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Table view (146 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		AANN01792448.1	N/A	seed	1,306	1,126	Erinaceus europaeus cont1.792447, whole genome shotgun sequence.	Erinaceus europaeus (western European hedgehog)
1		AACC02000013.1	N/A	seed	910,577	910,398	Homo sapiens chromosome 7 Contg13, whole genome shotgun sequence.	Homo sapiens (human)
2		AAWR02013862.1	N/A	seed	6,077	6,256	Equus caballus cont2.13861, whole genome shotgun sequence.	Equus caballus (horse)
3		ABRT010013038.1	N/A	seed	895	1,074	Tarsius syrichta cont1.13037, whole genome shotgun sequence.	Tarsius syrichta (Philippine tarsier)
4		ABVD01412771.1	N/A	seed	1,590	1,768	Choloepus hoffmanni cont1.412770, whole genome shotgun sequence.	Choloepus hoffmanni (Hoffmann's two-fingered sloth)
5		ABRR01115815.1	N/A	seed	1,629	1,807	Vicugna pacos cont1.115814, whole genome shotgun sequence.	Vicugna pacos (alpaca)
6		AAIY01400228.1	N/A	seed	2,213	2,392	Echinops telfairi cont1.400227, whole genome shotgun sequence.	Echinops telfairi (small Madagascar hedgehog)
7		ABRP01070477.1	N/A	seed	22,517	22,697	Pteropus vampyrus cont1.70476, whole genome shotgun sequence.	Pteropus vampyrus (large flying fox)
8		AAQQ01558328.1	N/A	seed	1,265	1,444	Spermophilus tridecemlineatus cont1.558327, whole genome shotgun sequence.	Spermophilus tridecemlineatus (thirteen-lined ground squirrel)
9		AAKN02016914.1	N/A	seed	5,934	6,110	Cavia porcellus strain inbred line 2N cont2.16913, whole genome shotgun sequence.	Cavia porcellus (Domestic guinea pig)
10		AC122240.4	N/A	seed	64,177	64,356	Mus musculus BAC clone RP23-145L9 from 6, complete sequence.	Mus musculus (house mouse)
11		AAPE02008847.1	N/A	seed	118,460	118,639	Myotis lucifugus cont2.8846, whole genome shotgun sequence.	Myotis lucifugus (little brown bat)
12		AACN010010072.1	N/A	seed	3,139	2,959	Canis familiaris ctg19866851899041, whole genome shotgun sequence.	Canis lupus familiaris (dog)
13		AAGU03015811.1	N/A	seed	27,774	27,618	Loxodonta africana cont3.15810, whole genome shotgun sequence.	Loxodonta africana (African savanna elephant)
14		AAGW02035474.1	N/A	seed	81,890	82,069	Oryctolagus cuniculus cont2.35473, whole genome shotgun sequence.	Oryctolagus cuniculus (rabbit)
0		GL873524.1	198.10	full	24,285,953	24,286,132	Otolemur garnettii unplaced genomic scaffold scaffold00005, whole genome shotgun sequence.	Otolemur garnettii (small-eared galago)
1		JAATJV010455200.1	196.80	full	288,999	289,178	JAATJV010455200.1 Sciurus carolinensis isolate SUZIE scaffold984, whole genome shotgun sequence	Sciurus carolinensis (gray squirrel)
2		LR738618.1	196.80	full	46,626,648	46,626,469	LR738618.1 Sciurus vulgaris genome assembly, chromosome: 8	Sciurus vulgaris (Eurasian red squirrel)
3		NW_012267443.1	196.10	full	442,173	441,994	NW_012267443.1 Dipodomys ordii isolate 6190 unplaced genomic scaffold, Dord_2.0 Scaffold227, whole genome shotgun sequence	Dipodomys ordii (Ord's kangaroo rat)
4		CM026977.1	195.90	full	34,944,109	34,944,288	CM026977.1 Rattus norvegicus strain BN/NHsdMcwi chromosome 4, whole genome shotgun sequence	Rattus norvegicus (Norway rat)
5		CM000999.3	195.50	full	6,820,942	6,821,121	CM000999.3 Mus musculus chromosome 6, GRCm39 reference primary assembly C57BL/6J	Mus musculus (house mouse)
6		CABDUW010000281.1	195.10	full	1,225,854	1,226,033	CABDUW010000281.1 Marmota monax genome assembly, contig: monax5_s00281, whole genome shotgun sequence	Marmota monax (woodchuck)
7		CM007671.1	194.90	full	61,969,471	61,969,650	CM007671.1 Microcebus murinus isolate mixed chromosome 11, whole genome shotgun sequence	Microcebus murinus (gray mouse lemur)
8		KQ013879.1	194.90	full	4,225,040	4,225,219	KQ013879.1 Propithecus coquereli isolate 6110/MARCELLA unplaced genomic scaffold Scaffold108, whole genome shotgun sequence	Propithecus coquereli (Coquerel's sifaka)
9		MPIZ01000094.1	194.90	full	3,425,845	3,425,666	MPIZ01000094.1 Prolemur simus strain KIAN8.4 scaffold94, whole genome shotgun sequence	Prolemur simus (greater bamboo lemur)
10		NW_017875902.1	194.50	full	108,630	108,809	NW_017875902.1 Castor canadensis isolate Ward unplaced genomic scaffold, C.can genome v1.0 scaffold_6575, whole genome shotgun sequence	Castor canadensis (American beaver)
11		JH721892.1	193.80	full	13,372,765	13,372,944	JH721892.1 Chinchilla lanigera unplaced genomic scaffold scaffold00031, whole genome shotgun sequence	Chinchilla lanigera
12		NW_004524626.1	193.70	full	838,663	838,484	NW_004524626.1 Octodon degus isolate 3935 unplaced genomic scaffold, OctDeg1.0 scaffold00050, whole genome shotgun sequence	Octodon degus (degu)
13		GL010032.1	193.20	full	52,494,657	52,494,478	Loxodonta africana unplaced genomic scaffold scaffold_5, whole genome shotgun sequence.	Loxodonta africana (African savanna elephant)
14		CM000321.4	193.10	full	99,835,842	99,836,021	Pan troglodytes isolate Yerkes chimp pedigree #C0471 (Clint) chromosome 7, whole genome shotgun sequence.	Pan troglodytes (chimpanzee)
15		CM000669.2	193.10	full	96,965,302	96,965,481	Homo sapiens chromosome 7, GRCh38 reference primary assembly.	Homo sapiens (human)
16		CM003390.1	193.10	full	102,501,608	102,501,787	CM003390.1 Pan paniscus isolate Ulindi chromosome 7, whole genome shotgun sequence	Pan paniscus (pygmy chimpanzee)
17		CM014338.1	193.10	full	109,158,011	109,157,832	CM014338.1 Macaca mulatta isolate AG07107 chromosome 3, whole genome shotgun sequence	Macaca mulatta (Rhesus monkey)
18		CM019247.1	193.10	full	75,225,159	75,224,980	CM019247.1 Piliocolobus tephrosceles isolate RC106 chromosome 8, whole genome shotgun sequence	Piliocolobus tephrosceles (Ugandan red Colobus)
19		CM021941.1	193.10	full	110,398,693	110,398,514	CM021941.1 Macaca fascicularis isolate cy0333 breed Mauritian cynomolgus macaque chromosome 3, whole genome shotgun sequence	Macaca fascicularis (crab-eating macaque)
20		FR853100.2	193.10	full	81,149,146	81,148,967	Gorilla gorilla gorilla genomic chromosome, chr7, whole genome shotgun sequence	Gorilla gorilla gorilla (western lowland gorilla)
21		KN973518.1	193.10	full	3,350,555	3,350,734	KN973518.1 Mandrillus leucophaeus isolate KB7577 unplaced genomic scaffold Scaffold148, whole genome shotgun sequence	Mandrillus leucophaeus (drill)
22		KQ009060.1	193.10	full	31,743,273	31,743,452	KQ009060.1 Macaca nemestrina isolate M95218 unplaced genomic scaffold Scaffold6, whole genome shotgun sequence	Macaca nemestrina (pig-tailed macaque)
23		KQ010206.1	193.10	full	3,846,836	3,847,015	KQ010206.1 Cercocebus atys isolate FAK unplaced genomic scaffold Scaffold165, whole genome shotgun sequence	Cercocebus atys (sooty mangabey)
24		JH170880.1	192.80	full	478,331	478,510	JH170880.1 Heterocephalus glaber unplaced genomic scaffold scaffold1076, whole genome shotgun sequence	Heterocephalus glaber (naked mole-rat)
25		QGOO02000023.1	192.80	full	3,386,980	3,387,159	QGOO02000023.1 Mus spicilegus strain ZRU musp714_scaffold_00023b, whole genome shotgun sequence	Mus spicilegus (steppe mouse)
26		CM000799.1	192.70	full	32,300,216	32,300,037	Oryctolagus cuniculus chromosome 10, whole genome shotgun sequence.	Oryctolagus cuniculus (rabbit)
27		CM022819.1	192.50	full	146,477,268	146,477,448	CM022819.1 Ailuropoda melanoleuca isolate Jingjing chromosome 1, whole genome shotgun sequence	Ailuropoda melanoleuca (giant panda)
28		JH393395.1	192.50	full	3,520,955	3,520,776	JH393395.1 Spermophilus tridecemlineatus unplaced genomic scaffold scaffold00117, whole genome shotgun sequence	Spermophilus tridecemlineatus (thirteen-lined ground squirrel)
29		KZ294929.1	192.50	full	164,211	164,032	KZ294929.1 Spermophilus dauricus unplaced genomic scaffold scaffold2150, whole genome shotgun sequence	Spermophilus dauricus (Daurian ground squirrel)
30		QVIC01000092.1	192.50	full	3,883,778	3,883,957	QVIC01000092.1 Urocitellus parryii isolate AGS 11-09-20 scaffold_91, whole genome shotgun sequence	Spermophilus parryii (Arctic ground squirrel)
31		CM001657.1	192.30	full	28,238,455	28,238,634	Nomascus leucogenys chromosome 11, whole genome shotgun sequence.	Nomascus leucogenys (Northern white-cheeked gibbon)
32		LZNR01002561.1	192.00	full	274,708	274,888	LZNR01002561.1 Ursus americanus isolate MABB319796 Contig2564, whole genome shotgun sequence	Ursus americanus (American black bear)
33		NW_024425563.1	192.00	full	65,789,103	65,788,923	NW_024425563.1 Ursus maritimus isolate PB19 unplaced genomic scaffold, ASM1731132v1 scaffold_3, whole genome shotgun sequence	Ursus maritimus (polar bear)
34		CM009952.1	191.80	full	107,026,165	107,025,986	CM009952.1 Theropithecus gelada isolate Dixy chromosome 3, whole genome shotgun sequence	Theropithecus gelada (gelada baboon)
35		CM018183.2	191.80	full	75,945,331	75,945,510	CM018183.2 Papio anubis isolate 15944 chromosome 4, whole genome shotgun sequence	Papio anubis (Olive baboon)
36		CM001962.2	191.70	full	52,096,398	52,096,219	Chlorocebus sabaeus isolate 1994-021 chromosome 21, whole genome shotgun sequence.	Chlorocebus sabaeus
37		KV389463.1	191.70	full	3,745,343	3,745,522	KV389463.1 Cebus capucinus imitator isolate Cc_AM_T3 unplaced genomic scaffold Scaffold37, whole genome shotgun sequence	Cebus imitator (Panamanian white-faced capuchin)
38		KZ201897.1	191.70	full	13,709,543	13,709,364	KZ201897.1 Aotus nancymaae isolate 86115 unplaced genomic scaffold Scaffold280, whole genome shotgun sequence	Aotus nancymaae (Ma's night monkey)
39		NW_022437021.1	191.70	full	373,657	373,478	NW_022437021.1 Sapajus apella isolate SASKATOON/1434 unplaced genomic scaffold, GSC_monkey_1.0 scaffold81, whole genome shotgun sequence	Cebus apella (Tufted capuchin)
40		KB321003.1	191.50	full	3,400,028	3,400,207	KB321003.1 Tupaia chinensis unplaced genomic scaffold Scaffold000544_1, whole genome shotgun sequence	Tupaia chinensis (Chinese tree shrew)
41		CM021922.1	191.30	full	49,910,596	49,910,417	CM021922.1 Callithrix jacchus isolate mCalJac1 chromosome 8, whole genome shotgun sequence	Callithrix jacchus (white-tufted-ear marmoset)
42		CZRN02000301.1	191.00	full	2,656,089	2,656,268	CZRN02000301.1 Marmota marmota marmota genome assembly, contig: chr6_part1, whole genome shotgun sequence	Marmota marmota marmota (Alpine marmot)
43		CM009269.2	190.20	full	67,744,684	67,744,505	CM009269.2 Pongo abelii isolate Susie chromosome 7, whole genome shotgun sequence	Pongo abelii (Sumatran orangutan)
44		KN979430.1	189.30	full	10,708,038	10,707,859	KN979430.1 Colobus angolensis palliatus isolate OR3802 unplaced genomic scaffold Scaffold104, whole genome shotgun sequence	Colobus angolensis palliatus
45		KN123705.1	189.10	full	385,437	385,258	KN123705.1 Fukomys damarensis unplaced genomic scaffold scaffold516, whole genome shotgun sequence	Fukomys damarensis (Damara mole-rat)
46		NW_007252336.1	189.00	full	432,061	431,882	NW_007252336.1 Carlito syrichta isolate Samal-C Ts95f unplaced genomic scaffold, Tarsius_syrichta-2.0.1 Scaffold308240, whole genome shotgun sequence	Carlito syrichta (Philippine tarsier)
47		JACDTQ010000550.1	188.70	full	44,943,066	44,942,886	JACDTQ010000550.1 Diceros bicornis minor isolate SBR-YM ScS9zPn_550, whole genome shotgun sequence	Diceros bicornis minor
48		KN295490.1	187.40	full	383,166	382,988	KN295490.1 Rhinopithecus roxellana isolate Xiao Hai unplaced genomic scaffold ENSRROG014872, whole genome shotgun sequence	Rhinopithecus roxellana (golden snub-nosed monkey)
49		MCGX01011147.1	187.40	full	932,117	931,939	MCGX01011147.1 Rhinopithecus bieti isolate Rb0 scaffold_31127, whole genome shotgun sequence	Rhinopithecus bieti (Black snub-nosed monkey)
50		KB030660.1	186.90	full	4,066,573	4,066,753	KB030660.1 Pteropus alecto unplaced genomic scaffold scaffold21, whole genome shotgun sequence	Pteropus alecto (black flying fox)
51		NW_011888785.1	186.90	full	11,965,013	11,964,833	NW_011888785.1 Pteropus vampyrus isolate Shadow unplaced genomic scaffold, Pvam_2.0 Scaffold4, whole genome shotgun sequence	Pteropus vampyrus (large flying fox)
52		JH378107.1	186.70	full	51,312,703	51,312,882	JH378107.1 Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00003, whole genome shotgun sequence	Saimiri boliviensis boliviensis (Bolivian squirrel monkey)
53		NW_004801743.1	186.10	full	3,322,275	3,322,453	NW_004801743.1 Mesocricetus auratus isolate Golden Hamster female 1 unplaced genomic scaffold, MesAur1.0 scaffold00140, whole genome shotgun sequence	Mesocricetus auratus (golden hamster)
54		JH725455.1	186.00	full	20,686,073	20,685,894	JH725455.1 Jaculus jaculus unplaced genomic scaffold scaffold00019, whole genome shotgun sequence	Jaculus jaculus (lesser Egyptian jerboa)
55		JH000272.1	185.60	full	1,175,471	1,175,649	JH000272.1 Cricetulus griseus cell line CHO-K1 unplaced genomic scaffold scaffold809, whole genome shotgun sequence	Cricetulus griseus (Chinese hamster)
56		NW_004444092.1	185.50	full	3,323,999	3,323,820	NW_004444092.1 Trichechus manatus latirostris isolate Lorelei unplaced genomic scaffold, TriManLat1.0 scaffold00156, whole genome shotgun sequence	Trichechus manatus latirostris
57		NC_058414.1	185.30	full	39,239,830	39,240,010	NC_058414.1 Neomonachus schauinslandi chromosome 12, ASM220157v2, whole genome shotgun sequence	Monachus schauinslandi (Hawaiian monk seal)
58		CAJHUB010000770.1	185.20	full	19,685,805	19,685,985	CAJHUB010000770.1 Nyctereutes procyonoides isolate TBG_1078 genome assembly, contig: Nypro792, whole genome shotgun sequence	Nyctereutes procyonoides (raccoon dog)
59		NW_006383776.1	184.80	full	165,259	165,079	NW_006383776.1 Leptonychotes weddellii isolate WS11-02 unplaced genomic scaffold, LepWed1.0 scaffold00736, whole genome shotgun sequence	Leptonychotes weddellii (Weddell seal)
60		CM014245.1	184.30	full	30,155,879	30,155,699	CM014245.1 Rhinolophus ferrumequinum isolate MPI-CBG mRhiFer1 chromosome 20, whole genome shotgun sequence	Rhinolophus ferrumequinum (greater horseshoe bat)
61		NW_006804525.1	184.30	full	1,457,997	1,457,817	NW_006804525.1 Erinaceus europaeus isolate Erinaceus europaeus_13Jul2011 unplaced genomic scaffold, EriEur2.0 scaffold00602, whole genome shotgun sequence	Erinaceus europaeus (western European hedgehog)
62		DS562866.1	184.20	full	28,223,386	28,223,562	Cavia porcellus supercont2_11 genomic scaffold, whole genome shotgun sequence.	Cavia porcellus (Domestic guinea pig)
63		KL204884.1	184.10	full	1,658,335	1,658,156	KL204884.1 Nannospalax galili isolate Female #2095 unplaced genomic scaffold scaffold187, whole genome shotgun sequence	Nannospalax galili (Upper Galilee mountains blind mole rat)
64		NW_020312848.1	184.00	full	21,497,989	21,498,169	NW_020312848.1 Callorhinus ursinus isolate GAN/ISIS: 27379988/994484 unplaced genomic scaffold, ASM326570v1 scaffold106, whole genome shotgun sequence	Callorhinus ursinus (northern fur seal)
65		CM009151.1	183.80	full	40,200,830	40,201,009	CM009151.1 Equus caballus isolate Twilight breed thoroughbred chromosome 4, whole genome shotgun sequence	Equus caballus (horse)
66		CM027690.2	183.80	full	61,945,331	61,945,152	CM027690.2 Equus asinus breed Dezhou chromosome 1, whole genome shotgun sequence	Equus asinus (ass)
67		JAATJU010023078.1	183.30	full	947,161	947,339	JAATJU010023078.1 Microtus ochrogaster isolate LTLLF scaffold384, whole genome shotgun sequence	Microtus ochrogaster (prairie vole)
68		CM025113.1	182.30	full	21,843,194	21,843,374	CM025113.1 Canis lupus familiaris isolate SID07034 breed Labrador retriever chromosome 14, whole genome shotgun sequence	Canis lupus familiaris (dog)
69		CM025470.1	182.30	full	21,809,077	21,809,257	CM025470.1 Canis lupus dingo isolate Sandy chromosome 14, whole genome shotgun sequence	Canis lupus dingo (dingo)
70		NW_020356483.1	182.00	full	5,758,548	5,758,728	NW_020356483.1 Vulpes vulpes strain TameXAggressive cross unplaced genomic scaffold, VulVul2.2 scaffold49, whole genome shotgun sequence	Vulpes vulpes (red fox)
71		NW_004450735.1	181.90	full	904,446	904,266	NW_004450735.1 Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold, Oros_1.0 Scaffold472, whole genome shotgun sequence	Odobenus rosmarus divergens (Pacific walrus)
72		NW_017731715.1	181.80	full	182,071	181,891	NW_017731715.1 Hipposideros armiger isolate ML-2016 unplaced genomic scaffold, ASM189008v1, whole genome shotgun sequence	Hipposideros armiger
73		NC_047042.1	181.60	full	45,687,090	45,686,911	NC_047042.1 Tursiops truncatus isolate mTurTru1 chromosome 9, mTurTru1.mat.Y, whole genome shotgun sequence	Tursiops truncatus (bottlenosed dolphin)
74		KE163803.1	181.50	full	3,590,516	3,590,337	KE163803.1 Myotis brandtii unplaced genomic scaffold scaffold48, whole genome shotgun sequence	Myotis brandtii
75		CYRY02043418.1	181.40	full	462,730	462,550	CYRY02043418.1 Gulo gulo genome assembly, contig: scaffold64, whole genome shotgun sequence	Gulo gulo (wolverine)
76		GL429782.1	181.20	full	5,075,353	5,075,532	Myotis lucifugus unplaced genomic scaffold scaffold_15, whole genome shotgun sequence.	Myotis lucifugus (little brown bat)
77		NC_041218.1	181.10	full	61,873,763	61,873,942	NC_041218.1 Physeter catodon isolate SW-GA chromosome 5, ASM283717v5, whole genome shotgun sequence	Physeter catodon (sperm whale)
78		NC_045793.1	181.10	full	61,300,336	61,300,515	NC_045793.1 Balaenoptera musculus isolate JJ_BM4_2016_0621 chromosome 9, mBalMus1.pri.v3, whole genome shotgun sequence	Balaenoptera musculus (Blue whale)
79		NW_006777108.1	181.10	full	1,438,088	1,437,909	NW_006777108.1 Lipotes vexillifer unplaced genomic scaffold, Lipotes_vexillifer_v1 scaffold107, whole genome shotgun sequence	Lipotes vexillifer (Yangtze River dolphin)
80		NW_020175410.1	181.10	full	9,752,435	9,752,256	NW_020175410.1 Neophocaena asiaeorientalis asiaeorientalis breed wild unplaced genomic scaffold, Neophocaena_asiaeorientalis_V1 scaffold70, whole genome shotgun sequence	Neophocaena asiaeorientalis asiaeorientalis (yangtze finless porpoise)
81		NW_022098064.1	181.10	full	60,435,609	60,435,788	NW_022098064.1 Delphinapterus leucas isolate GAN/ISIS: 26980492/103006 unplaced genomic scaffold, ASM228892v3 scaffoldscaffold73, whole genome shotgun sequence	Delphinapterus leucas (beluga whale)
82		RWIC01000208.1	181.10	full	303,431	303,610	RWIC01000208.1 Monodon monoceros isolate MVW Scaffold207, whole genome shotgun sequence	Monodon monoceros (narwhal)
83		CM016972.1	180.80	full	82,545,285	82,545,465	CM016972.1 Suricata suricatta isolate VVHF042 chromosome 2, whole genome shotgun sequence	Suricata suricatta (meerkat)
84		NTJE010039242.1	180.70	full	7,984	7,805	NTJE010039242.1 Eschrichtius robustus isolate AM-GW-M-EMB-4M-20130531 contig_43082, whole genome shotgun sequence	Eschrichtius robustus (grey whale)
85		KB199569.1	180.70	full	6,929,236	6,929,415	KB199569.1 Myotis davidii unplaced genomic scaffold scaffold187, whole genome shotgun sequence	Myotis davidii
86		NW_025421998.1	180.50	full	39,580,413	39,580,593	NW_025421998.1 Mustela putorius furo isolate JIRA1106 unplaced genomic scaffold, ASM1176430v1.1 tig00003845_pilon_pilon_pilon, whole genome shotgun sequence	Mustela putorius furo (domestic ferret)
87		NC_040912.2	180.30	full	27,210,593	27,210,414	NC_040912.2 Phyllostomus discolor isolate MPI-MPIP mPhyDis1 chromosome 10, mPhyDis1.pri.v3, whole genome shotgun sequence	Phyllostomus discolor (pale spear-nosed bat)
88		JAGFMF010011586.1	180.00	full	570,853	571,028	JAGFMF010011586.1 Galemys pyrenaicus isolate IBE-C5619 2611266, whole genome shotgun sequence	Galemys pyrenaicus
89		CM000820.5	179.90	full	76,586,489	76,586,668	Sus scrofa isolate TJ Tabasco breed Duroc chromosome 9, whole genome shotgun sequence.	Sus scrofa (pig)
90		JABWUV010000011.1	179.80	full	35,401,337	35,401,158	JABWUV010000011.1 Myotis myotis isolate mMyoMyo1 scaffold_m19_p_11, whole genome shotgun sequence	Myotis myotis
91		QWLN02006048.1	179.60	full	4,444,995	4,444,816	QWLN02006048.1 Sousa chinensis isolate MY-2018 scaffold112.1, whole genome shotgun sequence	Sousa chinensis (Indo-pacific humpbacked dolphin)
92		JACAGB010000010.1	179.50	full	35,814,045	35,813,866	JACAGB010000010.1 Pipistrellus kuhlii isolate mPipKuh1 scaffold_m20_p_10, whole genome shotgun sequence	Pipistrellus kuhlii (Kuhl's pipistrelle)
93		JACASE010000013.1	179.00	full	20,349,728	20,349,907	JACASE010000013.1 Rousettus aegyptiacus isolate mRouAeg1 scaffold_m13_p_13, whole genome shotgun sequence	Rousettus aegyptiacus (Egyptian rousette)
94		SGJD01000674.1	178.80	full	894,972	895,151	SGJD01000674.1 Balaenoptera physalus isolate FinWhale-01 scaffold814, whole genome shotgun sequence	Balaenoptera physalus (Fin whale)
95		NW_019154100.1	178.60	full	8,545,106	8,545,286	NW_019154100.1 Enhydra lutris kenyoni isolate GAN:26980312 unplaced genomic scaffold, ASM228890v2 scaffoldscaffold16, whole genome shotgun sequence	Enhydra lutris kenyoni
96		CM018164.1	178.40	full	60,725,068	60,725,247	CM018164.1 Phocoena sinus isolate mPhoSin1 chromosome 9, whole genome shotgun sequence	Phocoena sinus (vaquita)
97		PVHT020000174.1	177.70	full	4,015,772	4,015,593	PVHT020000174.1 Catagonus wagneri isolate BS18 Sc2sB16_147;HRSCAF=32195_1, whole genome shotgun sequence	Catagonus wagneri (Chacoan peccary)
98		JAULJE010000014.1	175.10	full	24,740,640	24,740,461	JAULJE010000014.1 Eptesicus nilssonii isolate BLF_Eptnil Scaffold_14, whole genome shotgun sequence	Eptesicus nilssoni (northern bat)
99		NW_006501346.1	174.90	full	2,036,885	2,037,063	NW_006501346.1 Peromyscus maniculatus bairdii unplaced genomic scaffold, Pman_1.0 Scaffold310, whole genome shotgun sequence	Peromyscus maniculatus bairdii (prairie deer mouse)
100		FNWR01000090.1	174.50	full	3,880,456	3,880,636	FNWR01000090.1 Neovison vison genome assembly, contig: scaffold90, whole genome shotgun sequence	Neovison vison
101		CM018462.1	173.20	full	94,141,411	94,141,591	CM018462.1 Panthera leo isolate Brooke chromosome A3, whole genome shotgun sequence	Panthera leo (lion)
102		LZPO01034949.1	173.20	full	58,186	58,364	Neotoma lepida isolate 417 scaffold_1342, whole genome shotgun sequence.	Neotoma lepida (desert woodrat)
103		NW_020834755.1	173.20	full	29,022,879	29,023,059	NW_020834755.1 Acinonyx jubatus isolate Rico unplaced genomic scaffold, Aci_jub_2 Primary Assembly Aci_jub_2_ph1_scaffold29, whole genome shotgun sequence	Acinonyx jubatus (cheetah)
104		KE721680.1	173.10	full	4,930,099	4,929,919	KE721680.1 Panthera tigris altaica isolate TaeGuk unplaced genomic scaffold scaffold1470, whole genome shotgun sequence	Panthera tigris altaica (Amur tiger)
105		VOAJ01003308.1	172.80	full	2,496,468	2,496,289	VOAJ01003308.1 Crocuta crocuta isolate KB4526 scaffold14, whole genome shotgun sequence	Crocuta crocuta (spotted hyena)
106		JACASF010000007.1	172.70	full	30,658,859	30,658,669	JACASF010000007.1 Molossus molossus isolate mMolMol1 scaffold_m16_p_7, whole genome shotgun sequence	Molossus molossus (Pallas's mastiff bat)
107		NW_020339852.1	171.00	full	29,865,632	29,865,812	NW_020339852.1 Puma concolor isolate SC36_Marlon unplaced genomic scaffold, PumCon1.0 scaffold_784, whole genome shotgun sequence	Puma concolor (puma)
108		CM001379.3	170.60	full	101,720,894	101,721,074	Felis catus isolate Cinnamon breed Abyssinian chromosome A2, whole genome shotgun sequence.	Felis catus (domestic cat)
109		CM016633.2	168.80	full	26,275,545	26,275,722	CM016633.2 Camelus dromedarius isolate Drom800 breed African chromosome 7, whole genome shotgun sequence	Camelus dromedarius (Arabian camel)
110		KB017833.1	168.80	full	128,930	129,107	Camelus ferus unplaced genomic scaffold scaffold1702, whole genome shotgun sequence.	Camelus ferus (Wild Bactrian camel)
111		NW_011511141.1	168.80	full	5,262,012	5,261,835	NW_011511141.1 Camelus bactrianus breed Alxa unplaced genomic scaffold, Ca_bactrianus_MBC_1.0 scaffold152, whole genome shotgun sequence	Camelus bactrianus (Bactrian camel)
112		NW_018337765.1	168.30	full	459,209	459,030	NW_018337765.1 Odocoileus virginianus texanus isolate animal Pink-7 unplaced genomic scaffold, Ovir.te_1.0 scaffold443, whole genome shotgun sequence	Odocoileus virginianus texanus
113		NW_021964167.1	168.10	full	5,305,846	5,305,669	NW_021964167.1 Vicugna pacos isolate Carlotta (AHFN-0088) chromosome 7 unlocalized genomic scaffold, VicPac3.1 ScfyRBE_8475;HRSCAF=10155, whole genome shotgun sequence	Vicugna pacos (alpaca)
114		CAAGRJ010026727.1	165.50	full	208,280	208,100	CAAGRJ010026727.1 Lynx pardinus genome assembly, contig: lp23s00207, whole genome shotgun sequence	Lynx pardinus (Spanish lynx)
115		CM017330.2	165.50	full	99,453,871	99,454,051	CM017330.2 Lynx canadensis isolate LIC74 chromosome A2, whole genome shotgun sequence	Lynx canadensis (Canada lynx)
116		NW_006408528.1	164.40	full	9,951,026	9,950,847	NW_006408528.1 Chrysochloris asiatica unplaced genomic scaffold, ChrAsi1.0 scaffold00010, whole genome shotgun sequence	Chrysochloris asiatica
117		PVHU021072348.1	161.90	full	4,477,358	4,477,179	PVHU021072348.1 Moschus moschiferus isolate BS20 Scw3uUT_1114135;HRSCAF=1217656_0, whole genome shotgun sequence	Moschus moschiferus (Siberian musk deer)
118		NW_006921650.1	161.00	full	336,492	336,316	NW_006921650.1 Orycteropus afer afer isolate SDZICR_OR568_19922 unplaced genomic scaffold, OryAfe1.0 scaffold00063, whole genome shotgun sequence	Orycteropus afer afer
119		CM018483.1	160.80	full	12,906,745	12,906,924	CM018483.1 Muntiacus reevesi isolate UCam_UCB_Mr chromosome 6, whole genome shotgun sequence	Muntiacus reevesi (Chinese muntjac)
120		CM008171.2	160.10	full	14,350,413	14,350,592	CM008171.2 Bos taurus isolate L1 Dominette 01449 registration number 42190680 breed Hereford chromosome 4, whole genome shotgun sequence	Bos taurus (cattle)
121		CM011777.1	160.10	full	105,460,068	105,459,889	CM011777.1 Bos indicus x Bos taurus breed Angus x Brahman F1 hybrid chromosome 4, whole genome shotgun sequence	Bos indicus x Bos taurus (hybrid cattle)
122		CM016693.1	160.10	full	115,208,917	115,208,738	CM016693.1 Bos grunniens isolate yakHY00 ecotype maiwa chromosome 4, whole genome shotgun sequence	Bos grunniens (domestic yak)
123		JH880300.1	160.10	full	709,210	709,031	JH880300.1 Bos grunniens mutus unplaced genomic scaffold scaffold40_1, whole genome shotgun sequence	Bos grunniens mutus
124		NW_011494706.1	160.10	full	2,603,879	2,603,700	NW_011494706.1 Bison bison bison isolate TAMUID 2011002044 unplaced genomic scaffold, Bison_UMD1.0 scf7180017864134, whole genome shotgun sequence	Bison bison bison (north american plains bison)
125		NC_032653.1	159.90	full	14,569,377	14,569,556	NC_032653.1 Bos indicus isolate QUIL7308 breed Nelore chromosome 4, Bos_indicus_1.0, whole genome shotgun sequence	Bos indicus
126		CM001585.2	157.30	full	14,216,393	14,216,572	Ovis aries breed Texel chromosome 4, whole genome shotgun sequence.	Ovis aries (sheep)
127		CM021209.1	156.60	full	12,958,226	12,958,404	CM021209.1 Cervus hanglu yarkandensis isolate CEY-2017 chromosome 18, whole genome shotgun sequence	Cervus elaphus yarkandensis
128		CM004565.1	148.70	full	106,323,309	106,323,130	CM004565.1 Capra hircus breed San Clemente chromosome 4, whole genome shotgun sequence	Capra hircus (goat)
129		NW_018344032.1	103.10	full	1,329,018	1,329,195	NW_018344032.1 Phascolarctos cinereus isolate Bilbo 61053 unplaced genomic scaffold, phaCin_unsw_v4.1 phaCin_unsw_v4.1.fa.scaf00081, whole genome shotgun sequence	Phascolarctos cinereus (koala)
130		UNPS02006874.1	97.80	full	11,166,600	11,166,777	UNPS02006874.1 Vombatus ursinus genome assembly, contig: WM1_genome_scaffold6874, whole genome shotgun sequence	Vombatus ursinus (common wombat)

There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.

Formatting options

You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Download

Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

In this page you can view static images showing the secondary structure of this family using a variety of colouring schemes:

Conservation (cons): this plot colours each character by how well conserved it is. A site with 100% sequence conservation is coloured red, 0% is violet.

Covariation (cov): this plot colours each base-pair according to how much the corresponding nucleotides are co-varying. A base-pair position at which every pair of nucleotides is co-variant with respect to every other pair in the alignment gets a score of 2 and is coloured red. Conversely, a base-pair position at every pair is anti-co-variant with respect to every other pair (e.g. lots of mutations to non-canonical pairs) gets a score of -2 and is coloured violet. Further information on this metric can be found in this document.

Sequence entropy (ent): this plot colours each character by how under- or over-represented the residues at the site are. Sites where one or more nucleotides are over-represented while the other nucleotides are either non-existent or near the background frequencies, receive positive scores; sites where all the nucleotides are under-represented receive negative scores. Further information on this metric can be found in this document.

Fraction of canonical basepairs (fcbp): this plot colours each base-pair by the percentage of canonical basepairs (A:U, C:G, G:U) which are found in the corresponding position in the alignment. A pair of sites with 100% canonical pairs is coloured red, a site with 0% is violet.

Maximum parse of the covariance model (maxcm): this plot takes the covariance model for the family and generates the sequence with the maximum possible score for that model. Each character is coloured by how many bits it contributes to the total score.

Sequence: for most of the above cases, the representative sequence used for the backbone is the most informative sequence (MIS). Any residue that has a higher frequency than than the background frequency is projected into the IUPAC redundancy codes.

Normal: this plot simply colours each stem loop

R-chie (rchie): arc diagrams showing secondary structure, calculated using the R-chie package. The consensus secondary structure is visualized as arc diagrams on top of each diagram, where a basepair in an arc, connect two columns of the block of sequences below. The block of sequences below represent the multiple sequence alignment of the Rfam seed, where each sequence is a horizontal strip. Sequences in the alignments are ordered so sequences that best fit the structure are on top, and those that do not fit as well are towards the bottom. For seed alignments for over 500 sequences, 500 random sequences were chosen. Rfam entries without sturcture have a blank plot. Colour information can be found on the R-chie FAQ.

You can also view the secondary structure in the VARNA applet. The applet is shown in a separate pop-up window.

Acknowledgements

The bulk of the code for generating these graphics was kindly supplied by Andreas Gruber and Ivo Hofacker. The statistics were implemented by Rfam.

The VARNA applet is developed by Yann Ponty et al:

The R-chie arc diagrams were calculated using R-chie:

These trees were generated using either a maximum likelihood approach or neighbour-joining. If the number of sequences in the alignment was less than or equal to 64 then the maximum likelihood approach of Rivas and Eddy was used [1]. For families with more than 64 sequences in the alignment the neighbour-joining approach with F84 distances as implemented in phylip was used [2].

Note: You can also download the data file for the seed tree.

We do not have tree information for this family. This is most likely due to the size of the family and the number of species covered. For very large families it is too computationally expensive to calculate trees and the resulting tree images would be too large to display in a browser.

There are 1 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order	Motif Accession	Motif Description	Number of Hits	Fraction of Hits	Sum of Bits	Image
7	RM00004	CRC binding motif	7	0.467	63.0