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You can either download the motif alignment or view it directly in your browser window. More...

Formatting options

You can view or download motif 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".

Alignment format:	Stockholm Pfam FASTA (gapped) FASTA (UNgapped)
Download/view:	Download View

There are 46 PDB entires which have been used to build the motif model.

The table of results below may be sorted by clicking on the column titles, or restored to the original order here.

Original order	PDB ID	PDB chain ID	PDB Residues
2	3OWI	A	41 - 61
2	2CDM	B	2 - 17
2	1C04		13 - 18
2	1G1X		588 - 651
2	1GRZ		149 - 154
2	1HMH		104 - 114
2	1HQ1		153 - 158
2	1HR2		149 - 154
2	1J5E		1012 - 1017
2	1JID		146 - 151
2	1KH6		28 - 33
2	1KXK		33 - 38
2	1L9A		146 - 151
2	1LNG		208 - 213
2	1M5O		74 - 79
2	1MFQ		197 - 202
2	1MME		154 - 164
2	1MZP		25 - 30
2	1NBS		204 - 209
2	1NYI		111 - 116
2	1Q96		13 - 18
2	1Q9A		2658 - 2663
2	1QZW		201 - 206
2	1RLG		9 - 14
2	1S72		1054 - 1060
2	1U6B		23 - 28
2	1U9S		204 - 209
2	1UN6		82 - 94
2	1X8W		149 - 154
2	1Y0Q		101 - 106
2	1Y69		2353 - 2358
2	2A2E		178 - 183
2	2AVY		1012 - 1017
2	2AW4		1222 - 1227
2	2BTE		46 - 51
2	2EZ6		11 - 16
2	2GIS		49 - 54
2	2J01		1222 - 1227
2	2NZ4		108 - 113
2	2OIU		10 - 15
2	2PXL		153 - 158
2	2R8S		149 - 154
2	2V3C		208 - 213
2	2Z75		113 - 118
2	430D		13 - 18
2	488D		154 - 164

There are 564 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. 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	Family Accession	Family Description	Number of Hits	Fraction of Hits	Sum of Bits	Image
3	RF00001	5S ribosomal RNA	279	0.392	2678.1
3	RF00004	U2 spliceosomal RNA	18	0.087	162.3
3	RF00007	U12 minor spliceosomal RNA	11	0.177	125.0
3	RF00008	Hammerhead ribozyme (type III)	8	0.094	81.7
3	RF00009	Nuclear RNase P	49	0.422	580.3
3	RF00010	Bacterial RNase P class A	453	0.989	17762.2
3	RF00011	Bacterial RNase P class B	102	0.895	2028.5
3	RF00012	Small nucleolar RNA U3	16	0.184	174.1
3	RF00013	6S / SsrS RNA	33	0.220	312.3
3	RF00014	DsrA RNA	3	0.600	24.0
3	RF00017	Metazoan signal recognition particle RNA	71	0.780	1144.2
3	RF00018	CsrB/RsmB RNA family	23	0.605	261.7
3	RF00021	Spot 42 RNA	11	0.579	103.0
3	RF00022	GcvB RNA	8	0.296	98.0
3	RF00023	transfer-messenger RNA	153	0.321	1591.1
3	RF00024	Vertebrate telomerase RNA	14	0.378	179.1
3	RF00028	Group I catalytic intron	10	0.833	178.6
3	RF00029	Group II catalytic intron	77	0.837	991.9
3	RF00030	RNase MRP	33	0.500	351.5
3	RF00040	RNase E 5' UTR element	6	1.000	59.5
3	RF00050	FMN riboswitch aptamer (RFN element)	30	0.205	312.3
3	RF00062	HgcC family RNA	5	1.000	55.8
3	RF00064	HgcG RNA (Pab40)	4	0.800	69.4
3	RF00066	U7 small nuclear RNA	3	0.061	25.3
3	RF00078	MicA sRNA	8	0.471	69.9
3	RF00079	OmrA-B family	11	0.478	124.4
3	RF00080	Manganese Mn2+ riboswitch aptamer (yybP-ykoY)	8	0.276	71.3
3	RF00082	SraG RNA	3	0.429	23.2
3	RF00083	GlmZ RNA activator of glmS mRNA	5	0.238	37.3
3	RF00084	CsrC RNA family	2	0.500	22.1
3	RF00096	U8 small nucleolar RNA	5	0.091	56.5
3	RF00099	Small nucleolar RNA SNORD22	11	0.224	91.5
3	RF00100	7SK RNA	3	0.067	29.9
3	RF00101	SraC/RyeA RNA	10	0.769	133.0
3	RF00102	VA RNA	13	0.236	102.8
3	RF00107	FinP	3	0.500	26.3
3	RF00113	Short Intergenic Abundant RNA	4	0.235	36.0
3	RF00126	ryfA RNA	8	0.889	91.3
3	RF00127	t44 RNA	13	0.167	140.7
3	RF00142	Small nucleolar RNA Z118/Z121/Z120	4	0.571	41.1
3	RF00156	Small nucleolar RNA SNORA70	13	0.302	100.6
3	RF00162	SAM riboswitch aptamer (S box leader)	86	0.188	1007.8
3	RF00166	PrrB/RsmZ RNA family	8	0.216	97.9
3	RF00168	Lysine riboswitch aptamer	18	0.383	168.1
3	RF00169	Bacterial small signal recognition particle RNA	102	0.391	850.9
3	RF00174	Cobalamin riboswitch aptamer	178	0.410	2225.7
3	RF00177	Bacterial small subunit ribosomal RNA	99	1.000	8325.7
3	RF00191	Small nucleolar RNA SNORA57	4	0.154	33.1
3	RF00199	SL2 RNA	21	0.700	224.8
3	RF00210	Aphthovirus internal ribosome entry site (IRES)	92	1.000	1166.0
3	RF00214	Retrovirus direct repeat 1 (dr1)	10	0.385	79.0
3	RF00222	Bag-1 internal ribosome entry site (IRES)	13	0.867	142.4
3	RF00223	bip internal ribosome entry site (IRES)	6	0.667	47.6
3	RF00224	FGF-2 internal ribosome entry site (IRES)	5	0.833	45.6
3	RF00226	n-myc internal ribosome entry site (IRES)	4	0.667	34.8
3	RF00229	Picornavirus internal ribosome entry site (IRES)	37	0.402	378.2
3	RF00230	T-box leader	10	0.208	98.3
3	RF00233	Tymovirus/Pomovirus/Furovirus tRNA-like 3' UTR element	3	0.103	29.1
3	RF00234	glmS glucosamine-6-phosphate activated ribozyme aptamer	11	0.611	125.7
3	RF00239	mir-124 microRNA precursor family	4	0.071	34.3
3	RF00243	traJ 5' UTR	3	0.500	22.3
3	RF00260	Hepatitis C virus (HCV) cis-acting replication element (CRE)	12	0.214	132.4
3	RF00261	L-myc internal ribosome entry site (IRES)	11	1.000	239.7
3	RF00286	Small Cajal body specific RNA 8	3	0.136	28.6
3	RF00302	Small nucleolar RNA SNORA65	2	0.143	16.4
3	RF00350	Small nucleolar RNA Z152/R70/R12/	3	0.333	26.6
3	RF00357	Small nucleolar RNA R44/J54/Z268 family	5	0.172	40.2
3	RF00368	sroB RNA	16	1.000	261.4
3	RF00369	sroC RNA	2	0.333	16.8
3	RF00371	sroE RNA	2	0.500	16.8
3	RF00373	Archaeal RNase P	59	0.843	1238.6
3	RF00379	c-di-AMP riboswitch aptamer (ydaO/yuaA leader)	26	0.245	300.0
3	RF00380	M-box riboswitch aptamer (ykoK leader)	114	0.717	1177.8
3	RF00391	RtT RNA	17	0.298	158.6
3	RF00397	Small nucleolar RNA SNORA14	3	0.167	24.7
3	RF00405	Small nucleolar RNA SNORA44	9	0.333	80.9
3	RF00408	Small nucleolar RNA SNORA1	3	0.103	26.0
3	RF00415	Small nucleolar RNA SNORA30/SNORA37 family	2	0.182	15.5
3	RF00419	Small nucleolar RNA SNORA52	2	0.095	25.4
3	RF00423	Small Cajal body specific RNA 4	2	0.083	16.4
3	RF00427	Small Cajal body specific RNA 23	4	0.222	29.9
3	RF00428	Small nucleolar RNA SNORA38	4	0.160	37.9
3	RF00431	Small nucleolar RNA SNORA55	6	0.207	55.6
3	RF00435	Repression of heat shock gene expression (ROSE) element	6	0.462	65.2
3	RF00438	Small nucleolar RNA SNORA33	4	0.143	40.1
3	RF00442	Guanidine-I riboswitch aptamer	24	0.240	297.2
3	RF00444	PrrF RNA	13	0.722	144.4
3	RF00447	Voltage-gated potassium-channel Kv1.4 IRES	2	0.333	17.9
3	RF00448	Epstein-Barr virus nuclear antigen (EBNA) IRES	2	0.333	23.4
3	RF00449	HIF-1 alpha IRES	5	0.294	50.1
3	RF00461	Vascular endothelial growth factor (VEGF) IRES A	7	1.000	110.9
3	RF00480	HIV Ribosomal frameshift signal	95	0.646	778.1
3	RF00485	Potassium channel RNA editing signal	23	0.271	218.9
3	RF00489	ctRNA	8	0.800	87.8
3	RF00490	S-element	8	0.276	83.5
3	RF00504	Glycine riboswitch aptamer	7	0.159	66.9
3	RF00506	Threonine operon leader	16	0.640	131.7
3	RF00512	Leucine operon leader	5	0.833	37.1
3	RF00514	Histidine operon leader	7	0.212	89.8
3	RF00515	PyrR binding site	10	0.244	81.0
3	RF00516	ylbH leader	2	0.667	23.5
3	RF00517	serC leader	13	0.186	112.8
3	RF00519	Makes More Granules Regulator RNA (mmgR)	35	0.402	388.2
3	RF00523	Prion pseudoknot	64	0.432	634.2
3	RF00524	R2 RNA element	2	0.133	16.6
3	RF00525	Flavivirus DB element	34	0.304	278.6
3	RF00542	Small nucleolar RNA psi28S-1192	3	0.200	28.8
3	RF00547	TrkB IRES	5	0.312	48.6
3	RF00548	U11 spliceosomal RNA	12	0.167	98.1
3	RF00549	c-sis internal ribosome entry site (IRES)	8	0.800	78.8
3	RF00552	rncO	5	0.278	55.1
3	RF00557	Ribosomal protein L10 leader	17	0.175	147.7
3	RF00558	Ribosomal protein L20 leader	17	0.395	186.2
3	RF00562	Small nucleolar RNA SNORA49	2	0.095	17.2
3	RF00564	Small Cajal body specific RNA 11	2	0.083	16.4
3	RF00567	Small nucleolar RNA SNORD17	3	0.158	24.0
3	RF00598	Small nucleolar RNA SNORA76	14	0.636	119.2
3	RF00602	Small Cajal body specific RNA 21	3	0.125	31.3
3	RF00603	Small nucleolar RNA SNORD23	5	0.333	43.2
3	RF00613	Small nucleolar RNA SNORD94	3	0.143	25.7
3	RF00618	U4atac minor spliceosomal RNA	9	0.148	76.2
3	RF00620	Hepatitis C alternative reading frame stem-loop	13	0.228	93.3
3	RF00625	Pseudomonas sRNA P11	11	0.733	186.2
3	RF00627	Pseudomonas sRNA P15	21	0.955	185.9
3	RF00628	RgsA sRNA	9	0.333	74.5
3	RF00629	Pseudomonas sRNA P24	6	0.429	66.5
3	RF00630	Pseudomonas sRNA P26	10	0.370	95.6
3	RF00634	SAM (S-adenosyl methionine) riboswitch aptamer	11	0.275	93.8
3	RF00637	microRNA mir-276	5	0.119	44.1
3	RF00639	mir-515 microRNA precursor family	4	0.100	33.9
3	RF00644	microRNA mir-27	9	0.110	73.1
3	RF00654	microRNA mir-216	4	0.070	35.6
3	RF00686	microRNA mir-338	2	0.095	20.1
3	RF00718	mir-431 microRNA precursor family	9	1.000	136.8
3	RF00742	MIR162_1 microRNA precursor family	5	0.139	51.8
3	RF00746	microRNA mir-454	4	0.235	32.1
3	RF00758	mir-346 microRNA precursor family	5	1.000	39.9
3	RF00770	microRNA mir-330	3	0.500	40.3
3	RF00779	microRNA MIR474	5	0.455	44.5
3	RF00784	microRNA mir-486	14	0.875	109.5
3	RF00957	mir-663 microRNA precursor family	4	0.333	36.4
3	RF00959	mir-612 microRNA precursor family	3	0.500	26.4
3	RF00960	microRNA mir-661	2	0.500	18.8
3	RF01008	microRNA mir-636	4	0.800	43.2
3	RF01010	microRNA mir-632	8	0.500	80.3
3	RF01016	mir-584 microRNA precursor family	2	0.125	14.7
3	RF01036	microRNA mir-567	3	0.333	24.9
3	RF01051	c-di-GMP-I riboswitch aptamer	86	0.555	955.8
3	RF01052	Arthropod 7SK RNA	6	0.316	42.4
3	RF01055	Molybdenum/Tungsten riboswitch aptamer (Moco RNA motif)	126	0.787	1315.5
3	RF01059	microRNA mir-598	3	0.125	29.0
3	RF01066	6C RNA	8	0.444	68.9
3	RF01069	purD RNA motif	8	0.381	83.9
3	RF01070	SucA RNA motif	7	0.200	66.1
3	RF01071	Ornate Large Extremophilic RNA	19	0.950	457.0
3	RF01084	Pseudoknot of tRNA-like structure	5	0.556	61.5
3	RF01116	Cyanobacterial functional RNA 1	7	0.189	69.8
3	RF01196	Small nucleolar RNA Z30a	10	1.000	125.4
3	RF01208	Small nucleolar RNA snoR99	2	0.222	14.7
3	RF01225	Small nucleolar RNA ACA64	4	0.133	32.0
3	RF01233	Small nucleolar RNA U109	3	0.115	23.6
3	RF01234	Small nucleolar RNA SNORA47	9	0.450	66.9
3	RF01252	Small nucleolar RNA snR5	2	0.182	17.2
3	RF01255	Small nucleolar RNA snR35	3	0.273	26.9
3	RF01263	Small nucleolar RNA snR191	2	0.182	23.4
3	RF01268	Small Cajal body-specific RNA 2	10	0.500	101.7
3	RF01294	Small nucleolar RNA U89	3	0.188	25.8
3	RF01295	Small Cajal body-specific RNA 7	5	0.278	40.2
3	RF01296	Small nucleolar RNA U85	5	0.238	48.4
3	RF01322	CRISPR RNA direct repeat element	4	0.571	48.4
3	RF01331	CRISPR RNA direct repeat element	6	1.000	63.0
3	RF01347	CRISPR RNA direct repeat element	3	1.000	31.5
3	RF01405	STnc490 Hfq binding RNA	67	0.882	491.2
3	RF01408	sraL Hfq binding RNA	3	0.500	22.9
3	RF01411	BsrF	3	0.273	22.8
3	RF01412	BsrG	4	0.667	45.0
3	RF01415	Flavivirus 3'UTR stem loop IV	2	0.095	16.0
3	RF01492	Listeria sRNA rli28	3	0.143	25.2
3	RF01502	Fungal signal recognition particle RNA	16	0.320	212.6
3	RF01521	caulobacter sRNA CC1840	3	1.000	48.0
3	RF01527	Caulobacter sRNA CrfA	4	2.000	35.8
3	RF01529	Cauldobacter sRNA CC3552	2	1.000	58.4
3	RF01541	Trypanosomatid snoRNA TB11Cs4H3	2	0.667	14.8
3	RF01581	Plasmodium RNA of unknown function RUF6-5	12	0.600	86.9
3	RF01610	Caenorhabditis snoRNA ceN104	2	0.400	16.5
3	RF01653	Caenorhabditis snoRNA ceN80	2	0.400	21.6
3	RF01670	Pseudomonas sRNA P17	3	1.000	25.1
3	RF01673	PhrS	3	0.231	22.9
3	RF01675	Pseudomonas sRNA CrcZ	9	0.474	85.4
3	RF01686	Acido-1 RNA	4	1.000	55.0
3	RF01687	Acido-Lenti-1 RNA	16	0.184	120.7
3	RF01691	Bacillus-plasmid RNA	5	0.161	50.8
3	RF01693	Bacteroidales-1 6S-Bacteroidales RNA suggested	3	0.073	23.2
3	RF01695	C4 antisense RNA	132	0.289	1741.0
3	RF01696	Chlorobi-1 RNA	4	0.267	38.9
3	RF01699	Clostridiales-1 RNA	94	0.485	1122.3
3	RF01700	Collinsella-1 RNA	2	0.333	22.6
3	RF01702	Cyano-2 RNA	30	0.526	288.2
3	RF01703	Dictyoglomi-1 RNA	3	0.750	55.1
3	RF01704	Glutamine-II riboswitch aptamer	61	0.097	703.5
3	RF01708	L17 ribosomal protein downstream element	9	0.173	104.2
3	RF01721	Pseudomon-groES RNA	11	0.611	143.9
3	RF01722	Pyrobac-1 RNA	3	0.375	25.3
3	RF01723	Rhizobiales-2 RNA	11	0.733	86.8
3	RF01725	SAM-I/IV (S-adenosyl methionine) riboswitch aptamer	76	0.182	878.4
3	RF01728	STAXI RNA	11	0.256	124.4
3	RF01729	Termite-flg RNA	2	0.154	14.4
3	RF01730	Termite-leu RNA	14	0.700	136.6
3	RF01731	TwoAYGGAY RNA	55	0.262	465.0
3	RF01732	MarS sRNA	4	0.129	46.5
3	RF01733	atoC RNA	5	0.625	47.9
3	RF01735	epsC RNA	3	0.100	24.8
3	RF01736	flg-Rhizobiales RNA	12	0.923	191.0
3	RF01739	Glutamine riboswitch aptamer (glnA leader)	114	0.121	1266.8
3	RF01740	gyrA RNA	4	0.222	29.6
3	RF01742	lactis-plasmid RNA	5	0.357	38.6
3	RF01745	manA RNA	99	0.600	920.7
3	RF01746	mraW RNA	7	0.156	60.0
3	RF01748	nuoG RNA	9	0.290	85.1
3	RF01750	ZMP/ZTP riboswitch aptamer (pfl RNA motif)	21	0.114	195.0
3	RF01752	psaA RNA	7	0.226	53.0
3	RF01753	psbNH RNA	7	0.179	60.2
3	RF01754	radC RNA	29	0.196	413.6
3	RF01755	rmf RNA	6	0.375	63.4
3	RF01756	rne-II RNA	5	0.312	55.0
3	RF01757	sbcD RNA	5	0.833	81.4
3	RF01758	sucA-II RNA	7	0.412	59.4
3	RF01761	wcaG RNA	12	0.111	109.8
3	RF01762	Whalefall-1 RNA	5	0.357	65.2
3	RF01766	cspA thermoregulator	6	0.400	46.8
3	RF01769	Enterobacteria greA leader	2	0.080	15.0
3	RF01772	Pseudomonas rnk leader	7	0.467	52.7
3	RF01773	Pseudomonas rpsL leader	5	0.556	43.9
3	RF01783	Mycobacterium B11	4	2.000	32.8
3	RF01793	ffh sRNA	8	0.090	62.5
3	RF01794	sok antitoxin (CssrC)	44	0.484	484.1
3	RF01796	Fumarate/nitrate reductase regulator sRNA	13	0.812	148.0
3	RF01807	GIR1 branching ribozyme	3	0.231	26.7
3	RF01808	MicX Vibrio cholerae sRNA	7	0.700	93.3
3	RF01809	SymR antitoxin	7	0.350	52.9
3	RF01811	Plasmid transferred anti-sense RNA	14	0.875	113.2
3	RF01820	RNA Staph. aureus E (RoxS)	2	0.133	19.0
3	RF01830	Salmonella enterica Typhi npcRNA 44	10	0.294	145.8
3	RF01835	ribosomal frameshift site	3	0.158	22.8
3	RF01844	SmY spliceosomal RNA	11	0.180	94.1
3	RF01846	Fungal small nucleolar RNA U3	21	0.318	295.2
3	RF01848	ACEA small nucleolar RNA U3	12	0.429	132.0
3	RF01849	Alphaproteobacteria transfer-messenger RNA	75	0.676	1655.1
3	RF01850	Betaproteobacteria transfer-messenger RNA	3	0.429	40.3
3	RF01852	Selenocysteine transfer RNA	27	0.248	283.7
3	RF01854	Bacterial large signal recognition particle RNA	29	0.315	221.5
3	RF01855	Plant signal recognition particle RNA	49	0.778	527.7
3	RF01856	Protozoan signal recognition particle RNA	9	0.500	110.6
3	RF01857	Archaeal signal recognition particle RNA	46	0.852	975.7
3	RF01859	Phenylalanine leader peptide	30	0.423	258.6
3	RF01867	caulobacter sRNA CC2171	12	0.923	227.1
3	RF01874	Myocardial infarction associated transcript exon 1	6	0.600	55.7
3	RF01877	Myocardial infarction associated transcript exon 5 conserved region 3	2	0.125	15.3
3	RF01895	microRNA mir-193	2	0.037	14.8
3	RF01909	CDKN2B antisense RNA 1 intronic convserved region	5	0.200	42.7
3	RF01946	KCNQ1 overlapping transcript 1 conserved region 1	3	0.375	25.7
3	RF01947	KCNQ1 overlapping transcript 1 conserved region 2	2	0.111	14.5
3	RF01953	SOX2 overlapping transcript exon 3	4	0.364	33.1
3	RF01955	Nuclear enriched abundant transcript 1 conserved region 1	2	0.118	19.3
3	RF01959	Archaeal small subunit ribosomal RNA	86	1.000	7662.3
3	RF01960	Eukaryotic small subunit ribosomal RNA	85	0.944	2878.5
3	RF01975	HOX antisense intergenic RNA myeloid 1 conserved region 1	6	0.429	53.5
3	RF01998	Group II catalytic intron D1-D4-1	117	0.494	1523.7
3	RF01999	Group II catalytic intron D1-D4-2	38	0.264	331.1
3	RF02001	Group II catalytic intron D1-D4-3	50	0.123	402.9
3	RF02003	Group II catalytic intron D1-D4-4	46	0.511	534.3
3	RF02004	Group II catalytic intron D1-D4-5	60	0.432	733.9
3	RF02005	Group II catalytic intron D1-D4-6	149	0.856	1920.6
3	RF02012	Group II catalytic intron D1-D4-7	177	0.725	2436.2
3	RF02025	microRNA mir-3017	12	0.333	104.6
3	RF02027	microRNA MIR2907	14	0.269	127.3
3	RF02030	tp2	4	0.167	30.2
3	RF02031	tpke11	14	0.500	182.7
3	RF02032	Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA	24	0.686	402.2
3	RF02033	HNH endonuclease-associated RNA and ORF (HEARO) RNA	96	0.691	1127.6
3	RF02035	IMES-2 RNA motif	244	0.762	2597.7
3	RF02037	IMES-4 RNA motif	23	0.767	217.4
3	RF02041	HOXA transcript at the distal tip, conserved region 2	5	0.200	52.3
3	RF02042	HOXA transcript at the distal tip, conserved region 3	7	0.304	61.7
3	RF02057	Salmonella enterica sRNA STnc40	5	0.294	58.5
3	RF02067	Salmonella enterica sRNA STnc310	4	0.500	32.5
3	RF02081	Enterobacterial sRNA STnc550	3	0.273	22.9
3	RF02089	CLRN1 antisense RNA 1 conserved region	2	0.105	17.2
3	RF02093	mir-2968 microRNA precursor	4	0.333	29.7
3	RF02100	Translational regulator of tfoXVC	4	0.400	48.9
3	RF02103	Deleted in lymphocytic leukemia 1 conserved region 1	5	0.192	44.7
3	RF02104	Deleted in lymphocytic leukemia 1 conserved region 2	8	0.500	62.7
3	RF02109	Deleted in lymphocytic leukemia 2 conserved region 5	8	0.267	65.6
3	RF02116	FAS antisense RNA 1 conserved region	2	0.105	16.6
3	RF02118	FMR1 antisense RNA 1 conserved region 2	12	0.480	118.1
3	RF02127	GNAS antisense RNA 1 conserved region 1	6	0.286	46.2
3	RF02137	HOXA11 antisense RNA 1 conserved region 1	3	0.200	27.9
3	RF02138	HOXA11 antisense RNA 1 conserved region 2	10	0.476	99.3
3	RF02141	HOXA11 antisense RNA 1 conserved region 5	3	0.107	27.2
3	RF02143	Hydatidiform mole associated and imprinted conserved region 1	6	0.375	72.2
3	RF02145	Maternally expressed 8 exon 1	5	0.217	45.0
3	RF02151	MER1 repeat containing imprinted transcript 1 conserved region 1	2	0.095	18.3
3	RF02160	Prostate androgen-regulated transcript 1 conserved region 2	5	0.172	49.6
3	RF02164	Pvt1 oncogene conserved region 1	7	0.412	81.7
3	RF02165	Pvt1 oncogene conserved region 2	3	0.176	25.7
3	RF02187	ST7 overlapping transcript 4 conserved region 1	2	0.083	18.1
3	RF02189	ST7 overlapping transcript 4 conserved region 3	3	0.150	27.1
3	RF02198	TTC28 antisense RNA 1 conserved region 1	5	0.357	43.1
3	RF02200	TTC28 antisense RNA 1 conserved region 3	3	0.500	32.4
3	RF02201	TTC28 antisense RNA 1 conserved region 4	3	0.167	25.1
3	RF02205	WT1 antisense RNA conserved region 3	10	0.526	105.0
3	RF02208	WT1 antisense RNA conserved region 6	3	0.158	23.2
3	RF02215	ZNFX1 antisense RNA 1 conserved region 1	11	0.733	88.4
3	RF02220	ZNRD1 antisense RNA 1 conserved region 3	6	0.667	45.5
3	RF02221	sRNA-Xcc1	31	0.419	261.6
3	RF02225	Proteobacterial sRNA sX6	8	1.000	70.5
3	RF02234	Xanthomonadaceae sRNA sX15	7	0.500	67.6
3	RF02235	Xanthomonadaceae sRNA asX1	11	0.733	159.6
3	RF02238	Xanthomonas sRNA asX4/Xoo4	4	0.500	31.3
3	RF02243	Proteobacterial sRNA Xoo8	4	1.000	79.4
3	RF02247	Six3os1 conserved region 2	4	0.267	30.4
3	RF02249	Six3os1 conserved region 4	3	0.429	23.2
3	RF02251	Six3os1 conserved region 6	4	1.000	53.6
3	RF02276	Hammerhead ribozyme (type II)	11	0.458	127.4
3	RF02278	Betaproteobacteria toxic small RNA	15	0.294	169.1
3	RF02343	Alphaproteobacterial sRNA ar9	20	0.714	270.5
3	RF02344	Alphaproteobacterial ar14	72	0.610	573.3
3	RF02345	Alphaproteobacterial ar15	5	0.082	64.1
3	RF02346	Alphaproteobacterial sRNA ar35	3	0.231	22.2
3	RF02349	Proteobacterial sRNA psRNA2	2	0.286	14.5
3	RF02351	Proteobacteria sRNA psRNA14	2	0.667	21.8
3	RF02353	Bradyrhizobiaceae sRNA BjrC68	12	1.000	221.4
3	RF02354	Bradyrhizobiaceae sRNA BjrC80	11	0.733	107.7
3	RF02355	Bradyrhizobiaceae sRNA BjrC174	11	0.733	172.4
3	RF02356	Alphaproteobacterial sRNA BjrC1505	20	0.800	290.3
3	RF02357	RNaseP truncated form	9	1.000	260.5
3	RF02363	Cyanobacterial functional RNA 11	2	0.500	15.7
3	RF02371	PyrG leader	5	0.500	76.0
3	RF02384	FasX small RNA	2	0.250	20.1
3	RF02399	Nitrogen stress-induced RNA 1	2	0.118	18.8
3	RF02401	ClpQY promoter	9	0.231	85.1
3	RF02405	Pseudomonas sRNA P34	6	1.200	57.3
3	RF02413	Small nucleolar RNA snoR145	3	0.158	28.0
3	RF02421	Burkholderia sRNA Bp1_Cand684_SIPHT	13	0.929	140.4
3	RF02422	Burkholderia sRNA Bp1_Cand738_SIPHT	9	0.429	83.5
3	RF02423	Burkholderia sRNA Bp1_Cand871_SIPHT	2	0.133	15.0
3	RF02424	Burkholderia sRNA Bp2_Cand287_SIPHT	3	0.214	32.9
3	RF02435	Streptococcus sRNA SpF41	3	0.333	51.9
3	RF02446	Streptococcus sRNA SpR18	5	0.217	37.7
3	RF02448	Streptococcus sRNA SpR20	5	0.714	42.9
3	RF02453	Bacillus sRNA ncr952	4	0.667	31.1
3	RF02457	Tombusvirus 3' cap-independent translation element	8	0.889	67.2
3	RF02461	Blackcurrant reversion virus cap-independent translation element	3	1.000	29.3
3	RF02462	Ascomycota telomerase RNA	4	1.000	128.5
3	RF02471	Actinobacteria sRNA Ms_IGR-5	16	0.762	189.0
3	RF02483	Small nucleolar RNA GlsR20	2	0.667	18.8
3	RF02488	Small nucleolar RNA GlsR25	3	1.000	23.8
3	RF02502	Rhizobiales sRNA Atu_C8	2	0.074	14.4
3	RF02506	Rhizobiales sRNA Atu_Ti1	2	0.143	17.4
3	RF02523	Repression of heat shock gene expression (ROSE) element	4	0.250	30.5
3	RF02531	Nrf2 internal ribosome entry site (IRES)	2	0.100	19.2
3	RF02540	Archaeal large subunit ribosomal RNA	91	1.000	14392.9
3	RF02541	Bacterial large subunit ribosomal RNA	102	1.000	9153.3
3	RF02542	Microsporidia small subunit ribosomal RNA	39	0.848	796.4
3	RF02543	Eukaryotic large subunit ribosomal RNA	87	0.989	5123.0
3	RF02553	Y RNA-like	2	0.333	17.1
3	RF02566	Mycobacterium smegmatis small RNA 1	3	0.750	29.3
3	RF02596	Cyanobacteria heterocyst sRNA	2	0.400	16.9
3	RF02605	Streptomyces sRNA scr5239	4	0.667	40.3
3	RF02645	Ruegeria cis2 sRNA	2	1.000	16.1
3	RF02649	Ruegeria trans44 sRNA	2	1.000	15.1
3	RF02673	Streptomyces sRNA 4677	5	0.417	51.9
3	RF02678	Hatchet ribozyme	69	0.451	655.5
3	RF02679	Pistol ribozyme	7	0.156	71.3
3	RF02680	PreQ1-III (pre queuosine) riboswitch aptamer	2	0.065	17.4
3	RF02681	Twister_sister_ribozyme	59	0.522	719.0
3	RF02682	HDV ribozyme from F. prausnitzii	4	0.083	31.5
3	RF02683	NiCo (Nickel/Cobalt) riboswitch aptamer	11	0.133	110.5
3	RF02684	Type-P5 twister ribozyme	72	0.335	815.7
3	RF02690	Burkholderia sRNA 1	5	1.000	64.4
3	RF02728	Haemophilus regulatory RNA responsive to iron	3	0.429	32.0
3	RF02743	Saccharopolyspora sRNA 389	2	1.000	33.5
3	RF02744	Soft rot Enterobacteriaceae Rev 39 5'UTR	4	1.000	68.4
3	RF02745	Soft rot Enterobacteriaceae Rev 42 5'UTR	2	0.667	18.8
3	RF02746	antisense RNA of rseC mRNA	6	0.857	64.8
3	RF02748	Francisella sRNA B	4	0.800	46.5
3	RF02778	FdoG-1 5' UTR thermometer	2	0.500	20.1
3	RF02790	sodF sRNA	6	1.000	73.7
3	RF02795	Pab91 RNA	3	1.000	25.1
3	RF02796	Pab160 RNA	3	0.750	22.2
3	RF02802	Pyrobaculum sRNA 204	3	0.600	27.1
3	RF02804	Pyrobaculum sRNA 206	4	1.000	31.6
3	RF02809	RsmW RNA family	3	1.000	44.7
3	RF02826	Streptomyces RNA 6925	3	0.750	22.6
3	RF02829	Streptomyces RNA 4115	5	0.833	48.0
3	RF02830	Streptomyces RNA 1601	5	0.833	58.0
3	RF02832	Streptomyces RNA 5676	5	1.000	102.7
3	RF02833	Streptomyces RNA 3202	2	0.500	15.0
3	RF02837	Burkholderia RNA 7 (anti-hemB)	9	0.346	71.6
3	RF02838	Enterococcus sRNA 55	2	0.500	20.1
3	RF02840	Enterococcus sRNA 68 (Lacto-3 RNA)	15	0.192	154.5
3	RF02848	Enterococcus sRNA B11	2	0.500	20.7
3	RF02855	Yersinia sRNA 251	2	0.400	15.1
3	RF02858	Actinobacillus sRNA 08	3	1.000	58.2
3	RF02868	Burkholderia sRNA 37	2	0.667	34.3
3	RF02877	Neisseria metabolic switch regulator b (RcoF1/NgncR163)	3	0.500	37.2
3	RF02886	Mycobacterium sRNA 6715	2	0.667	16.4
3	RF02887	Salmonella mgtC leader RNA	2	0.500	14.0
3	RF02893	RpsF leader	7	0.700	60.4
3	RF02913	pemK RNA	93	0.060	842.3
3	RF02915	DUF3800-VI RNA	11	0.126	111.6
3	RF02917	Burkholderiales-2 RNA	4	0.211	35.5
3	RF02919	ilvB-OMG RNA	6	0.214	45.0
3	RF02921	RT-14 RNA	24	0.168	209.9
3	RF02928	Actinomyces-1 RNA	30	0.127	287.1
3	RF02930	aspS RNA	30	0.517	300.5
3	RF02932	Betaproteobacteria-1 RNA	19	0.186	164.9
3	RF02933	ARRPOF RNA	10	0.286	112.3
3	RF02935	che1 RNA	48	0.490	687.6
3	RF02937	Clostridiales-2 RNA	4	0.091	31.9
3	RF02938	COG2827 RNA	10	0.208	81.3
3	RF02940	COG3860 RNA	11	0.262	106.9
3	RF02942	Clostridiales-3 RNA	39	0.248	334.0
3	RF02944	c4-2 RNA	180	0.804	1773.3
3	RF02949	Cupriavidus-1 RNA	2	0.400	18.1
3	RF02951	DABA-DC-AT RNA	21	0.167	194.4
3	RF02953	DUF1874 RNA	32	0.421	401.9
3	RF02954	DUF3577 RNA	44	0.512	526.1
3	RF02955	EGFOA RNA	31	0.425	336.4
3	RF02957	EFASI RNA	134	0.299	1663.5
3	RF02960	DUF2800 RNA	35	0.226	318.5
3	RF02961	DUF3800-II RNA	6	0.261	48.3
3	RF02962	DUF3800-III RNA	41	0.745	432.5
3	RF02964	DUF3800-V RNA	10	0.127	96.3
3	RF02965	CyVA-1 RNA	33	0.268	310.0
3	RF02966	DUF3268 RNA	23	0.213	200.1
3	RF02967	DUF3800-VII RNA	28	0.201	301.3
3	RF02968	DUF3800-IX RNA	94	0.410	839.6
3	RF02969	DUF3800-I RNA	97	0.302	1091.1
3	RF02972	engA RNA	28	0.182	224.7
3	RF02973	Enterococcus-1 RNA	39	0.500	341.0
3	RF02975	DUF3800-XI RNA	218	0.852	2534.9
3	RF02976	Flavobacterium-1 RNA	95	0.452	888.2
3	RF02977	THF-II riboswitch (folE RNA)	24	0.522	201.4
3	RF02981	FTHFS RNA	16	0.593	149.5
3	RF02984	DUF3800-X RNA	21	0.239	227.2
3	RF02985	ftsZ-DE RNA	6	0.600	47.4
3	RF02986	FuFi-1 RNA	47	0.276	449.7
3	RF02987	GA-cis RNA	126	0.262	1114.1
3	RF02988	GEBRO RNA	34	0.810	462.2
3	RF02989	gntR-DTE RNA	2	0.286	16.5
3	RF02992	hya RNA	2	0.074	17.2
3	RF02993	ilvH RNA	8	0.471	58.8
3	RF02995	IMES-5 RNA	23	0.442	186.2
3	RF02998	IS605-orfB-II RNA	12	0.214	111.0
3	RF03000	LOOT RNA	364	0.989	7069.0
3	RF03001	leuA-Halobacteria RNA	104	0.684	1521.1
3	RF03005	lysM-TM7 RNA	120	0.930	1449.3
3	RF03006	M23 RNA	23	0.742	217.9
3	RF03007	Mahella-1 RNA	8	0.421	74.2
3	RF03009	malK-III RNA	3	0.077	23.0
3	RF03011	Methylophilales-1 RNA	2	0.143	15.6
3	RF03013	nadA riboswitch	32	0.172	314.0
3	RF03015	Transposase-2 RNA	145	0.960	2473.1
3	RF03016	RT-12 RNA	11	0.262	91.5
3	RF03017	RT-13 RNA	6	0.462	53.7
3	RF03018	RT-15 RNA	27	0.422	315.3
3	RF03019	RT-16 RNA	19	0.183	192.0
3	RF03020	RT-17 RNA	10	0.159	106.3
3	RF03021	RT-18 RNA	30	0.213	266.2
3	RF03022	RT-10 RNA	12	0.106	103.0
3	RF03023	rpfG RNA	2	0.071	15.2
3	RF03026	RT-5 RNA	8	0.113	75.0
3	RF03027	RT-6 RNA	25	0.424	277.8
3	RF03028	RT-7 RNA	13	0.241	122.6
3	RF03033	NLPC-P60 RNA	3	0.176	25.0
3	RF03034	nrdJ RNA	22	0.301	203.0
3	RF03035	nqrA-Marinomonas RNA	4	0.800	35.7
3	RF03037	PAGEV RNA	25	0.291	226.6
3	RF03038	nhaA-II RNA	6	0.375	69.0
3	RF03039	Peptidase-S11 RNA	6	0.044	43.9
3	RF03041	poplar-1 RNA	10	0.455	140.1
3	RF03043	Prevotella-2 RNA	20	1.000	252.3
3	RF03044	Proteo-phage-1 RNA	23	0.343	244.7
3	RF03045	proV RNA	8	0.500	62.9
3	RF03049	RAGATH-24 RNA	11	0.500	105.4
3	RF03052	RAGATH-28 RNA	8	0.094	64.7
3	RF03057	nhaA-I RNA	37	0.132	327.6
3	RF03058	sul1 RNA	4	0.074	33.9
3	RF03059	raiA-hairpin RNA	50	0.625	441.4
3	RF03061	uxuA RNA	16	0.485	150.1
3	RF03063	Streptomyces-metK RNA	4	0.105	39.7
3	RF03067	terC RNA	14	0.109	138.5
3	RF03068	RT-3 RNA	82	0.355	1189.8
3	RF03069	malK-I RNA	222	0.689	2525.9
3	RF03072	raiA RNA	211	0.432	2303.7
3	RF03074	Rhodo-rpoB RNA	84	0.322	913.2
3	RF03076	Streptomyces-metH RNA	20	0.465	175.2
3	RF03077	RT-2 RNA	46	0.236	422.2
3	RF03078	chrB-a RNA	16	0.098	166.1
3	RF03079	MISL RNA	44	1.000	1579.7
3	RF03082	dinG RNA	52	0.605	459.3
3	RF03087	ROOL RNA	239	0.824	4046.5
3	RF03089	cold-seep-1 RNA	2	0.133	19.6
3	RF03090	lysM-Actino RNA	56	1.000	548.1
3	RF03094	LAGLIDADG-2 RNA	4	0.160	33.2
3	RF03096	RAGATH-19 RNA	4	0.364	33.4
3	RF03098	RAGATH-22 RNA	13	0.722	166.0
3	RF03102	RAGATH-33 RNA	2	0.286	19.7
3	RF03106	RT-11 RNA	2	0.667	19.9
3	RF03108	Methylosinus-1 RNA	11	0.917	225.5
3	RF03109	Thermales-rpoB RNA	11	0.786	96.5
3	RF03110	throat-1 RNA	20	0.741	296.5
3	RF03112	Staphylococcus-1 RNA	3	0.143	26.1
3	RF03113	Poribacteria-1 RNA	3	0.500	32.8
3	RF03115	KDPG-aldolase RNA	22	0.512	213.6
3	RF03117	Betacoronavirus 5'UTR	3	0.176	22.4
3	RF03120	Sarbecovirus 5'UTR	17	0.895	124.4
3	RF03132	L17-Actino-Proteobacteria ribosomal protein leader	78	0.191	672.4
3	RF03134	S6-S18-Chlorobi ribosomal protein leader	4	0.118	35.0
3	RF03135	L4-Archaeoglobi ribosomal protein leades	56	0.148	503.0
3	RF03136	S10-Clostridia ribosomal protein leader	118	0.593	1244.6
3	RF03137	S15-Methanomicrobia ribosomal protein leader	28	0.280	281.4
3	RF03140	S4-Clostridia ribosomal protein leader	25	0.179	281.9
3	RF03142	L2-Alphaproteobacteria ribosomal protein leader	91	0.201	977.3
3	RF03144	eL15-Euryarchaeota ribosomal protein leader	95	0.176	885.7
3	RF03147	RAGATH-10 RNA	25	0.168	272.6
3	RF03149	RAGATH-12 RNA	24	1.000	225.1
3	RF03153	RAGATH-4 RNA	9	0.600	84.7
3	RF03155	TD-1 RNA	13	0.464	142.2
3	RF03158	L31-Actinobacteria ribosomal protein leader	132	0.136	1154.7
3	RF03162	TD-2 RNA	21	0.583	290.5
3	RF03164	NiCo-AnGGAG riboswitch aptamer	5	0.385	57.1
3	RF03167	c-di-GMP-I-GGC riboswitch aptamer	21	0.525	242.6
3	RF03168	c-di-GMP-I-UAU riboswitch aptamer	5	0.833	49.8
3	RF03169	c-di-GMP-II-GAG riboswitch aptamer	133	0.282	1213.5
3	RF03170	c-di-GMP-II-GCG riboswitch aptamer	7	0.212	55.5
3	RF03532	Cis-regulator of HTH transcription factor	5	0.088	46.3
3	RF03534	Staphylococcus sRNA71 small RNA	4	0.308	43.9
3	RF03536	Tick-borne Flavivirus exoribonuclease-resistant RNA element	5	0.278	40.7
3	RF03538	Tick-borne Flavivirus 3' UTR cis-acting replication element (CRE)	7	0.875	95.2
3	RF03541	Insect-specific Flavivirus exoribonuclease-resistant RNA element	3	0.375	37.6
3	RF03546	Flavivirus 5' UTR	2	0.250	21.8
3	RF03547	General Flavivirus exoribonuclease-resistant RNA element	8	0.167	64.4
3	RF03582	mir-m22-1 microRNA precursor family	2	1.000	15.9
3	RF03668	mir-1788 microRNA precursor family	3	0.273	28.3
3	RF03819	mir-Ro6-3 microRNA precursor family	2	1.000	14.8
3	RF03990	mir-4888 microRNA precursor family	2	1.000	17.6
3	RF04011	mir-8515 microRNA precursor family	2	1.000	15.9
3	RF04063	MIR2629 microRNA precursor family	3	0.375	25.6
3	RF04163	mir-8364 microRNA precursor family	2	0.154	21.8
3	RF04180	Bacteroides sRNA BTnc231	7	1.000	147.3
3	RF04181	rteR sRNA	5	0.500	63.2
3	RF04183	Bacteroidales small SRP	3	0.097	24.2
3	RF04184	Bacteroides sRNA BTnc060	6	1.000	89.0
3	RF04188	Hovlinc ribozyme (hominin vlincRNA-located)	14	0.189	118.5
3	RF04190	Hairpin ribozyme 1 from viruses-like metatranscriptomes	11	0.131	128.6
3	RF04191	Hairpin ribozyme 2 from viruses-like metatranscriptomes	16	0.333	128.9
3	RF04198	MIR8670 microRNA precursor family	2	1.000	17.8
3	RF04218	Hepatitis C virus stem-loop I	4	0.070	32.0
3	RF04219	J750 non-coding RNA (containing SLSL761 and SL783)	22	0.386	203.1
3	RF04220	SL588 non-coding RNA	6	0.105	50.8
3	RF04248	MIR7486 microRNA precursor family	2	0.222	14.5
3	RF04306	Hepatitis C virus stem-loop SL8001 RNA	10	0.175	74.9