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For a good example of what is possible in wikipedia, look at the Hammerhead Ribozyme entry.

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Table view (31 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		AC002512.1	N/A	seed	12,119	11,569	Drosophila melanogaster (P1 DS00276 (D13)) DNA sequence, complete sequence.	Drosophila melanogaster (fruit fly)
1		AF466639.1	N/A	seed	3,212	3,762	Drosophila melanogaster isolate 116 bicoid (bcd) gene, complete cds.	Drosophila melanogaster (fruit fly)
2		AF465792.1	N/A	seed	2,973	3,522	Drosophila simulans bicoid protein (bicoid) gene, complete cds.	Drosophila simulans
3		AF466630.1	N/A	seed	3,213	3,763	Drosophila melanogaster isolate 157 bicoid (bcd) gene, complete cds.	Drosophila melanogaster (fruit fly)
4		M32122.1	N/A	seed	291	827	D.virilis bicoid (bcd) mRNA, 3' end.	Drosophila virilis
5		M32124.1	N/A	seed	262	812	D.sechellia bicoid (bcd) gene, 3' end.	Drosophila sechellia
6		M32126.1	N/A	seed	307	857	D.teissieri bicoid (bcd) mRNA, 3' end.	Drosophila picticornis
7		AF466626.1	N/A	seed	3,213	3,763	Drosophila melanogaster isolate 229 bicoid (bcd) gene, complete cds.	Drosophila melanogaster (fruit fly)
8		AF466636.1	N/A	seed	3,213	3,763	Drosophila melanogaster isolate 210 bicoid (bcd) gene, complete cds.	Drosophila melanogaster (fruit fly)
9		M32121.1	N/A	seed	250	792	D.teissieri bicoid (bcd) mRNA, 3' end.	Drosophila teissieri
10		M32123.1	N/A	seed	262	812	D.simulans bicoid (bcd) mRNA, 3' end.	Drosophila simulans
11		AF466631.1	N/A	seed	3,213	3,763	Drosophila melanogaster isolate 377 bicoid (bcd) gene, complete cds.	Drosophila melanogaster (fruit fly)
12		X55735.1	N/A	seed	2,601	3,156	D.pseudoobscura bcd (bicoid) gene involved in anterior positional specification during embryogenesis	Drosophila pseudoobscura
13		M32125.1	N/A	seed	227	779	D.heteroneura bicoid (bcd) gene, 3' end.	Drosophila heteroneura
14		X78058.1	N/A	seed	486	1,031	D.subobscura (H271) bcd and zen genes.	Drosophila subobscura
0		AE014297.3	638.70	full	6,756,504	6,755,954	Drosophila melanogaster chromosome 3R.	Drosophila melanogaster (fruit fly)
1		CH480821.1	610.80	full	2,673,569	2,673,019	CH480821.1 Drosophila sechellia strain Rob3c scaffold_6 genomic scaffold, whole genome shotgun sequence	Drosophila sechellia
2		CM000166.1	596.50	full	2,691,760	2,691,210	CM000166.1 Drosophila simulans strain white501 chromosome 3R, whole genome shotgun sequence	Drosophila simulans
3		NW_016046003.1	442.00	full	10,709	10,164	NW_016046003.1 Drosophila rhopaloa unplaced genomic scaffold, Drho_2.0 scf7180000763819, whole genome shotgun sequence	Drosophila rhopaloa
4		CM045922.1	427.20	full	25,906,863	25,907,404	CM045922.1 Drosophila gunungcola strain Sukarami chromosome 3R, whole genome shotgun sequence	Drosophila gunungcola
5		NW_016067551.1	376.00	full	294,524	293,963	NW_016067551.1 Drosophila kikkawai unplaced genomic scaffold, Dkik_2.0 scf7180000302619, whole genome shotgun sequence	Drosophila kikkawai
6		CH902617.1	359.00	full	5,464,718	5,465,247	CH902617.1 Drosophila ananassae strain TSC#14024-0371.13 scaffold_13340 genomic scaffold, whole genome shotgun sequence	Drosophila ananassae
7		NC_046679.1	326.40	full	20,633,835	20,634,390	NC_046679.1 Drosophila pseudoobscura strain MV2-25 chromosome 2, UCI_Dpse_MV25, whole genome shotgun sequence	Drosophila pseudoobscura pseudoobscura
8		CH479182.1	325.90	full	2,542,388	2,542,943	CH479182.1 Drosophila persimilis strain MSH-3 scaffold_3 genomic scaffold, whole genome shotgun sequence	Drosophila persimilis
9		CH916369.1	300.00	full	11,503,407	11,503,959	Drosophila grimshawi strain TSC#15287-2541.00 scaffold_14906 genomic scaffold, whole genome shotgun sequence.	Drosophila grimshawi
10		CH940650.1	286.00	full	6,166,369	6,166,903	CH940650.1 Drosophila virilis strain TSC#15010-1051.87 scaffold_13047 genomic scaffold, whole genome shotgun sequence	Drosophila virilis
11		CH933806.1	217.50	full	16,567,542	16,568,090	CH933806.1 Drosophila mojavensis strain TSC#15081-1352.22 scaffold_6540 genomic scaffold, whole genome shotgun sequence	Drosophila mojavensis
12		CP012526.1	202.40	full	19,882,718	19,883,256	Drosophila busckii chromosome 3R sequence.	Drosophila busckii
13		NC_047631.2	200.60	full	23,894,677	23,895,208	NC_047631.2 Drosophila albomicans strain 15112-1751.03 chromosome 2R, ASM965048v2, whole genome shotgun sequence	Drosophila albomicans
14		NW_022060548.1	195.50	full	6,608,900	6,609,448	NW_022060548.1 Scaptodrosophila lebanonensis strain 11010-0011.00,11010-0021.00 unplaced genomic scaffold, SlebRS2 tig00000053-arrow-pilon, whole genome shotgun sequence	Scaptodrosophila lebanonensis
15		LSRL02000006.1	187.90	full	1,458,630	1,458,084	LSRL02000006.1 Drosophila navojoa isolate navoj_Jal97 6, whole genome shotgun sequence	Drosophila navojoa

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	0.200	29.6