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Table view (101 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		S81809.1	N/A	seed	991	1,486	basic fibroblast growth factor {5' region, exon 1} [human, Genomic, 1701 nt].	Homo sapiens (human)
1		X04431.1	N/A	seed	477	973	Homo sapiens FGF gene, exon 1	Homo sapiens (human)
2		AC021205.6	N/A	seed	16,596	17,093	Homo sapiens BAC clone RP11-170N16 from 4, complete sequence.	Homo sapiens (human)
3		AAFC03058056.1	N/A	seed	47,679	47,194	Bos taurus Ctg86.CH240-409D14, whole genome shotgun sequence.	Bos taurus (cattle)
4		AC157217.2	N/A	seed	147,923	147,426	Pan troglodytes BAC clone CH251-305B5 from chromosome unknown, complete sequence.	Pan troglodytes (chimpanzee)
5		AAGV020630258.1	N/A	seed	3,728	3,245	Dasypus novemcinctus cont2.630257, whole genome shotgun sequence.	Dasypus novemcinctus (nine-banded armadillo)
0		CM000318.3	530.50	full	125,730,569	125,731,066	Pan troglodytes isolate Yerkes chimp pedigree #C0471 (Clint) chromosome 4, whole genome shotgun sequence.	Pan troglodytes (chimpanzee)
1		CM000666.2	528.20	full	122,826,680	122,827,177	Homo sapiens chromosome 4, GRCh38 reference primary assembly.	Homo sapiens (human)
2		CM009266.2	512.90	full	121,374,287	121,374,784	CM009266.2 Pongo abelii isolate Susie chromosome 4, whole genome shotgun sequence	Pongo abelii (Sumatran orangutan)
3		CM001653.1	509.00	full	33,621,896	33,621,399	Nomascus leucogenys chromosome 7b, whole genome shotgun sequence.	Nomascus leucogenys (Northern white-cheeked gibbon)
4		CM018182.1	485.50	full	66,686,666	66,686,169	CM018182.1 Papio anubis isolate 15944 chromosome 3, whole genome shotgun sequence	Papio anubis (Olive baboon)
5		CM009954.1	485.50	full	119,894,301	119,894,798	CM009954.1 Theropithecus gelada isolate Dixy chromosome 5, whole genome shotgun sequence	Theropithecus gelada (gelada baboon)
6		KQ010640.1	474.20	full	4,619,386	4,618,889	KQ010640.1 Cercocebus atys isolate FAK unplaced genomic scaffold Scaffold208, whole genome shotgun sequence	Cercocebus atys (sooty mangabey)
7		CM014340.1	473.90	full	120,667,276	120,667,773	CM014340.1 Macaca mulatta isolate AG07107 chromosome 5, whole genome shotgun sequence	Macaca mulatta (Rhesus monkey)
8		CM021943.1	463.50	full	119,878,583	119,879,078	CM021943.1 Macaca fascicularis isolate cy0333 breed Mauritian cynomolgus macaque chromosome 5, whole genome shotgun sequence	Macaca fascicularis (crab-eating macaque)
9		CM001947.1	459.00	full	70,089,796	70,090,293	Chlorocebus sabaeus isolate 1994-021 chromosome 7, whole genome shotgun sequence.	Chlorocebus sabaeus
10		CM019242.1	455.40	full	66,597,109	66,596,603	CM019242.1 Piliocolobus tephrosceles isolate RC106 chromosome 3, whole genome shotgun sequence	Piliocolobus tephrosceles (Ugandan red Colobus)
11		KQ004939.1	452.80	full	14,686,483	14,685,986	KQ004939.1 Macaca nemestrina isolate M95218 unplaced genomic scaffold Scaffold13, whole genome shotgun sequence	Macaca nemestrina (pig-tailed macaque)
12		CM021917.1	429.10	full	70,890,542	70,890,043	CM021917.1 Callithrix jacchus isolate mCalJac1 chromosome 3, whole genome shotgun sequence	Callithrix jacchus (white-tufted-ear marmoset)
13		KV389479.1	427.40	full	139,950	139,451	KV389479.1 Cebus capucinus imitator isolate Cc_AM_T3 unplaced genomic scaffold Scaffold53, whole genome shotgun sequence	Cebus imitator (Panamanian white-faced capuchin)
14		NW_022436967.1	425.50	full	16,215,448	16,214,949	NW_022436967.1 Sapajus apella isolate SASKATOON/1434 unplaced genomic scaffold, GSC_monkey_1.0 scaffold27, whole genome shotgun sequence	Cebus apella (Tufted capuchin)
15		KZ204805.1	387.60	full	5,838,897	5,839,401	KZ204805.1 Aotus nancymaae isolate 86115 unplaced genomic scaffold Scaffold53, whole genome shotgun sequence	Aotus nancymaae (Ma's night monkey)
16		CM003387.1	366.20	full	126,149,717	126,150,131	CM003387.1 Pan paniscus isolate Ulindi chromosome 4, whole genome shotgun sequence	Pan paniscus (pygmy chimpanzee)
17		CM004578.1	350.40	full	36,227,245	36,227,739	CM004578.1 Capra hircus breed San Clemente chromosome 17, whole genome shotgun sequence	Capra hircus (goat)
18		CM011790.1	349.50	full	34,570,396	34,569,911	CM011790.1 Bos indicus x Bos taurus breed Angus x Brahman F1 hybrid chromosome 17, whole genome shotgun sequence	Bos indicus x Bos taurus (hybrid cattle)
19		CM008184.2	344.80	full	34,861,229	34,860,744	CM008184.2 Bos taurus isolate L1 Dominette 01449 registration number 42190680 breed Hereford chromosome 17, whole genome shotgun sequence	Bos taurus (cattle)
20		MCGX01012098.1	344.40	full	1,320,665	1,321,343	MCGX01012098.1 Rhinopithecus bieti isolate Rb0 scaffold_33326, whole genome shotgun sequence	Rhinopithecus bieti (Black snub-nosed monkey)
21		NC_047038.1	341.40	full	18,713,646	18,713,150	NC_047038.1 Tursiops truncatus isolate mTurTru1 chromosome 5, mTurTru1.mat.Y, whole genome shotgun sequence	Tursiops truncatus (bottlenosed dolphin)
22		NW_024423453.1	341.30	full	16,303,787	16,304,285	NW_024423453.1 Ursus maritimus isolate PB19 unplaced genomic scaffold, ASM1731132v1 scaffold_11, whole genome shotgun sequence	Ursus maritimus (polar bear)
23		CM016705.1	332.70	full	38,298,658	38,298,176	CM016705.1 Bos grunniens isolate yakHY00 ecotype maiwa chromosome 16, whole genome shotgun sequence	Bos grunniens (domestic yak)
24		NW_019154087.1	330.40	full	9,134,744	9,134,248	NW_019154087.1 Enhydra lutris kenyoni isolate GAN:26980312 unplaced genomic scaffold, ASM228890v2 scaffoldscaffold3, whole genome shotgun sequence	Enhydra lutris kenyoni
25		CM009149.1	329.20	full	105,690,833	105,690,350	CM009149.1 Equus caballus isolate Twilight breed thoroughbred chromosome 2, whole genome shotgun sequence	Equus caballus (horse)
26		NW_025421456.1	328.30	full	3,208,043	3,208,539	NW_025421456.1 Mustela putorius furo isolate JIRA1106 unplaced genomic scaffold, ASM1176430v1.1 tig00000721_pilon_pilon_pilon, whole genome shotgun sequence	Mustela putorius furo (domestic ferret)
27		CM017332.2	326.50	full	101,981,691	101,981,195	CM017332.2 Lynx canadensis isolate LIC74 chromosome B1, whole genome shotgun sequence	Lynx canadensis (Canada lynx)
28		NW_020834726.1	326.50	full	102,314,315	102,314,811	NW_020834726.1 Acinonyx jubatus isolate Rico unplaced genomic scaffold, Aci_jub_2 Primary Assembly Aci_jub_2_ph1_scaffold0, whole genome shotgun sequence	Acinonyx jubatus (cheetah)
29		NW_006798658.1	325.40	full	133,598	134,094	NW_006798658.1 Lipotes vexillifer unplaced genomic scaffold, Lipotes_vexillifer_v1 scaffold1276, whole genome shotgun sequence	Lipotes vexillifer (Yangtze River dolphin)
30		CM027692.2	324.00	full	56,929,721	56,929,237	CM027692.2 Equus asinus breed Dezhou chromosome 3, whole genome shotgun sequence	Equus asinus (ass)
31		CM018160.1	322.70	full	18,916,110	18,915,614	CM018160.1 Phocoena sinus isolate mPhoSin1 chromosome 5, whole genome shotgun sequence	Phocoena sinus (vaquita)
32		NC_041220.1	322.20	full	126,468,454	126,468,948	NC_041220.1 Physeter catodon isolate SW-GA chromosome 7, ASM283717v5, whole genome shotgun sequence	Physeter catodon (sperm whale)
33		NW_020312855.1	322.00	full	9,509,198	9,509,684	NW_020312855.1 Callorhinus ursinus isolate GAN/ISIS: 27379988/994484 unplaced genomic scaffold, ASM326570v1 scaffold113, whole genome shotgun sequence	Callorhinus ursinus (northern fur seal)
34		CM001381.3	321.70	full	103,712,613	103,712,118	Felis catus isolate Cinnamon breed Abyssinian chromosome B1, whole genome shotgun sequence.	Felis catus (domestic cat)
35		PVHT020000256.1	314.70	full	7,823,477	7,823,979	PVHT020000256.1 Catagonus wagneri isolate BS18 Sc2sB16_220;HRSCAF=33664_3, whole genome shotgun sequence	Catagonus wagneri (Chacoan peccary)
36		KQ022881.1	314.60	full	2,318,006	2,318,484	KQ022881.1 Propithecus coquereli isolate 6110/MARCELLA unplaced genomic scaffold Scaffold323, whole genome shotgun sequence	Propithecus coquereli (Coquerel's sifaka)
37		CM018464.1	312.90	full	99,677,981	99,677,484	CM018464.1 Panthera leo isolate Brooke chromosome B2, whole genome shotgun sequence	Panthera leo (lion)
38		NW_004450408.1	311.60	full	240,719	240,233	NW_004450408.1 Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold, Oros_1.0 Scaffold145, whole genome shotgun sequence	Odobenus rosmarus divergens (Pacific walrus)
39		NC_045789.1	310.40	full	121,686,228	121,686,729	NC_045789.1 Balaenoptera musculus isolate JJ_BM4_2016_0621 chromosome 5, mBalMus1.pri.v3, whole genome shotgun sequence	Balaenoptera musculus (Blue whale)
40		NW_022098069.1	304.30	full	68,892,321	68,892,807	NW_022098069.1 Delphinapterus leucas isolate GAN/ISIS: 26980492/103006 unplaced genomic scaffold, ASM228892v3 scaffoldscaffold78, whole genome shotgun sequence	Delphinapterus leucas (beluga whale)
41		JACDTQ010001259.1	290.00	full	2,457,967	2,458,452	JACDTQ010001259.1 Diceros bicornis minor isolate SBR-YM ScS9zPn_1259, whole genome shotgun sequence	Diceros bicornis minor
42		RWIC01000113.1	288.80	full	1,209,748	1,210,217	RWIC01000113.1 Monodon monoceros isolate MVW Scaffold112, whole genome shotgun sequence	Monodon monoceros (narwhal)
43		CM018490.1	284.30	full	35,933,324	35,933,800	CM018490.1 Muntiacus reevesi isolate UCam_UCB_Mr chromosome 20, whole genome shotgun sequence	Muntiacus reevesi (Chinese muntjac)
44		LZNR01001827.1	284.10	full	189,329	188,826	LZNR01001827.1 Ursus americanus isolate MABB319796 Contig1830, whole genome shotgun sequence	Ursus americanus (American black bear)
45		KN295356.1	278.80	full	382,209	382,633	KN295356.1 Rhinopithecus roxellana isolate Xiao Hai unplaced genomic scaffold ENSRROG013391, whole genome shotgun sequence	Rhinopithecus roxellana (golden snub-nosed monkey)
46		CM000819.5	272.60	full	101,343,917	101,343,431	CM000819.5 Sus scrofa isolate TJ Tabasco breed Duroc chromosome 8, whole genome shotgun sequence	Sus scrofa (pig)
47		FR853097.2	267.20	full	134,793,295	134,793,812	Gorilla gorilla gorilla genomic chromosome, chr4, whole genome shotgun sequence	Gorilla gorilla gorilla (western lowland gorilla)
48		CM016628.2	266.70	full	35,045,859	35,045,367	CM016628.2 Camelus dromedarius isolate Drom800 breed African chromosome 2, whole genome shotgun sequence	Camelus dromedarius (Arabian camel)
49		NW_020339223.1	261.10	full	105,786,270	105,785,763	NW_020339223.1 Puma concolor isolate SC36_Marlon unplaced genomic scaffold, PumCon1.0 scaffold_2176, whole genome shotgun sequence	Puma concolor (puma)
50		PVHU021072365.1	256.70	full	38,100,140	38,100,635	PVHU021072365.1 Moschus moschiferus isolate BS20 Scw3uUT_1114142;HRSCAF=1217663_0, whole genome shotgun sequence	Moschus moschiferus (Siberian musk deer)
51		CM014243.1	253.60	full	5,339,247	5,339,734	CM014243.1 Rhinolophus ferrumequinum isolate MPI-CBG mRhiFer1 chromosome 18, whole genome shotgun sequence	Rhinolophus ferrumequinum (greater horseshoe bat)
52		NC_058404.1	240.80	full	100,700,681	100,699,809	NC_058404.1 Neomonachus schauinslandi chromosome 2, ASM220157v2, whole genome shotgun sequence	Monachus schauinslandi (Hawaiian monk seal)
53		CM007674.1	240.30	full	73,818,127	73,817,655	CM007674.1 Microcebus murinus isolate mixed chromosome 14, whole genome shotgun sequence	Microcebus murinus (gray mouse lemur)
54		NW_018336922.1	236.60	full	74,852	74,416	NW_018336922.1 Odocoileus virginianus texanus isolate animal Pink-7 unplaced genomic scaffold, Ovir.te_1.0 scaffold3671, whole genome shotgun sequence	Odocoileus virginianus texanus
55		CM022823.1	234.90	full	128,624,987	128,624,488	CM022823.1 Ailuropoda melanoleuca isolate Jingjing chromosome 5, whole genome shotgun sequence	Ailuropoda melanoleuca (giant panda)
56		NTJE010803330.1	228.40	full	350	1	NTJE010803330.1 Eschrichtius robustus isolate AM-GW-M-EMB-4M-20130531 contig_978648, whole genome shotgun sequence	Eschrichtius robustus (grey whale)
57		KN981380.1	208.30	full	1,534,456	1,534,702	KN981380.1 Colobus angolensis palliatus isolate OR3802 unplaced genomic scaffold Scaffold280, whole genome shotgun sequence	Colobus angolensis palliatus
58		JAULJE010000005.1	205.70	full	69,348,321	69,347,840	JAULJE010000005.1 Eptesicus nilssonii isolate BLF_Eptnil Scaffold_5, whole genome shotgun sequence	Eptesicus nilssoni (northern bat)
59		CM001598.2	201.30	full	34,536,234	34,535,762	Ovis aries breed Texel chromosome 17, whole genome shotgun sequence.	Ovis aries (sheep)
60		CM018163.1	187.60	full	30,358,340	30,358,811	CM018163.1 Phocoena sinus isolate mPhoSin1 chromosome 8, whole genome shotgun sequence	Phocoena sinus (vaquita)
61		NW_006921749.1	185.90	full	2,332,080	2,332,496	NW_006921749.1 Orycteropus afer afer isolate SDZICR_OR568_19922 unplaced genomic scaffold, OryAfe1.0 scaffold00162, whole genome shotgun sequence	Orycteropus afer afer
62		JABWUV010000006.1	183.10	full	39,548,008	39,548,481	JABWUV010000006.1 Myotis myotis isolate mMyoMyo1 scaffold_m19_p_6, whole genome shotgun sequence	Myotis myotis
63		NW_004444110.1	176.90	full	1,646,729	1,647,255	NW_004444110.1 Trichechus manatus latirostris isolate Lorelei unplaced genomic scaffold, TriManLat1.0 scaffold00174, whole genome shotgun sequence	Trichechus manatus latirostris
64		NW_020173215.1	174.90	full	1,966,170	1,966,457	NW_020173215.1 Neophocaena asiaeorientalis asiaeorientalis breed wild unplaced genomic scaffold, Neophocaena_asiaeorientalis_V1 scaffold65, whole genome shotgun sequence	Neophocaena asiaeorientalis asiaeorientalis (yangtze finless porpoise)
65		CM016971.1	174.80	full	95,767,418	95,766,864	CM016971.1 Suricata suricatta isolate VVHF042 chromosome 1, whole genome shotgun sequence	Suricata suricatta (meerkat)
66		CM008012.1	170.90	full	50,394,534	50,394,820	CM008012.1 Cervus elaphus hippelaphus isolate Hungarian chromosome 5, whole genome shotgun sequence	Cervus elaphus hippelaphus
67		NC_032666.1	170.00	full	36,953,578	36,954,063	NC_032666.1 Bos indicus isolate QUIL7308 breed Nelore chromosome 17, Bos_indicus_1.0, whole genome shotgun sequence	Bos indicus
68		CM021196.1	163.90	full	36,134,273	36,134,522	CM021196.1 Cervus hanglu yarkandensis isolate CEY-2017 chromosome 5, whole genome shotgun sequence	Cervus elaphus yarkandensis
69		GL010041.1	161.80	full	34,379,555	34,379,846	Loxodonta africana unplaced genomic scaffold scaffold_14, whole genome shotgun sequence.	Loxodonta africana (African savanna elephant)
70		NW_006383976.1	157.50	full	116,339	116,053	NW_006383976.1 Leptonychotes weddellii isolate WS11-02 unplaced genomic scaffold, LepWed1.0 scaffold00936, whole genome shotgun sequence	Leptonychotes weddellii (Weddell seal)
71		QWLN02000227.1	155.60	full	225	1	QWLN02000227.1 Sousa chinensis isolate MY-2018 scaffold16681.1, whole genome shotgun sequence	Sousa chinensis (Indo-pacific humpbacked dolphin)
72		NC_040910.2	134.20	full	3,052,724	3,053,170	NC_040910.2 Phyllostomus discolor isolate MPI-MPIP mPhyDis1 chromosome 8, mPhyDis1.pri.v3, whole genome shotgun sequence	Phyllostomus discolor (pale spear-nosed bat)
73		JACASF010000004.1	122.50	full	124,311,972	124,311,519	JACASF010000004.1 Molossus molossus isolate mMolMol1 scaffold_m16_p_4, whole genome shotgun sequence	Molossus molossus (Pallas's mastiff bat)
74		CM025118.1	113.90	full	17,578,933	17,578,301	CM025118.1 Canis lupus familiaris isolate SID07034 breed Labrador retriever chromosome 19, whole genome shotgun sequence	Canis lupus familiaris (dog)
75		CM025475.1	107.80	full	17,751,099	17,750,462	CM025475.1 Canis lupus dingo isolate Sandy chromosome 19, whole genome shotgun sequence	Canis lupus dingo (dingo)
76		NW_020184876.1	94.50	full	317	1	NW_020184876.1 Neophocaena asiaeorientalis asiaeorientalis breed wild unplaced genomic scaffold, Neophocaena_asiaeorientalis_V1 C48716377, whole genome shotgun sequence	Neophocaena asiaeorientalis asiaeorientalis (yangtze finless porpoise)
77		MPIZ01000396.1	81.70	full	875,286	875,127	MPIZ01000396.1 Prolemur simus strain KIAN8.4 scaffold396, whole genome shotgun sequence	Prolemur simus (greater bamboo lemur)
78		CYRY02004718.1	66.70	full	98	1	CYRY02004718.1 Gulo gulo genome assembly, contig: scaffold14243, whole genome shotgun sequence	Gulo gulo (wolverine)
79		NW_006939426.1	64.90	full	1	104	NW_006939426.1 Orycteropus afer afer isolate SDZICR_OR568_19922 unplaced genomic scaffold, OryAfe1.0 scaffold17839, whole genome shotgun sequence	Orycteropus afer afer
80		QWLN02000859.1	59.40	full	3,108,870	3,109,159	QWLN02000859.1 Sousa chinensis isolate MY-2018 scaffold24.1, whole genome shotgun sequence	Sousa chinensis (Indo-pacific humpbacked dolphin)
81		NW_017869625.1	59.10	full	755,716	756,082	NW_017869625.1 Castor canadensis isolate Ward unplaced genomic scaffold, C.can genome v1.0 scaffold_298, whole genome shotgun sequence	Castor canadensis (American beaver)
82		JACAGB010000008.1	58.80	full	35,031,141	35,031,558	JACAGB010000008.1 Pipistrellus kuhlii isolate mPipKuh1 scaffold_m20_p_8, whole genome shotgun sequence	Pipistrellus kuhlii (Kuhl's pipistrelle)
83		CAJHUB010000661.1	57.60	full	2,377,177	2,377,312	CAJHUB010000661.1 Nyctereutes procyonoides isolate TBG_1078 genome assembly, contig: Nypro694, whole genome shotgun sequence	Nyctereutes procyonoides (raccoon dog)
84		NTJE010681848.1	48.70	full	253	1	NTJE010681848.1 Eschrichtius robustus isolate AM-GW-M-EMB-4M-20130531 contig_811424, whole genome shotgun sequence	Eschrichtius robustus (grey whale)
85		NW_011512512.1	42.80	full	2,735,542	2,735,645	NW_011512512.1 Camelus bactrianus breed Alxa unplaced genomic scaffold, Ca_bactrianus_MBC_1.0 scaffold296, whole genome shotgun sequence	Camelus bactrianus (Bactrian camel)
86		LZNR01069930.1	42.60	full	1	52	LZNR01069930.1 Ursus americanus isolate MABB319796 Contig71044, whole genome shotgun sequence	Ursus americanus (American black bear)
87		CM016657.2	42.30	full	13,872,506	13,872,406	CM016657.2 Camelus dromedarius isolate Drom800 breed African chromosome 31, whole genome shotgun sequence	Camelus dromedarius (Arabian camel)
88		CAJHUB010000661.1	41.10	full	2,377,750	2,377,849	CAJHUB010000661.1 Nyctereutes procyonoides isolate TBG_1078 genome assembly, contig: Nypro694, whole genome shotgun sequence	Nyctereutes procyonoides (raccoon dog)
89		NW_006386812.1	38.50	full	1	48	NW_006386812.1 Leptonychotes weddellii isolate WS11-02 unplaced genomic scaffold, LepWed1.0 scaffold03772, whole genome shotgun sequence	Leptonychotes weddellii (Weddell seal)
90		SGJD01005432.1	37.20	full	34,040	34,143	SGJD01005432.1 Balaenoptera physalus isolate FinWhale-01 scaffold7165, whole genome shotgun sequence	Balaenoptera physalus (Fin whale)
91		NC_047036.1	37.00	full	86,227,831	86,227,945	NC_047036.1 Tursiops truncatus isolate mTurTru1 chromosome 3, mTurTru1.mat.Y, whole genome shotgun sequence	Tursiops truncatus (bottlenosed dolphin)
92		QWLN02004901.1	37.00	full	1,515,637	1,515,751	QWLN02004901.1 Sousa chinensis isolate MY-2018 scaffold252.1, whole genome shotgun sequence	Sousa chinensis (Indo-pacific humpbacked dolphin)
93		CYRY02045920.1	36.70	full	1	53	CYRY02045920.1 Gulo gulo genome assembly, contig: scaffold8650, whole genome shotgun sequence	Gulo gulo (wolverine)
94		JH174071.1	35.80	full	1,260,134	1,260,263	JH174071.1 Heterocephalus glaber unplaced genomic scaffold scaffold69, whole genome shotgun sequence	Heterocephalus glaber (naked mole-rat)

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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 4 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	RM00005	CsrA/RsmA binding motif	5	0.833	47.7
7	RM00008	GNRA tetraloop	5	0.833	45.6
7	RM00010	Kink turn 1, 3' bulge	2	0.333	38.3
7	RM00030	U-turn motif	4	0.667	41.9