Secondary structure and small RNA-seq evidence for dme-mir-1002

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:13747594-13747712 -	TGT----------AT-------------------CGGAATT--------AA-------TTAGAAATTATATATTTAAGTAGTGGATACAAAGGGCGAT-TTG-ATAT-AAA--AGTGTCGCATTGTATGACCTACTTAACTAGCTGATTTTGTATCCCAACATAATA--G
droSim1	chr2L:13506512-13506649 -	TGT----------CGGAATAAATATAATAATAATCGGAAAT--------AT-------TTAGAAATTATATATTTAAGTAGTGGATACAAAAGGCGAT-TTG-ATAT-AAA--AGTATCGCATTGTATGGCCTACTTAACTAGCTGATTTTGTATTCCAACATAAAA--T
droSec1	super_3:14439-14576 -	TGT----------CGGAATAAATATAATAATAATCGGAAAT--------AT-------TTAGAAATTATATATTTAAGTAGTGGATACAAAAGGCGAT-TTG-ATAT-AAA--AGTATCGCATTGTATGGCCTACTTAACTAGCTGATTTTGTATTCCAACATAAAA--T
droYak2	chr2L:10159916-10160031 -	TATGCTTCGAAGTTTTAA------------------------------------------AAAAATTATATATTTAAGTAGTGGATACAAAAGGCGAT-T-G-ATAT-AAA--AATGTCGCATTGTATGGCCTACTTAACTAGCTGATTTTGTATCCCAACTTA------
droEre2	scaffold_4929:11719022-11719139 +	TCT----------AT-------------------ATT----AATTG----A-------T-CAAAATTATATATCTAAGTAGTGGATACAAACGGCGAT-TTG-GTAT-AAA--AATGTCGCATTGTATGACCTGCTTAACTAGCTGATTTTGTATCCCAACGTACAA--A
droAna3	scaffold_12943:1815398-1815512 -	TCA----------TA-----------------------AATATCTGTGCAA-------A-CTAAATCATGTGTTTAAGTAGGCAATACAT-GGGCGAC-TAA-ATAA-AAT--ATACTCGCAATGTATAGCCTACATAACTAGTTGATTTTTGCAAGCATC--------C
dp4	chr4_group1:1722923-1723028 +	CCT----------CTCAA------------------------------------------AATAATCGGGCACCTAAGTAGTTGATACAA-GGGCGAT-AAT-GTAAAAGA--ACTTTCGCATTGTGTGACCTACTTAAATGCTCGATTGTTTCAAGCAACCT-------
droPer1	super_5:3483460-3483570 -	CCT----------CTCAA------------------------------------------AATAATCGGGCACCTAAGTAGTTGATACAA-GGGCGAT-AAT-GTAAAAGA--ACTTTCGCATTGTGTGACCTACTTAAATGCCCGATTGTTTCAAGCAACCTCTAA--A
droWil1	scaffold_180772:545437-545562 +	TCA----------TT--------------------TG----ATCTGGTCAT-------TGAAAAATGTTACACTTAAGTAGTTAATACAA-TGGCGAT-TCGTATTC-CATTGTACATCGCATTGTGTGAGTTACTTTGTTGAGAGATTTTTCCAAACAACAAGATAATC
droVir3	scaffold_12723:5043888-5043982 -	GCA----------AT---------------------------------------------GAAAATTGAACGCTTAAGTAGTTAATACAA-GGGCGAGTTTT-TTC----T--TGCATCGCATTGTGTGACCTACTTAAATGACAAATTTTCA--AG--AC--------A
droMoj3	scaffold_6500:16664711-16664807 +	TGA----------T----------------------------------------------GAAAATTCAGCACTTAAGTAGTTGATACAA-AGGCGAA-TTT-AT-T-AAA--TTTATCGCATTGTGTGAGCTACTTAAATGACAGATTTTTA-T-AGTAC--------G
droGri2	scaffold_15126:8057211-8057331 -	TGT----------AA------------------------ATATTTATAATCACTGTATT-GAAAATTTAACACTTAAGTAGTTGATACAA-GGGCGAGTTTC-ATA----A--AGTATCGCATTGTGTGACCTACTTGAATGAGAGATTTTTA--AGATACT--GTA--A

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:13747594-13747712 -	TGT----------AT-------------------CGGAATT--------AA-------TTAGAAATTATATATTTAAGTAGTGGATACAAAGGGCGAT-TTG-ATAT-AAA--AGTGTCGCATTGTATGACCTACTTAACTAGCTGATTTTGTATCCCAACATAATA--G
droSim1	chr2L:13506512-13506649 -	TGT----------CGGAATAAATATAATAATAATCGGAAAT--------AT-------TTAGAAATTATATATTTAAGTAGTGGATACAAAAGGCGAT-TTG-ATAT-AAA--AGTATCGCATTGTATGGCCTACTTAACTAGCTGATTTTGTATTCCAACATAAAA--T
droSec1	super_3:14439-14576 -	TGT----------CGGAATAAATATAATAATAATCGGAAAT--------AT-------TTAGAAATTATATATTTAAGTAGTGGATACAAAAGGCGAT-TTG-ATAT-AAA--AGTATCGCATTGTATGGCCTACTTAACTAGCTGATTTTGTATTCCAACATAAAA--T
droYak2	chr2L:10159916-10160031 -	TATGCTTCGAAGTTTTAA------------------------------------------AAAAATTATATATTTAAGTAGTGGATACAAAAGGCGAT-T-G-ATAT-AAA--AATGTCGCATTGTATGGCCTACTTAACTAGCTGATTTTGTATCCCAACTTA------
droEre2	scaffold_4929:11719022-11719139 +	TCT----------AT-------------------ATT----AATTG----A-------T-CAAAATTATATATCTAAGTAGTGGATACAAACGGCGAT-TTG-GTAT-AAA--AATGTCGCATTGTATGACCTGCTTAACTAGCTGATTTTGTATCCCAACGTACAA--A
droAna3	scaffold_12943:1815398-1815512 -	TCA----------TA-----------------------AATATCTGTGCAA-------A-CTAAATCATGTGTTTAAGTAGGCAATACAT-GGGCGAC-TAA-ATAA-AAT--ATACTCGCAATGTATAGCCTACATAACTAGTTGATTTTTGCAAGCATC--------C
dp4	chr4_group1:1722923-1723028 +	CCT----------CTCAA------------------------------------------AATAATCGGGCACCTAAGTAGTTGATACAA-GGGCGAT-AAT-GTAAAAGA--ACTTTCGCATTGTGTGACCTACTTAAATGCTCGATTGTTTCAAGCAACCT-------
droPer1	super_5:3483460-3483570 -	CCT----------CTCAA------------------------------------------AATAATCGGGCACCTAAGTAGTTGATACAA-GGGCGAT-AAT-GTAAAAGA--ACTTTCGCATTGTGTGACCTACTTAAATGCCCGATTGTTTCAAGCAACCTCTAA--A
droWil1	scaffold_180772:545437-545562 +	TCA----------TT--------------------TG----ATCTGGTCAT-------TGAAAAATGTTACACTTAAGTAGTTAATACAA-TGGCGAT-TCGTATTC-CATTGTACATCGCATTGTGTGAGTTACTTTGTTGAGAGATTTTTCCAAACAACAAGATAATC
droVir3	scaffold_12723:5043888-5043982 -	GCA----------AT---------------------------------------------GAAAATTGAACGCTTAAGTAGTTAATACAA-GGGCGAGTTTT-TTC----T--TGCATCGCATTGTGTGACCTACTTAAATGACAAATTTTCA--AG--AC--------A
droMoj3	scaffold_6500:16664711-16664807 +	TGA----------T----------------------------------------------GAAAATTCAGCACTTAAGTAGTTGATACAA-AGGCGAA-TTT-AT-T-AAA--TTTATCGCATTGTGTGAGCTACTTAAATGACAGATTTTTA-T-AGTAC--------G
droGri2	scaffold_15126:8057211-8057331 -	TGT----------AA------------------------ATATTTATAATCACTGTATT-GAAAATTTAACACTTAAGTAGTTGATACAA-GGGCGAGTTTC-ATA----A--AGTATCGCATTGTGTGACCTACTTGAATGAGAGATTTTTA--AGATACT--GTA--A

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGTCGGAATAAATATAATAATAATCGGAAATATTTAGAAATTATATATTTAAGTAGTGGATACAAAAGGCGATTTGATATAAA---AGTATCGCATTGTATGGCCTACTTAACTAGCTGATTTTGTATTCCAACATAAAAT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................................TTAAGTAGTGGATACAAAAGGCGA.....................................................................	24	1	3281.00	3281	3281
................................................TTAAGTAGTGGATACAAAAGGCG......................................................................	23	1	236.00	236	236
................................................TTAAGTAGTGGATACAAAAGGCGAT....................................................................	25	1	216.00	216	216
.................................................TAAGTAGTGGATACAAAAGGCGAT....................................................................	24	1	95.00	95	95
............................................................................................GCATTGTATGGCCTACTTAACT...........................	22	1	77.00	77	77
................................................TTAAGTAGTGGATACAAAAGGC.......................................................................	22	1	57.00	57	57
...........................................................................................CGCATTGTATGGCCTACTTAAC............................	22	1	51.00	51	51
.................................................TAAGTAGTGGATACAAAAGGCGA.....................................................................	23	1	41.00	41	41
................................................TTAAGTAGTGGATACAAAAGG........................................................................	21	1	18.00	18	18
.................................................TAAGTAGTGGATACAAAAGGCGATT...................................................................	25	1	12.00	12	12
...........................................................................................CGCATTGTATGGCCTACTTAACT...........................	23	1	10.00	10	10
.................................................TAAGTAGTGGATACAAAAGGC.......................................................................	21	1	8.00	8	8
............................................................................................GCATTGTATGGCCTACTTAAC............................	21	1	6.00	6	6
.............................................................................................CATTGTATGGCCTACTTAACT...........................	21	1	5.00	5	5
................................................TTAAGTAGTGGATACAAAAG.........................................................................	20	1	3.00	3	3
................................................TTAAGTAGTGGATACAAAAGGCGATT...................................................................	26	1	3.00	3	3
.................................................TAAGTAGTGGATACAAAAGGCG......................................................................	22	1	3.00	3	3

dp4

CCTCTCAA----------AATAATCGG-----------------GCACCTAAGTAGTTGATACA-AGGGCGATA--ATGTAAAAGAACTTTCGCATTGTGTGACCTACTTAAATGCTCGATTGTTTCAAGCAACCT-----	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................................CTAAGTAGTTGATACA-AGGGCGA.....................................................................	23	1	1684.00	1684	1684	0
.................................................TAAGTAGTTGATACA-AGGGCGA.....................................................................	22	1	223.00	223	223	0
............................................................................................GCATTGTGTGACCTACTTAAAT...........................	22	1	190.00	190	189	1
.................................................TAAGTAGTTGATACA-AGGGCGAT....................................................................	23	1	154.00	154	154	0
................................................CTAAGTAGTTGATACA-AGGGC.......................................................................	21	1	104.00	104	104	0
................................................CTAAGTAGTTGATACA-AGGGCG......................................................................	22	1	40.00	40	40	0
...........................................................................................CGCATTGTGTGACCTACTTAAA............................	22	1	37.00	37	37	0
................................................CTAAGTAGTTGATACA-AGGG........................................................................	20	1	36.00	36	36	0
.................................................TAAGTAGTTGATACA-AGGGC.......................................................................	20	1	31.00	31	31	0
............................................................................................GCATTGTGTGACCTACTTAAA............................	21	1	18.00	18	18	0
...............................................CCTAAGTAGTTGATACA-AGGGCG......................................................................	23	1	15.00	15	15	0
.................................................TAAGTAGTTGATACA-AGGGCG......................................................................	21	1	13.00	13	13	0
..........................................................................................TCGCATTGTGTGACCTACTTAAA............................	23	1	12.00	12	12	0
.........................................................................................TTCGCATTGTGTGACCTACTTA..............................	22	1	10.00	10	10	0
................................................CTAAGTAGTTGATACA-AGG.........................................................................	19	1	9.00	9	9	0
.........................................................................................TTCGCATTGTGTGACCTACTTAAA............................	24	1	7.00	7	7	0
..........................................................................................TCGCATTGTGTGACCTACTTAA.............................	22	1	6.00	6	6	0
.................................................TAAGTAGTTGATACA-AGGG........................................................................	19	1	6.00	6	6	0
...........................................................................................CGCATTGTGTGACCTACTTAA.............................	21	1	5.00	5	5	0
................................................CTAAGTAGTTGATACA-AGGGCGAT....................................................................	24	1	5.00	5	5	0
.............................................................................................CATTGTGTGACCTACTTAAATG..........................	22	1	4.00	4	4	0
............................................................................................GCATTGTGTGACCTACTTAA.............................	20	1	3.00	3	3	0
...................................................AGTAGTTGATACA-AGGGCGATA--ATG..............................................................	25	1	2.00	2	2	0
..............................................................................................ATTGTGTGACCTACTTAAAT...........................	20	1	2.00	2	2	0
...............................................CCTAAGTAGTTGATACA-AGGGCGA.....................................................................	24	1	2.00	2	2	0
.................................................TAAGTAGTTGATACA-AGGGCGATA--.................................................................	24	1	2.00	2	2	0
...................................................AGTAGTTGATACA-AGGGCGA.....................................................................	20	1	2.00	2	2	0
.........................................................................................TTCGCATTGTGTGACCTACTTAA.............................	23	1	2.00	2	2	0
.............................................................................................CATTGTGTGACCTACTTAAAT...........................	21	1	1.00	1	1	0
..................................................AAGTAGTTGATACA-AGGGCGATA--.................................................................	23	1	1.00	1	1	0
................................................CTAAGTAGTTGATACA-AG..........................................................................	18	1	1.00	1	1	0
....................................................GTAGTTGATACA-AGGGCG......................................................................	18	1	1.00	1	1	0
..................................................AAGTAGTTGATACA-AGGGCGA.....................................................................	21	1	1.00	1	1	0
....................................................GTAGTTGATACA-AGGGCGA.....................................................................	19	1	1.00	1	1	0
...............................................CCTAAGTAGTTGATACA-AGG.........................................................................	20	1	1.00	1	1	0
............................................................................................GCATTGTGTGACCTACTTAAATG..........................	23	1	1.00	1	1	0
................................................CTAAGTAGTTGATACA-AGGGCGATA--.................................................................	25	1	1.00	1	1	0
...............................................CCTAAGTAGTTGATACA-AGGGC.......................................................................	22	1	1.00	1	1	0

Secondary Structure

dm3

-21.7	-20.9	-20.7

droSim1

-21.4	-21.4	-20.4	-20.4

droSec1

-21.4	-21.4	-20.4	-20.4

droYak2

-21.4	-20.7	-20.4

droEre2

-23.0	-22.9	-22.5	-22.3

droAna3

-25.1	-25.1	-24.5	-24.4	-24.4	-24.1

dp4

-33.6	-33.2	-33.1	-32.7	-32.6

droPer1

-36.6	-36.2	-36.1	-35.7	-35.6

droWil1

-24.9	-24.9	-24.7	-24.7	-24.3	-24.3

droVir3

-25.2	-24.3

droMoj3

-26.9	-26.3

droGri2

-23.8	-22.9

Generated: 01/05/2013 at 05:05 PM