Search This Blog

Sunday, September 20, 2015

The Ketchum File IV: A Reassembly of Ketchum Raw Data: Can You Turn a Bear Sow’s Ear into a Sasquatch Silk Purse?



Caution:  Contains Ketchum Koolaid.  Please drink responsibly.


Dr. Melba Ketchum, DVM, posted the following last May on Facebook:

May 4, 2015

New Technology at Washington U Maps Human Genome in Days; Large-scale Studies now Possible. By Michele Munz (St. Louis Post-Dispatch)


http://www.stltoday.com/lifestyles/health-med-fit/medical/new-technology-at-wash-u-maps-human-genome-in-days/article_9ed22975-a385-5b53-897a-ff88cba2442b.html

 “This has been around for a while now because they used a supercomputer on our genomes. Of course they get faster each year. You have to have a supercomputer to analyze genomes. That's why the critics don't know what they're talking about. They don't even have the equipment to analyze the data. We had two bioinformaticists work on the genomes in our paper. We have more working on it now with a new (as of last fall) supercomputer like this one. Of course it takes a lot longer with a novel genome, because it has to be compared to all animals including mammals, birds, reptiles, amphibians plus plants, bacteria, fungi, Ancient DNA and viruses. In other words every DNA sequence ever mapped and not just GenBank but all depositories worldwide. This is what has been being (sic) done. I hope they will let us release the results!!!!!”



*************************************************************



Let’s get a few things straight first. The supercomputer is used to assemble the raw data into a sequence, and that’s something that “critics” like me have not attempted to do with the Ketchum et al. raw data because we do not have access to this raw data, not because we don’t have access to a supercomputer. I for one accepted her three sequences at face value and reinterpreted them by using an Internet connection to the servers at NCBI to align them against their GenBank® of known sequences. This is exactly what Ketchum et al. did through an Internet connection. No need to have a supercomputer in your garage to align assembled, complete sequences.

“GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (
Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration , which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis.“ (from the NCBI website)

Melba would have you believe that the search/match process takes a supercomputer a long time to do to cover all those “mammals, birds, reptiles, amphibians plus plants, bacteria, fungi, Ancient DNA and viruses .“ I’ve done high hundreds of searches through the shared NCBI servers, and none took longer than 30 min. The average time has been a minute or two, but it depends on the length of the query sequence and the time of day (since you share the resource with others). “Novel genomes” don’t take any longer to align than known species. Furthermore, as the NCBI website quote above says, GenBank® includes sequences from other important “depositories worldwide.” Anybody wanting their sequence to be available to the widest possible audience would contribute to one of these three databases, which share data with each other. There’s relatively little important, unique species data elsewhere. Access to a supercomputer does not give one access to more data. A real person needs to find the location of the data

Now for the interesting part of the above Ketchum Facebook post. Melba reveals that her raw data is being reassembled, and my communications with ”Jerry” (not his real name), one of her supporters, confirms that. Assembly involves putting together many short sequences in the right order to make the complete sequence. This involves looking for overlaps on the ends (de novo) or aligning with a reference sequence of the same or a closely related species. For complete genomes with billions of base pairs, this can require a supercomputer. But this is assembly, not identification.

According to Jerry, “… the assembly done on her raw data was about as appropriate as driving a square peg into a round hole. …She did not know enough to ask for a de Novo assembly. The University (University of Texas Southwestern Medical Center) should have known better though. Their bad, not hers.” Sorry, but the principle author has responsibility for everything in a scientific paper. She should have known better, too. A de novo assembly makes no assumptions about the species. In contrast, Ketchum et al. used a human reference sequence (chromosome 11) to assemble her sequences, because she believed human to be the closest species (her bias about her totally unprovenanced samples).

Jerry continues, “…you have just spent all your time and effort writing you (sic) treatises, trying to make sense of what was an imperfect reassembly. You might as well try comparing apples with oranges. … What was required all along was that the work be redone by a top notch bioinfomatician. Then we might get something meaningful from what I consider to be good raw data.” Not exactly a commendation for Fan Zhang, Melba’s “bioinformaticist,” whose degrees are in mechanical and aeronautical engineering from Harbin University in Manchuria and whom she continues to praise to this day. “Good raw data”? Maybe, but it’s not from a sasquatch, as I proved. Only if sasquatch is a feral human can Sample 31 be from a sasquatch.  Samples 26 and 140 are from a black bear and a dog (wolf, or coyote – all genus Canis) respectively.

And again from Jerry, “The only viable conclusion is that the assembled sequences were not entirely correct and it was quite clear to me that the whole of her nuDNA assembled data was less than reliable, as is any attempt to use that data to draw conclusions. I note that Melba said in May that her data has been reassembled again and she hopes those that did that will allow her to publish the results. I heard a whisper that this data crunching was underway but know absolutely none of the detail. All I can say is that it's a pity it was not done two or three years ago.” Is this bias, or what? May I humbly suggest another possible conclusion? The sequences are basically correct (but possibly incomplete), and Samples 26 and 140 are from a bear and a dog, respectively, as I’ve proven previously.

How about that!! An insider says that the Ketchum et al. assembly and sequencing is majorly flawed, and led to my “waste of time” trying to interpret the results by matching known species. “We can't make a silk purse from a sows (sic) ear,” says Jerry.   But that's exactly what Melba tried to do: make a sasquatch silk purse from a bear sow's ear. 

But who is “Jerry”?  Regular Google searches revealed nothing about him. I tried to find his publications through Google Scholar, but could not find even one. I searched the leadership and recent conference presenters and chairpersons of the major genetics societies in his country (he hails from outside the US according to his Facebook page), but did not find reference to Jerry. So, I cannot, without more information, consider him a peer-acknowledged authority on genetics; but for that matter, neither am I.  However, our Jerry does seem to have an ear to the ground, and he is knowledgeable about genetics, as judged by his several lengthy PMs to me.

However, I strongly disagree with him that a reassembly will change a black bear (Sample 26) sequence into a sasquatch sequence. Or a dog sequence (Sample 140) either, for that matter. Recall that three independent labs all showed S26 to be a black bear (See my blog, November 26, 2014, “Ketchum Sample 26, The Smeja Kill: Independent Lab Reports”). I compared S26 to sequences from five different NCBI databases and data from two literature sources. The results were consistent across all seven sources: Sample 26 is a black bear, with human and primate matches consistently much poorer. An incorrect assembly would likely not have produced sequence segments up to 2000 bp long matching a bear 99-100%. Such a sequence segment would involve a minimum 10-20 or likely more short raw sequences, not counting sequence coverage which was claimed to be 30X by Ketchum et al.: so, maybe 600 individual raw sequences total. It’s hard to imagine that software that “was about as appropriate as driving a square peg into a round hole,” could consistently produce relatively long sequence matches to a bear, with human and other primates consistently much poorer matches. If the software were that inappropriate, a much more likely scenario would be one in which the resulting sequence had random errors and hence matched no species consistently. How could software be so targeted as to always replace a sasquatch base with a bear base (where they differed) throughout the 2.7 million bases that were sequenced in S26? And why would the same software yield a bear for S26 and a dog for S140 if both were actually a sasquatch? Actually, use of a human reference would, if anything, result in a more human-like sequence, not a less human one. And this is precisely what we found: only conserved genes were assembled, those which matched human about 94-95%. This may also explain why only 2.7 million of the 135 million base pairs in chromosome 11 were sequenced, i.e. much of the rest was not sufficiently conserved to allow an assembly through a human reference. A similar argument is made for S140, the dog, with 2.1 million bases sequenced by Ketchum, et al. and conserved genes matching human 94-95% also.  

But Jerry has all kinds of excuses: (1) “…you have no idea what you are doing… ” A number of accomplished geneticists have told me otherwise. (2) “…there is an almost endless list of pipeline (software) approaches that can be used to reassemble short reads from Illumina data.” Does he really mean to imply that different software can give fundamentally different results, such as different, unrelated species? Show me please. (3) “…Genbank is known to have so much rubbish and unverified data in it's (sic) database…” Really? Then how would he plan to identify the newly reassembled sequences? Everybody uses GenBank®.  Whatever "rubbish" it contains won’t match a query sequence very well anyway and will not appear in the results, or if so with lower %ID. Also, “uncultured environmental samples,” which are not identified as to species, are clearly indicated as such. I used enough independent bear data, including polar bear and panda as cross checks to eliminate the possibility that one bad database sequence could result in a misidentification. (4) “You made incorrect assumptions”  Only that the published sequences are basically correct! (but possibly incomplete).  Other than that I made no assumptions; I simply compared these sequences to
GenBank®,
as Melba did, but with different results.

However, I do agree with Jerry when he says, “… you (Ketchum et al.) do not force a comparison of raw data against a known (human) genome even if the material is uncontaminated especially for a suspected unknown species.” This is what the Illumina HiSeq™ 2000 system, used by Ketchum et al., does. It is based on a human reference sequence, and is designed to detect small differences (SNPs), e.g. which may result in a disease, not large interspecies differences, e.g. which make a bear walk on four legs and a human on two. By this means, you’ll only map conserved genes, ones that involve common functions.



The bottom line question is: Can a human-based reference method, used by Ketchum et al. yield a consistent and basically correct, but incomplete, sequence which is different from human as for Samples 26 and 140?  I think it’s possible; Jerry does not. There are two reasons why I think so: (1) The sequencing of short segments is completely species blind, the reagents are completely neutral. None target a specific species. (2) Important genes are highly conserved. We found that human matched the S26 bear 94-95%, so in assembly some shorter sequences would also align with a human reference sequence well enough to assemble them (in the right order), at least for conserved genes. There will be some base mismatches (about 1 in 16 to 20 I found), but by and large the conserved genes will align correctly and will be identified as to species through a BLAST™ search of GenBank®.  No, this won’t work for assembling marijuana sequences with a Coho salmon reference, but bears and humans do have many functions in common and therefore have some, but not all, similar genes. We’ll have to see what the new team of hopefully “top notch bioinformaticians” comes up with. Hopefully, they’re sequencing some new and different samples by de novo assembly, not "wasting their time" with Samples 26 and 140.

It’s been over four months since Melba’s original post and the above St. Louis Post-Dispatch article, which claims that whole genomes can be sequenced in just a few days. And, as we noted above, searching GenBank® takes even less time (minutes). So where are the results? I asked Dr. Richard K. Wilson, the Director of the Washington University McDonnell Genome Institute whether the MGI was reassembling Melba’s raw data, but he did not respond. Similarly, Dr. Wes Warren, Assistant Director, whose field encompasses species identification, was also unresponsive to my inquiry. “Silence is Golden.” I take this as a “yes.” MGI may be involved in the reassembly of the Ketchum et al. raw data and has been sworn to secrecy by one of Melba’s famous NDAs. Of course, if their efforts fail they’d want that to be kept secret to protect their reputation. But wouldn’t it be refreshing for them to report such results, just as Bryan Sykes did with the 30 hair samples that turned out to be from known animals? I’ll make a prediction, too, that they will not find sasquatch or anything like it in Samples 26 and 140, over the published sequence ranges. Of course there are still the 99.9+% of the purported “three whole genomes” which was not assembled or published. I promised Jerry a case of his favorite national beer (largest container size) if MGI finds a sasquatch in just one of these samples. But I don’t think they will. I have the support of three independent laboratories which found S26 to be a black bear. 


Finally, you might wonder, “Why kick a dead horse?” Jerry calls it my “obsession with old news,” but it’s not “old news,” because Dr. Melba Ketchum, DVM, continues to appear on radio and TV shows expounding on her great discovery to mostly sensationalist interviewers. Science is based on a foundation of past work (“old news”), but only good, validated work, which is required to be cited as relevant references in each published scientific paper. Faulty results and conclusions need to be exposed and retracted, like polywater and cold fusion.  Jerry says, “Melba has some well qualified friends who think her work was an important start” (not exactly an endorsement of her conclusions). Actually, I agree to the extent that she and colleagues were the first to have used DNA analysis to attempt to prove the existence of sasquatch. If and when mistakes are admitted, previous results and conclusions retracted, and a reasonable interpretation of new results is presented (if there is one), I will cease and desist in my scientific criticism, but not before. Washington University of St. Louis McDonnell Genome Institute, we’re all waiting.

Note: More information on Illumina sequencing and assembly can be found on their website: 
illumina.com. It’s a good company. None of the above reflects badly on them in any way. Their machine got the right answers, even when using the wrong method selected by Ketchum et al.   

Saturday, September 19, 2015

The Ketchum File III: Gog and Magog are Not Bigfoot


Warning:  Contains Ketchum Koolaid.  Please drink responsibly.

On her Facebook page, Dr. Melba Ketchum, DVM, posted a picture of a statue outside the Cathedral at Avila (Spain) and said, "Here's the door of the Cathedral of Avila, Spain with a Sasquatch to the right, carved in the wall."

Actually there are two statues, one on either side of the entrance.  I know, I've been there.  A visit to the Cathedral website (http://catedralavila.es/la-catedral/puerta-occidental/), which has pictures of the entrance, reveals that the statues, which are on the door jambs, are not of sasquatch at all:
 
 
"In the jambs are one of the many curiosities of the Cathedral of Avila.  The presence of two wild men that guard and protect the entrance to the sacred enclosure are known as Gog and Magog, there to intimidate visitors into maintaining a good and devout behavior after crossing the doors."  (translated from Spanish).



West entrance to the Cathedral of Avila (begun in 1107 AD) showing Gog and Magog "intimidating" my wife Arlene (2014).  My photo.  

In the Bible Gog and Magog appear as individuals, as places, and as peoples or nations, often apocalyptically.  For example: 

Revelation 20:8  (New King James Version)


"Now when the thousand years have expired, Satan will be released from his prison and will go out to deceive the nations which are in the four corners of the earth, Gog and Magog, to gather them together to battle, whose number is as the sand of the sea."


In the Quran and other Islamic literature Gog and Magog are associated with peoples, e.g. Turkic and Mongol raiders, but also symbolized as demons.

Nice try, Melba, but the Cathedral of Avila does not validate your invalid study.  It's a great place to visit, however, next time you're in Spain.


Medieval wall of Avila, built around the Cathedral and inner city (11th - 14th Centuries).  My photo.       .




Roman tombstone from nearby cemetery incorporated into the wall around medieval Avila.  Circular shapes are faces of a husband and wife as was the custom, but their features have eroded with time.  These are not the eyes of a bigfoot or an ancient alien.   My photo.






Wednesday, June 24, 2015

The Ketchum File II: Melba on “The Conspiracy Show” (6-21-15) with Richard Syrett





WARNING: Contains Ketchum Koolaid. Please drink responsibly. Use an informed designated driver.
 

What a perfect radio show for Melba to appear on. While claiming that she’s a victim of a mainstream science “conspiracy” to deny her a place in the sun, Melba Ketchum continues to spin her yarn of having proven the existence of bigfoot. And don’t you know that the likes of sensationalist radio host Richard Syrett drank the Koolaid up. But you’re smarter than that.

First, some of the obvious falsehoods:

1. “The mtDNA is completely human,” she said. Some of the samples were. Others had too many mutations to fall nicely into the human mtDNA phylotree. Any sample with seven or more extra mutations has a less than 1% chance of actually being a real human sample. Several of her samples failed in this. One had 17 extra mutations. Average is only about three in the human population. The most likely explanation is contamination and degradation, which she continues to deny.

2. “The nuclear DNA is a mosaic of unknown and human.” - The three published sequences did not show that. I found that one is a black bear, one is completely human, and one is a dog.

3. “nDNA BLAST gave no hits at all.” - She doesn’t know how to do a proper search. See 2. above. Previously, Melba claimed on Facebook that she got 13 different species hits and still counting, and therefore the sample was unknown. Only a very few relatively short specific gene sequences gave no hits, I found. She claims they’re a hybrid, which would show both human and primate hits, but presented no evidence to support that claim in her paper. She can’t even stick to the same story.

4. “Passed peer review.” - The e-mail which she touts says “Accepted with revisions.” She did not make the requested revisions, but purchased the journal (with Wally Hersom’s funding) instead when the journal cancelled its so called “acceptance.”

Some pure speculations represented as facts:

5. “Crossbreeding is in the historical record. Maidens were stolen and came back with a hybrid baby. Offspring were not always healthy. Others lived normal lives.” - For “historical record” read “legend and mythology.” None of this was documented from personal experience by reputable civilized-world historians in a written language (not nebulous pictographs and totems subject to interpretation).

6. “The human was ‘bred out’ as the weaker species.” - Sample 31 nDNA was completely human. She concluded in her paper that the nDNA showed a “mosaic” pattern of a human hybrid. Furthermore, she continues to campaign against capture or killing because they are “human, just like us“ (she said previously). Just more inconsistencies.

7. “They bury their dead.” - Nobody has ever found verifiable skeletal remains, above or below the ground.  She claimed the government has some.

8. “Some are cannibalistic.” Evidence please?

A few other points. She claimed to have samples of Zana (the wild woman from Russia) and her son Kwit. These were shown by Bryan Sykes of Oxford to be of African origin (haplogroup). I doubt she has samples, and I doubt even more that she will add anything to this.


She claimed to have both samples and funding for her “Giants” study, but has not begun work because she is waiting for more of each. Why hasn’t the work begun on existing samples with existing funding? Even her believer, Chris Noel, asked this question on her Facebook page.

Finally, she continues to label her critics, including me, as “haters.” “The haters don’t give up… So many haters have torn it down,” she says. I don’t know anybody (including me) who has said that they hate Melba Ketchum or her coworkers. Personally, I reserve my hatred for more important people, like Hitler, Stalin, and a few other living dictators. The paper was “torn down” because it contained false conclusions, not because people hate her. 


 “The Galileo Effect?” I don’t think so.

Thursday, June 18, 2015

Ketchum Sample 26 (Justin Smeja’s) Matches Literature Black Bear Data Best


ABSTRACT

Black bear (Ursus americanus) genomic scaffolds from Cahill et al. were converted to a stand-alone PC BLAST™ database, which was queried with the Ketchum et al. Sample 26 (Smeja sample) nDNA sequence. Comparisons to polar bear (Ursus maritimus), giant panda (Ailuropoda melanoleuca), human, and other primates, showed conclusively that Sample 26 is a black bear. Human and other primates were much poorer matches than any of the bears. Sample 26 is a black bear, not a human-primate hybrid as claimed by Ketchum et al.



INTRODUCTION


Since the 2013 paper of Ketchum et al., “Novel North American Hominins…..” [1] was published we have attempted to verify the claim made therein:

“…the species (sasquatch) possesses a novel mosaic pattern of nuclear DNA comprising novel sequences that are related to primates interspersed with sequences that are closely homologous to humans.” 

The Ketchum paper included nDNA sequences for three samples, 26, 31, and 140. Our previous attempts [2] all resulted in the conclusion that Sample 26 (S26) was a bear, recently found to be a black bear. Here we compare the most comprehensive black bear data available to us so far [3] to S26, with the same conclusion.

Black bear nDNA data are relatively sparse in the NCBI databases, especially when compared to the whole genomes of the polar bear and the giant panda, both of which are endangered and of greater conservation interest. The only useful and significant black bear sequence lengths were found in the” Expressed sequence tags” and “RNA reference sequences” databases as previously reported.[4,5] Other useful black bear sequences, ultraconserved elements (UCE), were obtained from the literature [6].

This blog compares S26 to the black bear data of Cahill et al. in reference [3], which was the result of mapping black bear DNA to the 238 longest scaffolds (1Mb or greater in length) in the polar bear reference genome [7]. Coverage was 11.6 X. Their filtering reduced the error rate of each base to less than 1/1000 [3].

COMPUTATIONAL METHODS



S26 nDNA sequence was downloaded from the Sasquatch Genome Project website (see link at right). The black bear file [3], in FASTA format, was downloaded as a 600 Mb compressed gzip file, which was inflated to 2.1 Gb and converted to a stand-alone BLAST™ database for PC, using NCBI software (http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download). Each database entry was one of the 238 scaffolds mentioned above. The 2.7 Mb S26 nDNA sequence from [1] was queried against this database with PC BLAST™ software (above link). The hit table (converted from a text file to EXCEL®) was sorted by score, and the top 50 hits were examined and compared to the corresponding (in sequence range) best polar bear and giant panda matches to S26 from the NCBI “Reference genomic sequences database” (complete genomes). Additionally, the best human and other primate matches to S26 from the Reference genomic sequences database over the same sequence ranges were compared to the bear hits. All %IDs were computed based on mismatches only, excluding “N” designations, for unspecified bases, and gaps. This permitted the conservative base assignment approach of [3] to be compared consistently to the other matching sequences in our %ID comparisons.

RESULTS AND DISCUSSION


Table 1 shows partial results of our sequence comparisons. Within each grouping separated by a blank row, are, top to bottom, each in single row:

S26 match to black bear data in [3]

Best S26 match to polar bear

Best S26 match to giant panda

Best S26 match to human

Best S26 match to other primates (ex-human).

This table presents only the top 15 hits by score. When the top 50 hits were compared, 30 matched black bear best, eight matched polar bear best, 11 were tied between these two bears, and one was tied between polar bear and giant panda. Overall, black bear was the best species match to S26.

All the human and other primate hits were significantly poorer matches than any bear matches. For conserved genes with the highest scores, we found previously [2] that a few percentage points %ID can be the difference between phylogenetic orders (e.g. Carnivora (Ursidae family) vs. Primata), and such was the case here.



CONCLUSION



S26 is a black bear, consistent with our previous conclusions. Human and all primates don’t even come close to matching S26. The Ketchum et al. conclusion above IS WRONG. There are no good human or primate matches to S26 among the 50 highest scores.

Incomplete genomes can be useful in forensic investigations if the scaffolds are sufficiently long and well selected, coverage is good, and base assignment is conservative, as was the case here [3]. The sequence matches here were approximately twice as long as our previous best black bear matches

Beginning with this blog, S26 will no longer be referred to here as “The Smeja Kill” as it does not fit the description of what Justin Smeja (an experienced bear hunter) said he killed. Also, since this sample was collected five weeks later as a hand-sized patch of fur and flesh found under two feet of snow, it therefore has no verifiable connection to the actual “Smeja Kill.” Three other independent laboratory analyses found S26 to be a black bear [8]. Our computational analysis of the original Ketchum nDNA sequence is in agreement with these independent laboratory analyses and our own previous interpretations of the Ketchum et al. sequence [2].

ACKNOWLEDGEMENT

We are grateful to James Cahill and Prof. Beth Shapiro of the Department of Ecology and Evolutionary Biology, UC-Santa Cruz, for making the black bear data from [3] available for this study and also to the Sasquatch Genome Project for making the S26 nDNA sequence available on their website.



CONFLICT OF INTEREST

The author declares no conflict of interest.


REFERENCES

[1] See Sasquatch Genome Project link at right.

[2] See Paper 1 links at right and blogs under “Ketchum DNA Study” tab above.

[3] Cahill J A, et al., Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution, PLOS Genetics, March 14, 2013, DOI: 10.1371/journal.pgen.1003345. 

[4] See on this blog, May 22, 2015, “
New Black Bear Data Show Ketchum Sample 26 (the Smeja Kill) is a Bear.”

[5] See on this blog, June 4, 2015, “RNA Data Show Ketchum Sample 26 - the Smeja Kill - is a Black Bear.” 

[6] See on this blog, June 11, 2015, “New Genetic Markers for Bears Show that Ketchum Sample 26 - the Smeja Sample - is a BLACK BEAR” 

[7] Li B, Zhang G, Willerslev E, Wang J, Wang J (2011) Genomic data from the Polar Bear (Ursus maritimus). Available from:
http://dx.doi.org/10.5524/100008. GigaScience.

[8] See “The Tyler Huggins Report” under Pages at right and on this blog, November 26, 2014, “
Ketchum Sample 26, The Smeja Kill: Independent Lab Reports.”


  
Table 1. Top 15 Black Bear Hits and

Comparisons


Accession

%ID

Length

Start

End

Species

scaffold152

99.58

1681

1655920

1657569

black bear

NW_007907230.1

99.88

1679

1655920

1657569

polar bear

NW_003217478.1

99.59

1688

1655920

1657569

giant panda

NM_001039618.2

95.69

1695

1655921

1657569

human

XM_003254601.2

95.68

1690

1655921

1657569

northern white-

cheecked gibbon


scaffold156

99.92

1279*

189026

190304

black bear

NW_007929448.1

100.00

2139

189028

191141

polar bear

NW_003218202.1

100.00

2141

189026

191141

giant panda

BC038508.1

94.68

2142

189026

191141

human

XM_003951836.1

94.54

2142

189026

191141

chimpanzee

scaffold46

99.34

1359

759948

761288

black bear

NW_007907078.1

99.93

1359

759948

761288

polar bear

NW_003217489.1

99.49

1364

759948

761288

giant panda

NM_001278163.1

97.42

1354

759948

761288

human

XM_003254384.2

97.49

1353

759948

761288

northern white-

cheecked gibbon


scaffold46

100.00

1237

690618

691854

black bear

NW_007907078.1

99.92

1237

690618

691854

polar bear

NW_003217489.1

99.35

1237

690618

691854

giant panda

Z83001.1

98.79

1239

690618

691855

human

NC_006478.3|

98.87

1239

690618

691855

chimpanzee

scaffold180

99.84

1243

326857

328097

black bear

NW_007907318.1

99.69

1299

326857

328153

polar bear

NW_003217713.1

99.00

1300

326857

328153

giant panda

NG_012881.1

95.18

1308

326857

328153

human

NC_018435.1

95.03

1308

326857

328153

gorilla



scaffold180

99.84

1244

349476

350698

black bear

NW_007907318.1

99.92

1244

349476

350698

polar bear

NW_003217713.1

99.36

1243

349476

350698

giant panda

NC_000011.9

94.28

1241

349476

350700

human

NW_002885339.1

94.18

1237

349476

350697

orangutan

scaffold31

99.82

1112

2257274

2258385

black bear

NW_007907111.1

99.73

1112

2257274

2258385

polar bear

NW_003218653.1

99.28

1112

2257274

2258385

giant panda

NC_000011.9

94.96

1112

2257274

2258385

human

NC_013906.1

95.23

1112

2257274

2258385

white-tufted-

ear marmoset


scaffold24

99.66

1174

1835440

1836608

black bear

NW_007907090.1

99.66

1174

1835440

1836608

polar bear

NW_003218271.1

99.06

1174

1835440

1836608

giant panda

NW_004078072.1

94.47

1175

1835440

1836608

human

XM_004052006.1

94.38

1175

1835440

1836608

gorilla

scaffold46

100.00

1115

673215

674328

black bear

NW_007907078.1

100.00

1115

673215

674328

polar bear

NW_003217489.1

99.55

1114

673215

674328

giant panda

AC093262.2

98.30

1117

673215

674328

human

NC_022285.1

98.66

1118

673215

674327

crab-eating

 macaque


scaffold31

100.00

1140

2258573

2259712

black bear

NW_003218653.1

99.57

1173

2258573

2259743

polar bear

NW_007907111.1

99.65

1157

2258573

2259729

giant panda

NG_027813.1

96.37

1156

2258575

2259729

human

DQ977225.1

96.45

1156

2258575

2259729

pygmy

chimpanzee


scaffold137

99.92

1260

1624428

1625637

black bear

NW_007907229.1

99.44

1260

1624428

1625637

polar bear

NW_003218719.1

99.13

1260

1624428

1625637

giant panda

XM_005273811.1

95.71

1374

1624428

1625746

human

NW_010810287.1

95.39

1259

1624428

1625637

golden snub-

nosed monkey


scaffold93

99.83

1151

1508093

1509231

black bear

NW_007907285.1

100.00

1151

1508093

1509231

polar bear

NW_003217421.1

99.04

1151

1508093

1509231

giant panda

AP000609.5

94.59

1147

1508092

1509231

human

XM_003808137.1

94.77

1147

1508090

1509231

chimpanzee

scaffold46

99.91

1141

710570

711698

black bear

NW_007907078.1|

99.91

1141

710570

711698

polar bear

NW_003217489.1

98.16

1140

710570

711698

giant panda

AC_000143.1

95.90

1146

710568

711698

human

NW_002885202.1

96.06

1142

710570

711698

orangutan

scaffold46

99.91

1080

630428

631502

black bear

NW_007907078.1

99.07

1079

630428

631501

polar bear

NW_003218059.1

98.24

1082

630426

631502

giant panda

AC_000143.1

94.38

1085

630427

631501

human

NC_019830.1

94.37

1083

630428

631501

northern white-

cheecked gibbon


scaffold180

100.00

1083

321092

322174

black bear

NW_007907318.1

99.82

1083

321092

322174

polar bear

NW_003217713.1

99.35

1083

321092

322174

giant panda

NG_012881.1

95.87

1090

321092

322174

human

NC_018435.1

96.24

1091

321092

322174

gorilla

Top 15 hits only – top 50 were compared in text. 
%ID is based on mismatches only.  Length is in bp.  Start and End sequence positions refer to S26 sequence.

*   Note shorter sequence length.