Secondary structure and small RNA-seq evidence for dme-mir-996

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:25042891-25043017 +	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAA-CGAA----G----A------GAGC
droSim1	chr3R:24713787-24713913 +	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAA-CGAA----G----A------GAGC
droSec1	super_4:3905684-3905810 +	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAA-CGAA----G----A------GAGC
droYak2	chr3R:21454418-21454540 -	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACTA-CGAA----G----A----------
droEre2	scaffold_4820:2987415-2987537 -	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACTA-CGAA----G----A----------
droAna3	scaffold_13340:14198945-14199070 -	GGTCT----------------------------------------------------------------------------------------------------------TTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GTTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAC-CAAA----G----AGTCGGATAGT
dp4	chr2:1883607-1883737 +	CAGCGT---------------------------------------------------------------------------------------------------TTGCTCTTCTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAACACAA-CGAACCGAA----A------GAGC
droPer1	super_7:2047020-2047150 +	CAGCGT---------------------------------------------------------------------------------------------------TTGCTCTTCTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAACACAA-CGAACCGAA----A------GAGC
droWil1	scaffold_181108:1735977-1736125 +	GGATGGATGGAGTCCTTTCTATGTGGCAGCG----------------------------------------------------------------------------TCTCT----TGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGTTTGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAA-C-AA----G----A---GCGCAGC
droVir3	scaffold_12822:2333349-2333515 +	GAGAGG-----------------CTGCAGCTGCTGCCTGATTTTTGATTTTTTTTT-TTTTTTTGTTTC--GCT----------------------------CTTTTGCTCTTCTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAACACA--------------------------
droMoj3	scaffold_6540:26449231-26449397 +	GAGAGG---GAGGT----CTCTACTGCAGCTGCTGCCTGAT-----ATTTCTTTTT------------------------------------------------TTTGCTCTTCTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAATACACACAGC----G----A------AAAC
droGri2	scaffold_14624:3251484-3251700 +	AGAGAGAGAGAGA---------------G--------AAATGTTTGCTTGCTCTCTATCTCTCTGTCTCTCGCCCACTTTCTAGCTTCAACTGCAACTGCAACTGCTGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAACACAC-AACACAAAAAAAAAAGAGGAGAGC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:25042891-25043017 +	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAA-CGAA----G----A------GAGC
droSim1	chr3R:24713787-24713913 +	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAA-CGAA----G----A------GAGC
droSec1	super_4:3905684-3905810 +	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAA-CGAA----G----A------GAGC
droYak2	chr3R:21454418-21454540 -	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACTA-CGAA----G----A----------
droEre2	scaffold_4820:2987415-2987537 -	GGAAGG---------------------------------------------------------------------------------------------------ATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACTA-CGAA----G----A----------
droAna3	scaffold_13340:14198945-14199070 -	GGTCT----------------------------------------------------------------------------------------------------------TTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-GTTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAC-CAAA----G----AGTCGGATAGT
dp4	chr2:1883607-1883737 +	CAGCGT---------------------------------------------------------------------------------------------------TTGCTCTTCTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAACACAA-CGAACCGAA----A------GAGC
droPer1	super_7:2047020-2047150 +	CAGCGT---------------------------------------------------------------------------------------------------TTGCTCTTCTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAACACAA-CGAACCGAA----A------GAGC
droWil1	scaffold_181108:1735977-1736125 +	GGATGGATGGAGTCCTTTCTATGTGGCAGCG----------------------------------------------------------------------------TCTCT----TGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGTTTGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAA-C-AA----G----A---GCGCAGC
droVir3	scaffold_12822:2333349-2333515 +	GAGAGG-----------------CTGCAGCTGCTGCCTGATTTTTGATTTTTTTTT-TTTTTTTGTTTC--GCT----------------------------CTTTTGCTCTTCTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAACACA--------------------------
droMoj3	scaffold_6540:26449231-26449397 +	GAGAGG---GAGGT----CTCTACTGCAGCTGCTGCCTGAT-----ATTTCTTTTT------------------------------------------------TTTGCTCTTCTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAATACACACAGC----G----A------AAAC
droGri2	scaffold_14624:3251484-3251700 +	AGAGAGAGAGAGA---------------G--------AAATGTTTGCTTGCTCTCTATCTCTCTGTCTCTCGCCCACTTTCTAGCTTCAACTGCAACTGCAACTGCTGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGT-TGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAACACAC-AACACAAAAAAAAAAGAGGAGAGC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GGAAGGATGCTCTTTTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGTGGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAGCACAACGAA----GAGAGC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...........................................................................TGACTAGATTTCATGCTCGTCT..................................	22	1	922.00	922	922
...........................................................................TGACTAGATTTCATGCTCGTCTA.................................	23	1	814.00	814	814
...........................................................................TGACTAGATTTCATGCTCGT....................................	20	1	401.00	401	401
.................................GCGAACATGGATCTAGTGCACG............................................................................	22	1	312.00	312	312
................................GGCGAACATGGATCTAGTGCACG............................................................................	23	1	309.00	309	309
...........................................................................TGACTAGATTTCATGCTCGTC...................................	21	1	216.00	216	216
..........................................................................GTGACTAGATTTCATGCTCGTCT..................................	23	1	50.00	50	50
.......................................................GTGGTTCATGATTAAGTTCG........................................................	20	1	31.00	31	31
.................................GCGAACATGGATCTAGTGCACGG...........................................................................	23	1	19.00	19	19
................................GGCGAACATGGATCTAGTGCA..............................................................................	21	1	18.00	18	18
................................GGCGAACATGGATCTAGTGCAC.............................................................................	22	1	15.00	15	15
................................GGCGAACATGGATCTAGTGC...............................................................................	20	1	14.00	14	14
..................................CGAACATGGATCTAGTGCACGG...........................................................................	22	1	13.00	13	13
..........................................................................GTGACTAGATTTCATGCTCGTC...................................	22	1	10.00	10	10
.................................GCGAACATGGATCTAGTGCAC.............................................................................	21	1	7.00	7	7
..........................................................................GTGACTAGATTTCATGCTCGT....................................	21	1	6.00	6	6
...............................CGGCGAACATGGATCTAGTGCACG............................................................................	24	1	5.00	5	5
.................................GCGAACATGGATCTAGTGC...............................................................................	19	1	4.00	4	4
.............................................................................ACTAGATTTCATGCTCGTCT..................................	20	1	4.00	4	4
.............................................................................ACTAGATTTCATGCTCGTCTA.................................	21	1	3.00	3	3
.................................GCGAACATGGATCTAGTGCA..............................................................................	20	1	3.00	3	3
.................................GCGAACATGGATCTAGTGCACGGT..........................................................................	24	1	3.00	3	3
...........................................................................TGACTAGATTTCATGCTC......................................	18	1	2.00	2	2
...........................................................................TGACTAGATTTCATGCTCGTCTAT................................	24	1	2.00	2	2
............................................................................GACTAGATTTCATGCTCGT....................................	19	1	2.00	2	2
...................................GAACATGGATCTAGTGCACG............................................................................	20	1	2.00	2	2
..................................CGAACATGGATCTAGTGCACG............................................................................	21	1	1.00	1	1
............................................................................GACTAGATTTCATGCTCGTC...................................	20	1	1.00	1	1
...........................................................................TGACTAGATTTCATGCTCG.....................................	19	1	1.00	1	1
.............................................................................ACTAGATTTCATGCTCGTC...................................	19	1	1.00	1	1
................................GGCGAACATGGATCTAGTGCACGG...........................................................................	24	1	1.00	1	1

dp4

CAGCGTTTGCTCTTCTCTGACTCTATTTTGTCGGCGAACATGGATCTAGTGCACGGTTGTTCATGATTAAGTTCGTGACTAGATTTCATGCTCGTCTATTAAGTTGGGTCAACACAACGAACCGAAAGAGC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...........................................................................TGACTAGATTTCATGCTCGTCT..................................	22	1	7778.00	7778	1658	6120
...........................................................................TGACTAGATTTCATGCTCGTCTA.................................	23	1	2344.00	2344	1471	873
...........................................................................TGACTAGATTTCATGCTCGTC...................................	21	1	1740.00	1740	435	1305
...........................................................................TGACTAGATTTCATGCTCGT....................................	20	1	1635.00	1635	787	848
................................GGCGAACATGGATCTAGTGCACG............................................................................	23	1	607.00	607	517	90
.................................GCGAACATGGATCTAGTGCACG............................................................................	22	1	526.00	526	413	113
...........................................................................TGACTAGATTTCATGCTCG.....................................	19	1	88.00	88	31	57
................................GGCGAACATGGATCTAGTGCA..............................................................................	21	1	50.00	50	44	6
.................................GCGAACATGGATCTAGTGCAC.............................................................................	21	1	49.00	49	19	30
.................................GCGAACATGGATCTAGTGCA..............................................................................	20	1	30.00	30	8	22
................................GGCGAACATGGATCTAGTGC...............................................................................	20	1	25.00	25	24	1
................................GGCGAACATGGATCTAGTGCAC.............................................................................	22	1	23.00	23	21	2
..........................................................................GTGACTAGATTTCATGCTCGTCT..................................	23	1	18.00	18	14	4
...........................................................................TGACTAGATTTCATGCTCGTCTAT................................	24	1	9.00	9	4	5
.................................GCGAACATGGATCTAGTGCACGG...........................................................................	23	1	8.00	8	7	1
...........................................................................TGACTAGATTTCATGCTC......................................	18	1	7.00	7	4	3
..........................................................................GTGACTAGATTTCATGCTCGTC...................................	22	1	6.00	6	2	4
.......................................................GTTGTTCATGATTAAGTTCG........................................................	20	1	5.00	5	4	1
............................................................................GACTAGATTTCATGCTCGTCT..................................	21	1	4.00	4	1	3
..........................................................................GTGACTAGATTTCATGCTCGT....................................	21	1	4.00	4	2	2
.................................GCGAACATGGATCTAGTGC...............................................................................	19	1	3.00	3	1	2
..................................CGAACATGGATCTAGTGCACGG...........................................................................	22	1	3.00	3	3	0
.............................................................................ACTAGATTTCATGCTCGTCT..................................	20	1	2.00	2	1	1
............................................................................GACTAGATTTCATGCTCGTC...................................	20	1	2.00	2	0	2
.............................................................................ACTAGATTTCATGCTCGTC...................................	19	1	2.00	2	0	2
..................................CGAACATGGATCTAGTGCACG............................................................................	21	1	2.00	2	2	0
.................................GCGAACATGGATCTAGTGCACGGT..........................................................................	24	1	2.00	2	2	0
...................................GAACATGGATCTAGTGCACGGT..........................................................................	22	1	1.00	1	1	0