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Table view (94 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		URS00000C1F14_7238	N/A	seed	3	78	Drosophila sechellia microRNA dse-mir-6 precursor (dse-mir-6-3)	Drosophila sechellia
1		URS00000C1F14_7240	N/A	seed	3	78	Drosophila simulans microRNA dsi-mir-6 precursor (dsi-mir-6-3)	Drosophila simulans
2		URS00004C64F6_7220	N/A	seed	3	78	Drosophila erecta microRNA der-mir-6 precursor (der-mir-6-3)	Drosophila erecta
3		URS00007ADB71_7227	N/A	seed	3	78	Drosophila melanogaster (fruit fly) microRNA dme-mir-6 precursor (dme-mir-6-3)	Drosophila melanogaster (fruit fly)
4		URS000014217A_7245	N/A	seed	3	78	Drosophila yakuba microRNA dya-mir-6 precursor (dya-mir-6-3)	Drosophila yakuba
5		URS0000798419_7227	N/A	seed	2	73	Drosophila melanogaster (fruit fly) microRNA dme-mir-6 precursor (dme-mir-6-2)	Drosophila melanogaster (fruit fly)
6		URS00000D1B9E_7220	N/A	seed	2	72	Drosophila erecta microRNA der-mir-6 precursor (der-mir-6-2)	Drosophila erecta
7		URS000000AB74_7217	N/A	seed	2	83	Drosophila ananassae microRNA dan-mir-6 precursor (dan-mir-6-2)	Drosophila ananassae
8		URS00002409C4_7260	N/A	seed	1	94	Drosophila willistoni microRNA dwi-mir-6 precursor (dwi-mir-6-2)	Drosophila willistoni
9		URS00003F656F_7238	N/A	seed	2	73	Drosophila sechellia microRNA dse-mir-6 precursor (dse-mir-6-2)	Drosophila sechellia
10		URS00003F656F_7240	N/A	seed	2	73	Drosophila simulans microRNA dsi-mir-6 precursor (dsi-mir-6-2)	Drosophila simulans
11		URS00000371AF_7245	N/A	seed	2	73	Drosophila yakuba microRNA dya-mir-6 precursor (dya-mir-6-2)	Drosophila yakuba
12		URS00001CEE65_7222	N/A	seed	2	78	Drosophila grimshawi microRNA dgr-mir-6 precursor (dgr-mir-6-2, dgr-mir-6-5)	Drosophila grimshawi
13		URS000040C604_7230	N/A	seed	2	80	Drosophila mojavensis microRNA dmo-mir-6 precursor (dmo-mir-6-2)	Drosophila mojavensis
14		URS00003C043C_7244	N/A	seed	2	79	Drosophila virilis microRNA dvi-mir-6 precursor (dvi-mir-6-2)	Drosophila virilis
15		URS00004CE695_7237	N/A	seed	3	83	Drosophila pseudoobscura microRNA dps-mir-6 precursor (dps-mir-6-2)	Drosophila pseudoobscura
16		URS00004CE695_7234	N/A	seed	3	83	Drosophila persimilis microRNA dpe-mir-6 precursor (dpe-mir-6-3)	Drosophila persimilis
17		URS0000620E9A_7222	N/A	seed	1	74	Drosophila grimshawi microRNA dgr-mir-6 precursor (dgr-mir-6-3, dgr-mir-6-6)	Drosophila grimshawi
18		URS000012212F_7230	N/A	seed	2	77	Drosophila mojavensis microRNA dmo-mir-6 precursor (dmo-mir-6-3)	Drosophila mojavensis
19		URS00004656CC_7244	N/A	seed	1	73	Drosophila virilis microRNA dvi-mir-6 precursor (dvi-mir-6-3)	Drosophila virilis
20		URS0000067C92_7260	N/A	seed	1	76	Drosophila willistoni microRNA dwi-mir-6 precursor (dwi-mir-6-3)	Drosophila willistoni
21		URS0000131F58_7237	N/A	seed	3	78	Drosophila pseudoobscura microRNA dps-mir-6 precursor (dps-mir-6-3)	Drosophila pseudoobscura
22		URS00000EBB92_7234	N/A	seed	3	78	Drosophila persimilis microRNA dpe-mir-6 precursor (dpe-mir-6-2)	Drosophila persimilis
23		URS00005F1170_7217	N/A	seed	3	74	Drosophila ananassae microRNA dan-mir-6 precursor (dan-mir-6-3)	Drosophila ananassae
24		URS00007A4E86_7227	N/A	seed	5	77	Drosophila melanogaster (fruit fly) microRNA dme-mir-6 precursor (dme-mir-6-1)	Drosophila melanogaster (fruit fly)
25		URS000030A165_7240	N/A	seed	1	71	Drosophila simulans microRNA dsi-mir-6 precursor (dsi-mir-6-1)	Drosophila simulans
26		URS0000084558_7237	N/A	seed	5	75	Drosophila pseudoobscura microRNA dps-mir-6 precursor (dps-mir-6-1)	Drosophila pseudoobscura
27		URS0000376FBE_7234	N/A	seed	1	69	Drosophila persimilis microRNA dpe-mir-6 precursor (dpe-mir-6-1)	Drosophila persimilis
28		URS000055EF9A_7222	N/A	seed	1	70	Drosophila grimshawi microRNA dgr-mir-6 precursor (dgr-mir-6-1, dgr-mir-6-4)	Drosophila grimshawi
29		URS00001E0A17_7230	N/A	seed	1	66	Drosophila mojavensis microRNA dmo-mir-6 precursor (dmo-mir-6-1)	Drosophila mojavensis
30		URS0000278918_7260	N/A	seed	1	69	Drosophila willistoni microRNA dwi-mir-6 precursor (dwi-mir-6-1)	Drosophila willistoni
31		URS00001ACC18_7244	N/A	seed	1	70	Drosophila virilis microRNA dvi-mir-6 precursor (dvi-mir-6-1)	Drosophila virilis
32		URS00000A9366_7217	N/A	seed	1	68	Drosophila ananassae microRNA dan-mir-6 precursor (dan-mir-6-1)	Drosophila ananassae
33		URS0000237498_7220	N/A	seed	1	71	Drosophila erecta microRNA der-mir-6 precursor (der-mir-6-1)	Drosophila erecta
34		URS0000249CC8_7238	N/A	seed	1	71	Drosophila sechellia microRNA dse-mir-6 precursor (dse-mir-6-1)	Drosophila sechellia
35		URS00002DE950_7245	N/A	seed	1	71	Drosophila yakuba microRNA dya-mir-6 precursor (dya-mir-6-1)	Drosophila yakuba
0		NC_047629.2	85.60	full	2,752,915	2,752,986	NC_047629.2 Drosophila albomicans strain 15112-1751.03 chromosome 3, ASM965048v2, whole genome shotgun sequence	Drosophila albomicans
1		CH902619.1	83.10	full	9,732,124	9,732,195	CH902619.1 Drosophila ananassae strain TSC#14024-0371.13 scaffold_13266 genomic scaffold, whole genome shotgun sequence	Drosophila ananassae
2		CP012524.1	82.30	full	11,349,054	11,348,982	Drosophila busckii chromosome 2R sequence.	Drosophila busckii
3		NW_016067610.1	82.10	full	88,757	88,681	NW_016067610.1 Drosophila kikkawai unplaced genomic scaffold, Dkik_2.0 scf7180000302679, whole genome shotgun sequence	Drosophila kikkawai
4		CH479181.1	81.60	full	8,906,791	8,906,866	CH479181.1 Drosophila persimilis strain MSH-3 scaffold_2 genomic scaffold, whole genome shotgun sequence	Drosophila persimilis
5		NC_046680.1	81.60	full	16,471,518	16,471,443	NC_046680.1 Drosophila pseudoobscura strain MV2-25 chromosome 3, UCI_Dpse_MV25, whole genome shotgun sequence	Drosophila pseudoobscura pseudoobscura
6		NW_016062090.1	81.30	full	74,235	74,305	NW_016062090.1 Drosophila rhopaloa unplaced genomic scaffold, Drho_2.0 scf7180000780066, whole genome shotgun sequence	Drosophila rhopaloa
7		AE013599.5	81.00	full	19,660,793	19,660,718	Drosophila melanogaster chromosome 2R.	Drosophila melanogaster (fruit fly)
8		CP012524.1	80.80	full	11,348,914	11,348,840	Drosophila busckii chromosome 2R sequence.	Drosophila busckii
9		CH480816.1	80.10	full	13,063,031	13,062,956	Drosophila sechellia strain Rob3c scaffold_1 genomic scaffold, whole genome shotgun sequence.	Drosophila sechellia
10		CM000164.1	80.10	full	14,706,379	14,706,304	CM000164.1 Drosophila simulans strain white501 chromosome 2R, whole genome shotgun sequence	Drosophila simulans
11		AE013599.5	79.80	full	19,660,941	19,660,870	Drosophila melanogaster chromosome 2R.	Drosophila melanogaster (fruit fly)
12		NW_016062090.1	79.60	full	74,382	74,457	NW_016062090.1 Drosophila rhopaloa unplaced genomic scaffold, Drho_2.0 scf7180000780066, whole genome shotgun sequence	Drosophila rhopaloa
13		CH933808.1	79.40	full	20,936,035	20,935,960	CH933808.1 Drosophila mojavensis strain TSC#15081-1352.22 scaffold_6496 genomic scaffold, whole genome shotgun sequence	Drosophila mojavensis
14		CH480816.1	79.10	full	13,063,179	13,063,108	Drosophila sechellia strain Rob3c scaffold_1 genomic scaffold, whole genome shotgun sequence.	Drosophila sechellia
15		CM000164.1	79.10	full	14,706,527	14,706,456	CM000164.1 Drosophila simulans strain white501 chromosome 2R, whole genome shotgun sequence	Drosophila simulans
16		NC_047629.2	78.90	full	2,753,062	2,753,131	NC_047629.2 Drosophila albomicans strain 15112-1751.03 chromosome 3, ASM965048v2, whole genome shotgun sequence	Drosophila albomicans
17		NW_016067610.1	78.60	full	88,904	88,834	NW_016067610.1 Drosophila kikkawai unplaced genomic scaffold, Dkik_2.0 scf7180000302679, whole genome shotgun sequence	Drosophila kikkawai
18		CH479181.1	78.60	full	8,906,645	8,906,725	CH479181.1 Drosophila persimilis strain MSH-3 scaffold_2 genomic scaffold, whole genome shotgun sequence	Drosophila persimilis
19		NC_046680.1	78.60	full	16,471,664	16,471,584	NC_046680.1 Drosophila pseudoobscura strain MV2-25 chromosome 3, UCI_Dpse_MV25, whole genome shotgun sequence	Drosophila pseudoobscura pseudoobscura
20		CH916375.1	78.50	full	2,108,163	2,108,087	Drosophila grimshawi strain TSC#15287-2541.00 scaffold_15112 genomic scaffold, whole genome shotgun sequence.	Drosophila grimshawi
21		CH920867.1	78.50	full	3,536	3,612	CH920867.1 Drosophila grimshawi strain TSC#15287-2541.00 scaffold_5621 genomic scaffold, whole genome shotgun sequence	Drosophila grimshawi
22		CH933808.1	78.40	full	20,936,216	20,936,138	CH933808.1 Drosophila mojavensis strain TSC#15081-1352.22 scaffold_6496 genomic scaffold, whole genome shotgun sequence	Drosophila mojavensis
23		LSRL02000014.1	78.40	full	1,253,995	1,253,917	LSRL02000014.1 Drosophila navojoa isolate navoj_Jal97 14, whole genome shotgun sequence	Drosophila navojoa
24		NC_047629.2	78.00	full	2,752,767	2,752,838	NC_047629.2 Drosophila albomicans strain 15112-1751.03 chromosome 3, ASM965048v2, whole genome shotgun sequence	Drosophila albomicans
25		CH916375.1	77.80	full	2,107,997	2,107,922	Drosophila grimshawi strain TSC#15287-2541.00 scaffold_15112 genomic scaffold, whole genome shotgun sequence.	Drosophila grimshawi
26		CH920867.1	77.80	full	3,700	3,775	CH920867.1 Drosophila grimshawi strain TSC#15287-2541.00 scaffold_5621 genomic scaffold, whole genome shotgun sequence	Drosophila grimshawi
27		LSRL02000014.1	77.50	full	1,253,814	1,253,739	LSRL02000014.1 Drosophila navojoa isolate navoj_Jal97 14, whole genome shotgun sequence	Drosophila navojoa
28		CH963850.1	77.00	full	1,651,077	1,651,000	Drosophila willistoni strain TSC#14030-0811.24 scf2_1100000004514 genomic scaffold, whole genome shotgun sequence.	Drosophila willistoni
29		NW_022060529.1	76.40	full	28,701,585	28,701,658	NW_022060529.1 Scaptodrosophila lebanonensis strain 11010-0011.00,11010-0021.00 unplaced genomic scaffold, SlebRS2 tig00000001-arrow-pilon, whole genome shotgun sequence	Scaptodrosophila lebanonensis
30		CH940648.1	76.10	full	4,112,959	4,113,033	CH940648.1 Drosophila virilis strain TSC#15010-1051.87 scaffold_12875 genomic scaffold, whole genome shotgun sequence	Drosophila virilis
31		CH480816.1	75.90	full	13,063,317	13,063,245	Drosophila sechellia strain Rob3c scaffold_1 genomic scaffold, whole genome shotgun sequence.	Drosophila sechellia
32		NW_022060529.1	75.90	full	28,701,741	28,701,818	NW_022060529.1 Scaptodrosophila lebanonensis strain 11010-0011.00,11010-0021.00 unplaced genomic scaffold, SlebRS2 tig00000001-arrow-pilon, whole genome shotgun sequence	Scaptodrosophila lebanonensis
33		JAMKOV010000007.1	75.80	full	2,057,974	2,057,904	JAMKOV010000007.1 Drosophila gunungcola strain Sukarami chromosome 2R 000006F, whole genome shotgun sequence	Drosophila gunungcola
34		CM000164.1	75.60	full	14,706,668	14,706,596	CM000164.1 Drosophila simulans strain white501 chromosome 2R, whole genome shotgun sequence	Drosophila simulans
35		JAMKOV010000007.1	75.50	full	2,057,827	2,057,752	JAMKOV010000007.1 Drosophila gunungcola strain Sukarami chromosome 2R 000006F, whole genome shotgun sequence	Drosophila gunungcola
36		CH963850.1	75.20	full	1,651,241	1,651,147	Drosophila willistoni strain TSC#14030-0811.24 scf2_1100000004514 genomic scaffold, whole genome shotgun sequence.	Drosophila willistoni
37		CH940648.1	74.60	full	4,112,785	4,112,862	CH940648.1 Drosophila virilis strain TSC#15010-1051.87 scaffold_12875 genomic scaffold, whole genome shotgun sequence	Drosophila virilis
38		NW_016062090.1	74.20	full	74,101	74,172	NW_016062090.1 Drosophila rhopaloa unplaced genomic scaffold, Drho_2.0 scf7180000780066, whole genome shotgun sequence	Drosophila rhopaloa
39		AE013599.5	73.70	full	19,661,080	19,661,008	Drosophila melanogaster chromosome 2R.	Drosophila melanogaster (fruit fly)
40		CH902619.1	72.70	full	9,731,964	9,732,045	CH902619.1 Drosophila ananassae strain TSC#14024-0371.13 scaffold_13266 genomic scaffold, whole genome shotgun sequence	Drosophila ananassae
41		JAMKOV010000007.1	71.70	full	2,058,116	2,058,044	JAMKOV010000007.1 Drosophila gunungcola strain Sukarami chromosome 2R 000006F, whole genome shotgun sequence	Drosophila gunungcola
42		CH479181.1	71.10	full	8,906,499	8,906,569	CH479181.1 Drosophila persimilis strain MSH-3 scaffold_2 genomic scaffold, whole genome shotgun sequence	Drosophila persimilis
43		CH940648.1	71.00	full	4,112,631	4,112,702	CH940648.1 Drosophila virilis strain TSC#15010-1051.87 scaffold_12875 genomic scaffold, whole genome shotgun sequence	Drosophila virilis
44		CH916375.1	70.80	full	2,108,302	2,108,231	Drosophila grimshawi strain TSC#15287-2541.00 scaffold_15112 genomic scaffold, whole genome shotgun sequence.	Drosophila grimshawi
45		CH920867.1	70.80	full	3,397	3,468	CH920867.1 Drosophila grimshawi strain TSC#15287-2541.00 scaffold_5621 genomic scaffold, whole genome shotgun sequence	Drosophila grimshawi
46		NW_004765279.1	69.00	full	70,241	70,320	NW_004765279.1 Musca domestica strain aabys unplaced genomic scaffold, Musca_domestica-2.0.2 Scaffold19303, whole genome shotgun sequence	Musca domestica (house fly)
47		NC_046680.1	68.60	full	16,471,810	16,471,740	NC_046680.1 Drosophila pseudoobscura strain MV2-25 chromosome 3, UCI_Dpse_MV25, whole genome shotgun sequence	Drosophila pseudoobscura pseudoobscura
48		CH902619.1	68.10	full	9,731,820	9,731,887	CH902619.1 Drosophila ananassae strain TSC#14024-0371.13 scaffold_13266 genomic scaffold, whole genome shotgun sequence	Drosophila ananassae
49		NW_004765279.1	67.80	full	70,622	70,696	NW_004765279.1 Musca domestica strain aabys unplaced genomic scaffold, Musca_domestica-2.0.2 Scaffold19303, whole genome shotgun sequence	Musca domestica (house fly)
50		CP012524.1	65.90	full	11,349,191	11,349,118	Drosophila busckii chromosome 2R sequence.	Drosophila busckii
51		JRES01000195.1	65.70	full	382,489	382,411	Lucilia cuprina strain LS Scaffold3, whole genome shotgun sequence.	Lucilia cuprina
52		CH963850.1	64.30	full	1,651,399	1,651,329	Drosophila willistoni strain TSC#14030-0811.24 scf2_1100000004514 genomic scaffold, whole genome shotgun sequence.	Drosophila willistoni
53		NW_016067610.1	63.40	full	89,041	88,975	NW_016067610.1 Drosophila kikkawai unplaced genomic scaffold, Dkik_2.0 scf7180000302679, whole genome shotgun sequence	Drosophila kikkawai
54		NW_004765279.1	62.50	full	70,426	70,505	NW_004765279.1 Musca domestica strain aabys unplaced genomic scaffold, Musca_domestica-2.0.2 Scaffold19303, whole genome shotgun sequence	Musca domestica (house fly)
55		NW_011876347.1	61.70	full	203,147	203,074	NW_011876347.1 Bactrocera dorsalis strain Punador unplaced genomic scaffold, ASM78921v2 scaffold00054, whole genome shotgun sequence	Bactrocera dorsalis (oriental fruit fly)
56		CH933808.1	59.50	full	20,936,381	20,936,314	CH933808.1 Drosophila mojavensis strain TSC#15081-1352.22 scaffold_6496 genomic scaffold, whole genome shotgun sequence	Drosophila mojavensis
57		LSRL02000014.1	59.50	full	1,254,151	1,254,084	LSRL02000014.1 Drosophila navojoa isolate navoj_Jal97 14, 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	RM00023	Rho independent terminator 2	9	0.375	109.1