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Table view (73 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		Z49629.1	N/A	seed	469	662	S.cerevisiae chromosome X reading frame ORF YJR129c	Saccharomyces cerevisiae (baker's yeast)
1		AABZ01000024.1	N/A	seed	46,395	46,589	Saccharomyces mikatae IFO 1815 contig_741, whole genome shotgun sequence.	Saccharomyces mikatae IFO 1815
2		AACA01000267.1	N/A	seed	4,921	4,730	Saccharomyces bayanus MCYC 623 contig_717, whole genome shotgun sequence.	Saccharomyces bayanus MCYC 623
3		AAZN01000275.1	N/A	seed	150,002	149,819	Vanderwaltozyma polyspora DSM 70294 KpolContig1028c, whole genome shotgun sequence.	Vanderwaltozyma polyspora DSM 70294
0		BK006943.2	236.60	full	663,749	663,942	TPA: Saccharomyces cerevisiae S288C chromosome X, complete sequence.	Saccharomyces cerevisiae S288c
1		JH797810.1	234.70	full	5,564	5,757	Saccharomyces kudriavzevii IFO 1802 unplaced genomic scaffold c1503, whole genome shotgun sequence.	Saccharomyces kudriavzevii IFO 1802
2		CM001572.1	218.80	full	642,557	642,748	Saccharomyces arboricola H-6 chromosome X, whole genome shotgun sequence.	Saccharomyces arboricola H-6
3		DS480385.1	180.00	full	183,325	183,142	Vanderwaltozyma polyspora DSM 70294 KpolScaffold1028 genomic scaffold, whole genome shotgun sequence.	Vanderwaltozyma polyspora DSM 70294
4		HE612867.1	122.80	full	47,146	46,964	Tetrapisispora phaffii CBS 4417 chromosome 12, complete genome	Tetrapisispora phaffii CBS 4417
5		CP058608.1	117.00	full	332,827	332,645	CP058608.1 Zygotorulaspora mrakii strain NRRL Y-6702 chromosome 5	Zygosaccharomyces mrakii
6		CP059269.1	112.20	full	1,093,315	1,093,489	CP059269.1 Torulaspora sp. CBS 2947 strain CBS2947 chromosome 3	Torulaspora sp. CBS 2947
7		LT598487.1	100.00	full	145,592	145,384	Lachancea fermentati genome assembly, chromosome: A	Lachancea fermentati
8		HE806317.1	98.20	full	1,452,775	1,452,599	Tetrapisispora blattae CBS 6284 chromosome 2, complete genome	Tetrapisispora blattae CBS 6284
9		CAIF01000292.1	97.40	full	8,433	8,252	Wickerhamomyces ciferrii, NRRL Y-1031 F-60-10, WGS project CAIF01000000 data, contig: 00292	Wickerhamomyces ciferrii NRRL Y-1031
10		KV454215.1	93.40	full	116,694	116,514	Wickerhamomyces anomalus NRRL Y-366-8 unplaced genomic scaffold WICANscaffold_8, whole genome shotgun sequence.	Wickerhamomyces anomalus NRRL Y-366-8
11		HE616745.1	93.10	full	114,718	114,538	Torulaspora delbrueckii CBS 1146 chromosome 4, complete genome	Torulaspora delbrueckii CBS 1146
12		HE650825.1	92.10	full	864,701	864,933	Kazachstania africana CBS 2517 chromosome 5, complete genome	Kazachstania africana CBS 2517
13		HE580276.1	91.50	full	713,264	713,466	Naumovozyma dairenensis CBS 421 chromosome 10, complete genome	Naumovozyma dairenensis CBS 421
14		HE576761.1	91.10	full	415,582	415,790	Naumovozyma castellii CBS 4309 complete genome, chromosome 10	Naumovozyma castellii CBS 4309
15		LT598460.1	88.60	full	687,408	687,646	Lachancea dasiensis CBS 10888 genome assembly, chromosome: A	Lachancea dasiensis CBS 10888
16		CR382122.1	85.70	full	398,851	398,571	Kluyveromyces lactis strain NRRL Y-1140 chromosome B complete sequence.	Kluyveromyces lactis
17		FXLY01000009.1	80.60	full	715,041	715,234	Kazachstania saulgeensis genome assembly, contig: scaffold_08	Kazachstania saulgeensis
18		CR380959.2	80.40	full	69,266	69,039	Candida glabrata strain CBS138 chromosome M complete sequence.	Candida glabrata
19		LN736367.1	80.10	full	509,233	509,463	Lachancea lanzarotensis strain CBS 12615 genome assembly, scaffold: LALA0S08	Lachancea lanzarotensis
20		CU928168.1	79.60	full	1,492,779	1,492,553	Lachancea thermotolerans CBS 6340 chromosome D complete sequence.	Lachancea thermotolerans CBS 6340
21		JAEUBF010000390.1	77.00	full	47,111	47,307	JAEUBF010000390.1 Wickerhamomyces mucosus strain CBS6341 scaffold12, whole genome shotgun sequence	Wickerhamomyces mucosus
22		LT598469.1	76.20	full	783,668	783,461	Lachancea mirantina genome assembly, chromosome: G	Lachancea mirantina
23		HE978315.1	74.70	full	1,329,172	1,329,415	Kazachstania naganishii CBS 8797 chromosome 2, complete genome	Kazachstania naganishii CBS 8797
24		AE016818.2	71.00	full	938,751	938,974	Ashbya gossypii ATCC 10895 chromosome V, complete sequence.	Ashbya gossypii ATCC 10895
25		JAEUBG010000350.1	69.90	full	2,452	2,284	JAEUBG010000350.1 Wickerhamomyces pijperi strain CBS2887 scaffold261, whole genome shotgun sequence	Pichia pijperi
26		CU928174.1	68.20	full	1,216,461	1,216,642	Zygosaccharomyces rouxii strain CBS732 chromosome B complete sequence.	Zygosaccharomyces rouxii CBS 732
27		CP002497.1	65.80	full	263,886	263,637	Eremothecium cymbalariae DBVPG#7215 chromosome 1, complete sequence.	Eremothecium cymbalariae DBVPG#7215
28		KV454432.1	63.40	full	255,228	255,424	Babjeviella inositovora NRRL Y-12698 unplaced genomic scaffold BABINscaffold_7, whole genome shotgun sequence.	Babjeviella inositovora NRRL Y-12698
29		GL996512.1	62.40	full	653,214	652,993	Candida tenuis ATCC 10573 unplaced genomic scaffold CANTEscaffold_00006, whole genome shotgun sequence.	Candida tenuis ATCC 10573
30		CP034457.1	61.50	full	1,661,830	1,661,612	CP034457.1 Metschnikowia aff. pulcherrima strain APC 1.2 chromosome II, complete sequence	Metschnikowia aff. pulcherrima
31		JACBPP010000004.1	61.50	full	358,370	358,588	JACBPP010000004.1 Metschnikowia pulcherrima strain KIOM G15050 contig4, whole genome shotgun sequence	Metschnikowia pulcherrima
32		CH981524.1	58.70	full	3,069,699	3,069,407	Lodderomyces elongisporus NRRL YB-4239 supercont1.1 genomic scaffold, whole genome shotgun sequence.	Lodderomyces elongisporus NRRL YB-4239
33		BIMT01000016.1	57.90	full	160,830	160,608	BIMT01000016.1 Metschnikowia sp. JCM 33374 DNA, tig00000046, whole genome shotgun sequence	Metschnikowia sp. JCM 33374
34		LT635758.1	57.80	full	1,582,147	1,581,926	[Candida] intermedia strain CBS 141442 genome assembly, chromosome: III	Candida intermedia
35		LXTC01000004.1	57.50	full	654,003	653,782	Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993 METBIscaffold_4, whole genome shotgun sequence.	Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993
36		LPNM01000006.1	55.50	full	465,143	465,347	Hanseniaspora osmophila strain AWRI3579 Hanseniaspora_osmophila_AWRI3579_scaffold6, whole genome shotgun sequence.	Hanseniaspora osmophila
37		PYFQ01000001.1	54.70	full	1,167,132	1,166,915	PYFQ01000001.1 [Candida] pseudohaemuli strain B12108 scaffold00001, whole genome shotgun sequence	Candida pseudohaemulonii
38		GG692396.1	54.70	full	303,291	303,551	Candida tropicalis MYA-3404 genomic scaffold supercont3.2, whole genome shotgun sequence.	Candida tropicalis MYA-3404
39		KV454542.1	54.60	full	617,072	617,304	Hyphopichia burtonii NRRL Y-1933 unplaced genomic scaffold HYPBUscaffold_5, whole genome shotgun sequence.	Hyphopichia burtonii NRRL Y-1933
40		CP028776.1	54.40	full	1,154,919	1,154,793	CP028776.1 Pichia kudriavzevii strain CBS573 chromosome 4, complete sequence	Pichia kudriavzevii
41		CR382133.2	53.70	full	182,047	182,263	Debaryomyces hansenii CBS767 chromosome A complete sequence.	Debaryomyces hansenii CBS767
42		MPUK01000006.1	53.60	full	339,112	338,800	Cyberlindnera fabianii strain 65 BON22_Sc06, whole genome shotgun sequence.	Cyberlindnera fabianii
43		AOGT01000022.1	52.60	full	9,059	9,319	Candida maltosa Xu316 contig25_scaffold2, whole genome shotgun sequence.	Candida maltosa Xu316
44		NSDU01000007.1	52.60	full	897,324	897,538	NSDU01000007.1 Meyerozyma sp. JA9 scaffold_3, whole genome shotgun sequence	Meyerozyma sp. JA9
45		PKFO01000003.1	52.50	full	1,690,777	1,690,995	PKFO01000003.1 [Candida] haemuli strain B11899 C_2014730914, whole genome shotgun sequence	Candida haemulonis
46		CP000496.1	52.20	full	231,590	231,818	Scheffersomyces stipitis CBS 6054 chromosome 2, complete sequence.	Scheffersomyces stipitis CBS 6054
47		CH408160.1	51.90	full	659,300	659,514	Pichia guilliermondii ATCC 6260 scaffold_6 genomic scaffold, whole genome shotgun sequence.	Meyerozyma guilliermondii ATCC 6260
48		QLNQ01000001.1	51.80	full	2,516,423	2,516,162	QLNQ01000001.1 Candida viswanathii strain ATCC 20962 contig1, whole genome shotgun sequence	Candida viswanathii
49		JAEUBE010000042.1	51.20	full	81,609	81,427	JAEUBE010000042.1 Ogataea philodendri strain CBS6075 scaffold17, whole genome shotgun sequence	Ogataea philodendri
50		QLNQ01000030.1	51.10	full	240,699	240,960	QLNQ01000030.1 Candida viswanathii strain ATCC 20962 contig2, whole genome shotgun sequence	Candida viswanathii
51		KV453911.1	50.80	full	349,549	349,311	Candida tanzawaensis NRRL Y-17324 unplaced genomic scaffold CANTAscaffold_3, whole genome shotgun sequence.	Candida tanzawaensis NRRL Y-17324
52		JAGSYN010000118.1	49.50	full	16,981	17,219	JAGSYN010000118.1 [Candida] subhashii strain CBS 10753 scaffold117, whole genome shotgun sequence	Candida subhashii
53		KV454014.1	49.50	full	1,386,598	1,386,805	Pachysolen tannophilus NRRL Y-2460 unplaced genomic scaffold PACTA_scaffold_4, whole genome shotgun sequence.	Pachysolen tannophilus NRRL Y-2460
54		CH408077.1	49.40	full	1,049,960	1,049,742	Clavispora lusitaniae ATCC 42720 scaffold_2 genomic scaffold, whole genome shotgun sequence.	Clavispora lusitaniae ATCC 42720
55		CM076438.1	48.90	full	1,892,839	1,893,058	CM076438.1 [Candida] auris strain B8441 chromosome 1, whole genome shotgun sequence	Candida auris
56		CP017624.1	46.50	full	204,466	204,338	Candida albicans SC5314 chromosome 2 sequence.	Candida albicans SC5314
57		JABWAD010000059.1	46.50	full	18,280	18,152	JABWAD010000059.1 Candida albicans strain FDAARGOS_656 tig00000159_pilon, whole genome shotgun sequence	Candida albicans
58		CM002301.1	46.10	full	458,444	458,629	Ogataea parapolymorpha DL-1 chromosome II, whole genome shotgun sequence.	Ogataea parapolymorpha DL-1
59		JAEUBD010000146.1	46.00	full	524,710	524,521	JAEUBD010000146.1 Ogataea polymorpha strain NCAIM Y.01608 scaffold5, whole genome shotgun sequence	Ogataea polymorpha
60		HE605206.1	45.90	full	2,962,641	2,962,946	Candida parapsilosis strain CDC317 annotated contig 005809	Candida parapsilosis CDC317
61		GL996501.1	45.70	full	1,856,282	1,856,533	Spathaspora passalidarum NRRL Y-27907 unplaced genomic scaffold SPAPAscaffold_3, whole genome shotgun sequence.	Spathaspora passalidarum NRRL Y-27907
62		FO082050.1	45.30	full	85,920	86,128	Pichia sorbitophila strain CBS 7064 chromosome J complete sequence.	Millerozyma farinosa CBS 7064 (Pichia farinosa CBS 7064)
63		CAKXYY010000014.1	45.20	full	70,222	70,437	CAKXYY010000014.1 [Candida] railenensis strain CLIB 1423 genome assembly, contig: CLIB1423_14S, whole genome shotgun sequence	Candida railenensis
64		BSXN01001010.1	43.90	full	732	932	BSXN01001010.1 [Candida] boidinii NBRC 10035 DNA, scf7180000049316, whole genome shotgun sequence	Candida boidinii
65		NSGQ01000014.1	43.40	full	214,196	213,948	NSGQ01000014.1 Spathaspora sp. JA1 scaffold_13, whole genome shotgun sequence	Spathaspora sp. JA1
66		FO082054.1	43.20	full	88,167	88,375	Pichia sorbitophila strain CBS 7064 chromosome F complete sequence.	Millerozyma farinosa CBS 7064 (Pichia farinosa CBS 7064)
67		KN984465.1	41.80	full	11,563,327	11,563,461	KN984465.1 Colobus angolensis palliatus isolate OR3802 unplaced genomic scaffold Scaffold57, whole genome shotgun sequence	Colobus angolensis palliatus
68		CM017444.1	41.70	full	16,347,894	16,347,705	CM017444.1 Eragrostis curvula cultivar Victoria chromosome 6, whole genome shotgun sequence	Eragrostis curvula (weeping love grass)

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.