Secondary structure and small RNA-seq evidence for dme-mir-988

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:8046362-8046490 -	CAAAAGAA---CAT------AGTT-G-----------------------------ACGGCGGTA--------------------CCGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGATGA-TCTG-CGA---------A----------------ATACA-CAGTGGTAT
droSim1	chr2R_random:2089209-2089337 -	CTAGAGAA---CAT------TTTT-G-----------------------------ATGGCGGTA--------------------CCGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGATGA-TCTG-AGA---------A----------------ATACA-CAGTGATAT
droSec1	super_1:5591420-5591548 -	CTAGAGAA---CAT------TTTT-G-----------------------------ATGGCGGTA--------------------CCGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGATGA-TCTG-CGA---------A----------------ATACA-CAGTGTTTT
droYak2	chr2R:8904838-8904966 +	CTAAATAA---CAT------TTTT-C-----------------------------ATGGCGTTA--------------------CTGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGGTGA-CCTG-CGA---------A----------------ATACA-CAGGGATAT
droEre2	scaffold_4845:17747735-17747863 +	CAGAAAAA---CAT------ATTT-G-----------------------------ATGACGGTA--------------------CCGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--GAAGGTGA-CCTG-CGA---------A----------------ATACA-CAGTGTTAT
droAna3	scaffold_13266:2579688-2579821 +	TAATGGAA---TCA---GTAAGTG-G-----------------------------AAAGGTGTA--------------------CTGGACATTTTGGGTGTGTGATTTGTGGCAAAGTGATAGGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--CAAGGTGC-TTTC-CAACGG-----CA------------------ACA-TATCAGCAA
dp4	chr3:405625-405769 -	CCGGATAA---C---------T-----------------GGGTATCCAGGAATCCAGACT------------------------GTGGACATTTTGGGTGTGTGATTTGTGGCAAAGTGATATGCATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGTTGAAT--CCC-ACACCTA-----CACTCTCAT------ATAAT----GATCAT
droPer1	super_2:590063-590227 -	AAGAAAAA---AGT------TGTTATATCCCGGATAACTGGGTATCCAGGAATCCAGACT------------------------GTGGACATTTTGGGTGTGTGATTTGTGGCAAAGTGATATGCATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGTTGAAT--CCC-ACACCTA-----CACTCTCAG------ATAAT----GATCAT
droWil1	scaffold_181141:3254354-3254482 +	AAGT---A---CATTTGTTTAGTT-A-----------------------------AAACGAATT--------------------GTGGGCATTTCGGGCGTGTGATTTGTAGCAAAGTGATATGTACT-TGAT--AATCCCCTTGTTGCAAACCTCACGCCGGAAAGATGT-C-TC--CA---------A----------------ATACATCAG-----T
droVir3	scaffold_12875:19840344-19840491 +	TATGCACAGATCAT------GT-------------------------------CCAGAGTGT--GTAATA-----------TATCTGCGCATTTTGGGCGTGTGATTTGTGGCAAAGTGATGAGC--TTGGATTCCATCCCCTTGTTGCAAACCTCACGCC--AAAGGTGG-C------GCATTTAACCAGCA-----AT------ATAAA-GATTCATGT
droMoj3	scaffold_6496:6364073-6364233 -	TGGATAAA---GAC------TATT-C-----------------------------GGAGTGTTA----TATCTATCATGTGTATTTGCGCATTTTGGTCGTGTGATTTGTGGCAAAGTGATGAGC-TA-TGATTCCATCCCCTTGTTGCAAACCTCACGCT--GAAGGTGA-C------GCATAGCAGCAACA-----ATTGAAAGATATT-CGATTAAAC
droGri2	scaffold_15245:18189031-18189168 +	TAAA---G---CAT------ATTA-A----------------ATTC---------CGAGTGT--G--GTA-----------TTTCTGTGCATTTTGGGCGTGTGATTTGTGGCAAAGTGATGAGC--T-TGATTCCATCCCCTTGTTGCAAACCTCACGCC--GAAGGTGG-C------GCATCTAAGCA----------------ACA-A-TATTAATAT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:8046362-8046490 -	CAAAAGAA---CAT------AGTT-G-----------------------------ACGGCGGTA--------------------CCGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGATGA-TCTG-CGA---------A----------------ATACA-CAGTGGTAT
droSim1	chr2R_random:2089209-2089337 -	CTAGAGAA---CAT------TTTT-G-----------------------------ATGGCGGTA--------------------CCGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGATGA-TCTG-AGA---------A----------------ATACA-CAGTGATAT
droSec1	super_1:5591420-5591548 -	CTAGAGAA---CAT------TTTT-G-----------------------------ATGGCGGTA--------------------CCGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGATGA-TCTG-CGA---------A----------------ATACA-CAGTGTTTT
droYak2	chr2R:8904838-8904966 +	CTAAATAA---CAT------TTTT-C-----------------------------ATGGCGTTA--------------------CTGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGGTGA-CCTG-CGA---------A----------------ATACA-CAGGGATAT
droEre2	scaffold_4845:17747735-17747863 +	CAGAAAAA---CAT------ATTT-G-----------------------------ATGACGGTA--------------------CCGGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--GAAGGTGA-CCTG-CGA---------A----------------ATACA-CAGTGTTAT
droAna3	scaffold_13266:2579688-2579821 +	TAATGGAA---TCA---GTAAGTG-G-----------------------------AAAGGTGTA--------------------CTGGACATTTTGGGTGTGTGATTTGTGGCAAAGTGATAGGTATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--CAAGGTGC-TTTC-CAACGG-----CA------------------ACA-TATCAGCAA
dp4	chr3:405625-405769 -	CCGGATAA---C---------T-----------------GGGTATCCAGGAATCCAGACT------------------------GTGGACATTTTGGGTGTGTGATTTGTGGCAAAGTGATATGCATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGTTGAAT--CCC-ACACCTA-----CACTCTCAT------ATAAT----GATCAT
droPer1	super_2:590063-590227 -	AAGAAAAA---AGT------TGTTATATCCCGGATAACTGGGTATCCAGGAATCCAGACT------------------------GTGGACATTTTGGGTGTGTGATTTGTGGCAAAGTGATATGCATT-TGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGTTGAAT--CCC-ACACCTA-----CACTCTCAG------ATAAT----GATCAT
droWil1	scaffold_181141:3254354-3254482 +	AAGT---A---CATTTGTTTAGTT-A-----------------------------AAACGAATT--------------------GTGGGCATTTCGGGCGTGTGATTTGTAGCAAAGTGATATGTACT-TGAT--AATCCCCTTGTTGCAAACCTCACGCCGGAAAGATGT-C-TC--CA---------A----------------ATACATCAG-----T
droVir3	scaffold_12875:19840344-19840491 +	TATGCACAGATCAT------GT-------------------------------CCAGAGTGT--GTAATA-----------TATCTGCGCATTTTGGGCGTGTGATTTGTGGCAAAGTGATGAGC--TTGGATTCCATCCCCTTGTTGCAAACCTCACGCC--AAAGGTGG-C------GCATTTAACCAGCA-----AT------ATAAA-GATTCATGT
droMoj3	scaffold_6496:6364073-6364233 -	TGGATAAA---GAC------TATT-C-----------------------------GGAGTGTTA----TATCTATCATGTGTATTTGCGCATTTTGGTCGTGTGATTTGTGGCAAAGTGATGAGC-TA-TGATTCCATCCCCTTGTTGCAAACCTCACGCT--GAAGGTGA-C------GCATAGCAGCAACA-----ATTGAAAGATATT-CGATTAAAC
droGri2	scaffold_15245:18189031-18189168 +	TAAA---G---CAT------ATTA-A----------------ATTC---------CGAGTGT--G--GTA-----------TTTCTGTGCATTTTGGGCGTGTGATTTGTGGCAAAGTGATGAGC--T-TGATTCCATCCCCTTGTTGCAAACCTCACGCC--GAAGGTGG-C------GCATCTAAGCA----------------ACA-A-TATTAATAT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTAGAGAACATTTTTGATGGCGGTACC----------------GGGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATTTGATCATCCCCTTGTTGCAAACCTCACGCCAAAGATGA-TCTGAGAAATACACAGTGATAT---------	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................................................................................CCCCTTGTTGCAAACCTCACG..........................................	21	1	401.00	401	401
............................................................................................CCCCTTGTTGCAAACCTCACGC.........................................	22	1	211.00	211	211
........................................................GTGTGATTTGTAGCAAAGTGAT.............................................................................	22	1	21.00	21	21
........................................................GTGTGATTTGTAGCAAAGTGA..............................................................................	21	1	11.00	11	11
........................................................GTGTGATTTGTAGCAAAGTGATA............................................................................	23	1	10.00	10	10
.............................................................................................CCCTTGTTGCAAACCTCACG..........................................	20	1	8.00	8	8
............................................................................................CCCCTTGTTGCAAACCTCAC...........................................	20	1	7.00	7	7
.........................................................TGTGATTTGTAGCAAAGTGATA............................................................................	22	1	5.00	5	5
........................................................GTGTGATTTGTAGCAAAGTG...............................................................................	20	1	3.00	3	3
...........................................................................................TCCCCTTGTTGCAAACCTCACG..........................................	22	1	3.00	3	3
..............................................................................................CCTTGTTGCAAACCTCACGC.........................................	20	1	3.00	3	3
............................................................................................CCCCTTGTTGCAAACCTCA............................................	19	1	2.00	2	2
.........................................................TGTGATTTGTAGCAAAGTGAT.............................................................................	21	1	2.00	2	2
...........................................................................................TCCCCTTGTTGCAAACCTCACGC.........................................	23	1	1.00	1	1
........................................................GTGTGATTTGTAGCAAAGT................................................................................	19	1	1.00	1	1
.........................................................TGTGATTTGTAGCAAAGTGATATG..........................................................................	24	1	1.00	1	1
.....................GGTACC----------------GGGCATTTTGGGT...................................................................................................	19	1	1.00	1	1
.............................................................................................CCCTTGTTGCAAACCTCACGC.........................................	21	1	1.00	1	1

dp4

CCGGATAACTG----------GGTATCCAGGAATCCAGACTGTGGACATTTTGGGTGTGTGATTTGTGGCAAAGTGATATGCATTTGATCATCCCCTTGTTGCAAACCTCACGCCAAAGTTGAATCCCACACCTACACTCTCATATAATGATCAT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................................................................................CCCCTTGTTGCAAACCTCACG..........................................	21	1	456.00	456	290	166
............................................................................................CCCCTTGTTGCAAACCTCACGC.........................................	22	1	420.00	420	199	221
........................................................GTGTGATTTGTGGCAAAGTGAT.............................................................................	22	1	45.00	45	17	28
........................................................GTGTGATTTGTGGCAAAGTG...............................................................................	20	1	38.00	38	3	35
.........................................................TGTGATTTGTGGCAAAGTGAT.............................................................................	21	1	27.00	27	5	22
........................................................GTGTGATTTGTGGCAAAGTGA..............................................................................	21	1	24.00	24	6	18
.........................................................TGTGATTTGTGGCAAAGTGA..............................................................................	20	1	16.00	16	0	16
.........................................................TGTGATTTGTGGCAAAGTGATA............................................................................	22	1	10.00	10	3	7
............................................................................................CCCCTTGTTGCAAACCTCAC...........................................	20	1	8.00	8	5	3
.............................................................................................CCCTTGTTGCAAACCTCACG..........................................	20	1	8.00	8	6	2
.............................................................................................CCCTTGTTGCAAACCTCACGC.........................................	21	1	7.00	7	2	5
........................................................GTGTGATTTGTGGCAAAGT................................................................................	19	1	7.00	7	1	6
...........................................................................................TCCCCTTGTTGCAAACCTCACG..........................................	22	1	6.00	6	4	2
.......................................................TGTGTGATTTGTGGCAAAGTG...............................................................................	21	1	4.00	4	0	4
.....................................GACTGTGGACATTTTGGGT...................................................................................................	19	1	4.00	4	4	0
........................................................GTGTGATTTGTGGCAAAG.................................................................................	18	1	3.00	3	1	2
.......................................................TGTGTGATTTGTGGCAAAGTGAT.............................................................................	23	1	3.00	3	2	1
...............................................................................................CTTGTTGCAAACCTCACGC.........................................	19	1	3.00	3	3	0
.......................................................TGTGTGATTTGTGGCAAAGTGA..............................................................................	22	1	2.00	2	0	2
............................................................................................CCCCTTGTTGCAAACCTCA............................................	19	1	2.00	2	1	1
............................................................................................CCCCTTGTTGCAAACCTCACGCC........................................	23	1	1.00	1	1	0
........................................................GTGTGATTTGTGGCAAAGTGATA............................................................................	23	1	1.00	1	0	1
.......................................................TGTGTGATTTGTGGCAAAG.................................................................................	19	1	1.00	1	0	1
................................................................................................TTGTTGCAAACCTCACGC.........................................	18	1	1.00	1	1	0
...............................................................................................CTTGTTGCAAACCTCACG..........................................	18	1	1.00	1	1	0
...........................................................TGATTTGTGGCAAAGTGAT.............................................................................	19	1	1.00	1	0	1