj(d)
|
% C(e)
|
Norm. %C(f)
|
Ave. %ID(c)
|
Nj(d)
|
vs. S26
|
<< %ID ≥ 95%,
Length ≥ 200 bp >>
|
<<<<< Whole
Genome >>>>>
| ||||||
Panda
|
1929
|
7117
|
98.3
|
3417
|
74.2
|
≡100
|
98.1
|
11865
|
Dog
|
1299
|
3684
|
97.2
|
2198
|
49.7
|
67.0
|
96.3
|
11472
|
Human
|
833
|
1711
|
96.3
|
696
|
40.7
|
54.9
|
96.0
|
78085
|
vs. S31
|
<< %ID ≥ 95%,
Length ≥ 100 bp >>
|
<<<<< Whole
Genome >>>>>
| ||||||
Human
|
891
|
4261
|
99.6
|
4308
|
86.4
|
≡100
|
97.5
|
163491
|
Dog
|
795
|
3623
|
99.1
|
110
|
3.3
|
3.9
|
98.6
|
406
|
Panda
|
742
|
3188
|
98.9
|
73
|
2.4
|
2.8
|
98.5
|
126
|
vs. S140
|
<< %ID ≥ 95%,
Length ≥ 150 bp >>
|
<<<<< Whole
Genome >>>>>
| ||||||
Dog
|
1902
|
8523
|
99.0
|
3887
|
81.3
|
≡100
|
98.3
|
34764
|
Panda
|
1084
|
3208
|
97.3
|
2198
|
48.0
|
59.1
|
96.3
|
4605
|
Human
|
779
|
1953
|
96.6
|
933
|
38.6
|
47.5
|
95.9
|
115702
|
Table 6.
(a) First Moment, Equn.
1.3, score x %. (b) Second Moment, Equn 1.4, score x %2.
(c) Equation
1.5. (d) Number of hits. (e)
Equn. 1.6. %s not additive
because sequences are conserved. (f)
Normalized to highest %C ≡ 100.
Of all the numbers presented in Tables 1-6,
only the reversal above: 97.5 average % ID (in red in Table 6)
for the S31 vs. the human reference
genomic sequence hits seems too low and out of line with other S31 statistics. We found that many low %ID hits in the 85% - 90%ID
range had corresponding high %ID hits over the same sequence range. Reasons for these sequence ranges being so
hypervariable were not immediately obvious but might merit further
investigation. We do believe, however,
that the 99.6 average %ID over 4308 hits with %ID ≥ 95% is a very strong
indication that the sample is human.
These results are consistent with the previous
highest score results in Tables 1, 4, and 5: In Table 6 S26 best matches the panda, S31
human, and S140 dog, as measured by highest first and second moments (Equns. 1.3
and 1.4), average %ID, number of hits, and % coverage.
Although these summary statistics are convincing,
we decided to display individual hits graphically to examine the coverage
across the entire sample sequences, as seen in Figs. 1-6. We added results of
Nucleotide Database searches of other primates (OP) for perspective. The same matching sequence length criteria
and %ID minimum (95%) were used in Figs.
1-6 as in Table 6. The dense horizontal lines of points in
Figures 3, 4 and 5 contain most of
the data points of these three Figures. Clearly
S26 matches panda; S31 matches human; and S140 matches dog best, as judged by
highest concentrations of data points near 100% ID in Figs. 1, 3,
and 5 and highest overall second
moments in Figs. 2, 4, and 6, confirming the overall statistics in Table 6. Furthermore, these best
matches apply across the entire sample sequence, i.e. there is no significant
“mosaicity” - the interspersion of hit sequences with equally high match
statistics from different groups. For
example, there are relatively much fewer nonhuman data points (Table 6) in Fig. 3, and these are not concentrated in the 99-100%ID range.
(See Figures in Separate Page)
We observed well established phylogenic
relationships in the overall distributions of the data points: human closer to other primates, dog closer to
panda, the same as was found in Tables 1,
4, and 5. The vertical banding seen in Figs. 1, 2, 5,
and to a lesser degree 6, is
likely due to a higher concentration of database sequences at well studied, important,
conserved genes.
CONTINUED
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