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Table view (86 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		AF064267.1	N/A	seed	1	98	Saccharomyces cerevisiae snR55 small nucleolar RNA, complete sequence.	Saccharomyces cerevisiae (baker's yeast)
1		AJ002157.1	N/A	seed	1	98	Saccharomyces cerevisiae Z10 small nucleolar RNA gene	Saccharomyces cerevisiae (baker's yeast)
2		CR380953.1	N/A	seed	76,850	76,759	Candida glabrata strain CBS138 chromosome G complete sequence.	Candida glabrata
3		CR382122.1	N/A	seed	550,960	551,053	Kluyveromyces lactis strain NRRL Y-1140 chromosome B complete sequence.	Kluyveromyces lactis
4		AJ575660.1	N/A	seed	49,019	49,094	Yarrowia lipolytica iah1, mts1, stl1, sip3, coq6, cdc37, aep2, tRNA-Gly, tRNA-Thr and 5S rRNA genes and ORF1, ORF2, ORFX, ORF6, ORF7, ORF12, ORF13, ORF15, ORFY, ORF18 and retrotransposon Ylt1	Yarrowia lipolytica
5		CR382138.2	N/A	seed	1,137,390	1,137,465	Debaryomyces hansenii strain CBS767 chromosome F complete sequence.	Debaryomyces hansenii
0		BK006945.2	98.20	full	794,794	794,697	TPA: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.	Saccharomyces cerevisiae S288c
1		CM001574.1	97.30	full	737,620	737,523	Saccharomyces arboricola H-6 chromosome XII, whole genome shotgun sequence.	Saccharomyces arboricola H-6
2		JH796419.1	93.40	full	12,576	12,479	Saccharomyces kudriavzevii IFO 1802 unplaced genomic scaffold c2002, whole genome shotgun sequence.	Saccharomyces kudriavzevii IFO 1802
3		CU928171.1	88.70	full	1,562,754	1,562,845	Lachancea thermotolerans CBS 6340 chromosome G complete sequence.	Lachancea thermotolerans CBS 6340
4		HE580276.1	88.70	full	382,030	381,934	Naumovozyma dairenensis CBS 421 chromosome 10, complete genome	Naumovozyma dairenensis CBS 421
5		FXLY01000013.1	88.70	full	52,029	51,933	Kazachstania saulgeensis genome assembly, contig: scaffold_12	Kazachstania saulgeensis
6		HE576761.1	86.30	full	127,561	127,465	Naumovozyma castellii CBS 4309 complete genome, chromosome 10	Naumovozyma castellii CBS 4309
7		LN736374.1	85.90	full	11,835	11,928	Lachancea lanzarotensis strain CBS 12615 genome assembly, scaffold: LALA0S15	Lachancea lanzarotensis
8		HE612866.1	83.30	full	276,947	277,041	Tetrapisispora phaffii CBS 4417 chromosome 11, complete genome	Tetrapisispora phaffii CBS 4417
9		HE616745.1	82.80	full	551,613	551,711	Torulaspora delbrueckii CBS 1146 chromosome 4, complete genome	Torulaspora delbrueckii CBS 1146
10		CP002498.1	79.40	full	811,014	811,113	Eremothecium cymbalariae DBVPG#7215 chromosome 2, complete sequence.	Eremothecium cymbalariae DBVPG#7215
11		LT598489.1	78.80	full	711,275	711,362	Lachancea fermentati genome assembly, chromosome: B	Lachancea fermentati
12		HE978315.1	78.60	full	1,090,974	1,090,880	Kazachstania naganishii CBS 8797 chromosome 2, complete genome	Kazachstania naganishii CBS 8797
13		DS480417.1	77.90	full	54,073	53,979	Vanderwaltozyma polyspora DSM 70294 KpolScaffold526 genomic scaffold, whole genome shotgun sequence.	Vanderwaltozyma polyspora DSM 70294
14		LT598464.1	77.20	full	206,280	206,188	Lachancea mirantina genome assembly, chromosome: B	Lachancea mirantina
15		HE650821.1	76.60	full	1,307,542	1,307,639	Kazachstania africana CBS 2517 chromosome 1, complete genome	Kazachstania africana CBS 2517
16		CP058604.1	74.60	full	1,636,027	1,635,925	CP058604.1 Zygotorulaspora mrakii strain NRRL Y-6702 chromosome 1	Zygosaccharomyces mrakii
17		AE016815.5	74.30	full	457,747	457,660	Ashbya gossypii ATCC 10895 chromosome II, complete sequence.	Ashbya gossypii ATCC 10895
18		LT598459.1	72.40	full	990,472	990,566	Lachancea dasiensis CBS 10888 genome assembly, chromosome: C	Lachancea dasiensis CBS 10888
19		HE806322.1	71.80	full	310,824	310,914	Tetrapisispora blattae CBS 6284 chromosome 7, complete genome	Tetrapisispora blattae CBS 6284
20		CP059270.1	65.60	full	869,110	869,015	CP059270.1 Torulaspora sp. CBS 2947 strain CBS2947 chromosome 4	Torulaspora sp. CBS 2947
21		JAGSYN010000156.1	65.40	full	40,513	40,591	JAGSYN010000156.1 [Candida] subhashii strain CBS 10753 scaffold103, whole genome shotgun sequence	Candida subhashii
22		GL996500.1	63.50	full	856,831	856,907	Spathaspora passalidarum NRRL Y-27907 unplaced genomic scaffold SPAPAscaffold_2, whole genome shotgun sequence.	Spathaspora passalidarum NRRL Y-27907
23		KV454012.1	63.10	full	2,101,680	2,101,763	Pachysolen tannophilus NRRL Y-2460 unplaced genomic scaffold PACTA_scaffold_2, whole genome shotgun sequence.	Pachysolen tannophilus NRRL Y-2460
24		JAEUBG010002298.1	63.00	full	160	240	JAEUBG010002298.1 Wickerhamomyces pijperi strain CBS2887 scaffold26, whole genome shotgun sequence	Pichia pijperi
25		CR382127.1	62.40	full	889,985	890,060	Yarrowia lipolytica strain CLIB122 chromosome A complete sequence.	Yarrowia lipolytica
26		CU928173.1	61.00	full	972,733	972,649	Zygosaccharomyces rouxii strain CBS732 chromosome A complete sequence.	Zygosaccharomyces rouxii CBS 732
27		QLNQ01000027.1	60.50	full	1,133,069	1,133,152	QLNQ01000027.1 Candida viswanathii strain ATCC 20962 contig5, whole genome shotgun sequence	Candida viswanathii
28		KV454540.1	60.30	full	1,621,523	1,621,601	Hyphopichia burtonii NRRL Y-1933 unplaced genomic scaffold HYPBUscaffold_3, whole genome shotgun sequence.	Hyphopichia burtonii NRRL Y-1933
29		QLNQ01000025.1	59.80	full	1,301,473	1,301,388	QLNQ01000025.1 Candida viswanathii strain ATCC 20962 contig7, whole genome shotgun sequence	Candida viswanathii
30		NSGQ01000041.1	59.40	full	106,869	106,948	NSGQ01000041.1 Spathaspora sp. JA1 scaffold_40, whole genome shotgun sequence	Spathaspora sp. JA1
31		KV454486.1	59.20	full	216,755	216,679	Ascoidea rubescens DSM 1968 unplaced genomic scaffold ASCRUscaffold_12, whole genome shotgun sequence.	Ascoidea rubescens DSM 1968
32		CANTUO010000001.1	59.10	full	545,551	545,632	CANTUO010000001.1 Candida verbasci genome assembly, contig: chrA, whole genome shotgun sequence	Candida verbasci
33		PNEN01000230.1	59.00	full	146,129	146,053	PNEN01000230.1 Cercospora berteroae strain CBS538.71 Cbert_1_scaffold230, whole genome shotgun sequence	Cercospora berteroae
34		CP017630.1	58.90	full	1,324,552	1,324,466	Candida albicans SC5314 chromosome R sequence.	Candida albicans SC5314
35		JABWAD010000055.1	58.90	full	606,086	606,172	JABWAD010000055.1 Candida albicans strain FDAARGOS_656 tig00000154_pilon, whole genome shotgun sequence	Candida albicans
36		KV453910.1	58.90	full	1,830,517	1,830,595	Candida tanzawaensis NRRL Y-17324 unplaced genomic scaffold CANTAscaffold_2, whole genome shotgun sequence.	Candida tanzawaensis NRRL Y-17324
37		CAKXYY010000006.1	58.30	full	273,490	273,413	CAKXYY010000006.1 [Candida] railenensis strain CLIB 1423 genome assembly, contig: CLIB1423_06S, whole genome shotgun sequence	Candida railenensis
38		CP000500.1	58.00	full	1,136,189	1,136,264	Scheffersomyces stipitis CBS 6054 chromosome 6, complete sequence.	Scheffersomyces stipitis CBS 6054
39		CAIF01000217.1	57.90	full	88,270	88,349	Wickerhamomyces ciferrii, NRRL Y-1031 F-60-10, WGS project CAIF01000000 data, contig: 00217	Wickerhamomyces ciferrii NRRL Y-1031
40		JAEUBF010000974.1	57.80	full	181,962	181,884	JAEUBF010000974.1 Wickerhamomyces mucosus strain CBS6341 scaffold11, whole genome shotgun sequence	Wickerhamomyces mucosus
41		CP099426.1	55.60	full	1,240,840	1,240,916	CP099426.1 Septoria linicola strain SE15195 chromosome 9	Mycosphaerella linicola
42		BSXN01001071.1	55.40	full	6,061	5,979	BSXN01001071.1 [Candida] boidinii NBRC 10035 DNA, scf7180000049377, whole genome shotgun sequence	Candida boidinii
43		MPUK01000001.1	55.10	full	1,797,238	1,797,318	Cyberlindnera fabianii strain 65 BON22_Sc01, whole genome shotgun sequence.	Cyberlindnera fabianii
44		BSXU01000515.1	54.80	full	8,868	8,785	BSXU01000515.1 Ambrosiozyma monospora NBRC 1965 DNA, scf7180000088408, whole genome shotgun sequence	Ambrosiozyma monospora
45		BSXU01003818.1	54.80	full	2,609	2,692	BSXU01003818.1 Ambrosiozyma monospora NBRC 1965 DNA, scf7180000092393, whole genome shotgun sequence	Ambrosiozyma monospora
46		PUHW01000024.1	54.30	full	8,590	8,674	PUHW01000024.1 [Candida] californica strain Olga-1 scaffold_24, whole genome shotgun sequence	Candida californica
47		UFAJ01000118.1	54.30	full	4,190	4,092	UFAJ01000118.1 Saccharomycodes ludwigii strain UTAD17 genome assembly, contig: SCODWIG_contig_0118, whole genome shotgun sequence	Saccharomycodes ludwigii
48		BDGI01000125.1	54.10	full	32,658	32,742	Pichia membranifaciens DNA, contig: CON125, strain: KS47-1.	Pichia membranifaciens
49		SELW01000220.1	54.00	full	46,000	45,916	SELW01000220.1 [Candida] inconspicua strain CBS 180 scaffold21_size184832, whole genome shotgun sequence	Candida inconspicua
50		KV454001.1	53.80	full	280,903	280,987	Pichia membranifaciens NRRL Y-2026 unplaced genomic scaffold PICMEscaffold_1, whole genome shotgun sequence.	Pichia membranifaciens NRRL Y-2026
51		KV454208.1	53.70	full	689,691	689,614	Wickerhamomyces anomalus NRRL Y-366-8 unplaced genomic scaffold WICANscaffold_1, whole genome shotgun sequence.	Wickerhamomyces anomalus NRRL Y-366-8
52		CH408076.1	53.70	full	2,299,052	2,299,129	Clavispora lusitaniae ATCC 42720 scaffold_1 genomic scaffold, whole genome shotgun sequence.	Clavispora lusitaniae ATCC 42720
53		ML742199.1	53.40	full	28,579	28,498	ML742199.1 Aspergillus avenaceus strain IBT 18842 unplaced genomic scaffold BDV25scaffold_177, whole genome shotgun sequence	Aspergillus avenaceus
54		GL996515.1	53.10	full	462,092	462,164	Candida tenuis ATCC 10573 unplaced genomic scaffold CANTEscaffold_00009, whole genome shotgun sequence.	Candida tenuis ATCC 10573
55		QQZK01000056.1	52.80	full	119,416	119,504	QQZK01000056.1 Geotrichum candidum strain LMA-70 Scaffold56, whole genome shotgun sequence	Geotrichum candidum (oospora lactis)
56		LXTC01000007.1	52.30	full	270,537	270,461	Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993 METBIscaffold_7, whole genome shotgun sequence.	Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993
57		CP014502.1	52.30	full	2,182,713	2,182,791	Sugiyamaella lignohabitans strain CBS 10342 chromosome D, complete sequence.	Candida lignohabitans
58		MU003812.1	52.30	full	106,127	106,051	MU003812.1 Polychaeton citri CBS 116435 unplaced genomic scaffold K431scaffold_48, whole genome shotgun sequence	Polychaeton citri CBS 116435
59		CH981527.1	51.90	full	429,973	430,057	Lodderomyces elongisporus NRRL YB-4239 supercont1.4 genomic scaffold, whole genome shotgun sequence.	Lodderomyces elongisporus NRRL YB-4239
60		CP028773.1	51.70	full	534,936	535,020	CP028773.1 Pichia kudriavzevii strain CBS573 chromosome 1, complete sequence	Pichia kudriavzevii
61		ML992663.1	51.60	full	2,097,407	2,097,331	ML992663.1 Cercospora zeae-maydis SCOH1-5 unplaced genomic scaffold CERZMscaffold_2, whole genome shotgun sequence	Cercospora zeae-maydis SCOH1-5
62		LT635760.1	51.60	full	158,211	158,288	[Candida] intermedia strain CBS 141442 genome assembly, chromosome: V	Candida intermedia
63		NAJP01000089.1	51.50	full	147,342	147,418	NAJP01000089.1 Friedmanniomyces endolithicus strain CCFEE 5311 scaffold_89, whole genome shotgun sequence	Friedmanniomyces endolithicus
64		NAJP01000090.1	51.50	full	6,099	6,023	NAJP01000090.1 Friedmanniomyces endolithicus strain CCFEE 5311 scaffold_90, whole genome shotgun sequence	Friedmanniomyces endolithicus
65		NAJQ01000034.1	51.50	full	80,932	80,856	NAJQ01000034.1 Friedmanniomyces simplex strain CCFEE 5184 scaffold_34, whole genome shotgun sequence	Friedmanniomyces simplex
66		NAJQ01001283.1	51.50	full	4,606	4,682	NAJQ01001283.1 Friedmanniomyces simplex strain CCFEE 5184 scaffold_1283, whole genome shotgun sequence	Friedmanniomyces simplex
67		ML121527.1	50.90	full	506,928	507,008	ML121527.1 Terfezia boudieri ATCC MYA-4762 unplaced genomic scaffold L211scaffold_1, whole genome shotgun sequence	Terfezia boudieri ATCC MYA-4762
68		MUNK01000370.1	50.80	full	32,836	32,912	Hortaea werneckii EXF-2000 unitig_343, whole genome shotgun sequence.	Hortaea werneckii EXF-2000
69		KZ111175.1	50.50	full	173,008	172,933	Rachicladosporium sp. CCFEE 5018 unplaced genomic scaffold Supercontig_40, whole genome shotgun sequence.	Rachicladosporium sp. CCFEE 5018
70		NAJO01000036.1	50.50	full	401,315	401,390	Rachicladosporium antarcticum strain CCFEE 5527 scaffold_36, whole genome shotgun sequence.	Rachicladosporium antarcticum
71		JAHMUF010000012.1	50.50	full	149,770	149,849	JAHMUF010000012.1 Scheffersomyces spartinae strain ARV_011 scaffold_12, whole genome shotgun sequence	Scheffersomyces spartinae
72		KV453855.1	50.40	full	330,826	330,735	Candida arabinofermentans NRRL YB-2248 unplaced genomic scaffold CANARscaffold_9, whole genome shotgun sequence.	Candida arabinofermentans NRRL YB-2248
73		LFZN01000178.1	50.30	full	61,690	61,615	Mycosphaerella eumusae strain CBS 114824 scaffold178, whole genome shotgun sequence.	Mycosphaerella eumusae
74		SNSC02000003.1	50.30	full	1,024,062	1,023,987	SNSC02000003.1 Venturia nashicola strain PRI2 Scaffold_03, whole genome shotgun sequence	Venturia nashicola
75		WNWQ01000290.1	50.30	full	31,760	31,685	WNWQ01000290.1 Venturia inaequalis isolate bline_iso_100314 BLS_290, whole genome shotgun sequence	Venturia inaequalis
76		QWIM01001498.1	50.20	full	8,137	8,213	QWIM01001498.1 Hortaea werneckii strain EXF-6651 contig-180_1497, whole genome shotgun sequence	Hortaea werneckii
77		AOGT01000963.1	50.10	full	6,924	6,843	Candida maltosa Xu316 contig1236_scaffold20, whole genome shotgun sequence.	Candida maltosa Xu316
78		CP034456.1	50.10	full	1,083,257	1,083,181	CP034456.1 Metschnikowia aff. pulcherrima strain APC 1.2 chromosome I, complete sequence	Metschnikowia aff. pulcherrima
79		JACBPP010000003.1	50.10	full	1,824,139	1,824,215	JACBPP010000003.1 Metschnikowia pulcherrima strain KIOM G15050 contig3, whole genome shotgun sequence	Metschnikowia pulcherrima

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	RM00029	UNCG tetraloop	3	0.500	32.6