Secondary structure and small RNA-seq evidence for dme-mir-958

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:22662374-22662495 -	GGATT-TTCC-------------------------ACGATCGGCGTGTCTATGGCAAGTAGAATAGCAGGCTTATCACATGTTTAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCACACCCG---------A
droSim1	chr3L:21947666-21947787 -	GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCACACCCG---------A
droSec1	super_11:2578674-2578788 -	GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCA----------------
droYak2	chr3L:23128644-23128763 -	GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTTAACTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCGAACCC-----------
droEre2	scaffold_4784:22312266-22312387 -	GGATT-GTCT-------------------------ACGATCGGCGTGGCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTTACATCAAACCCG---------A
droAna3	scaffold_13337:22380395-22380515 -	GAATA-TTCCA------------------------ACGACCGGTGGGTTTTTAGCAAGTAGAATAGCAGGCTTATCACAGGTTCC-TTTA-ACCCACTGTGAGATTCTTCTATTCTACTTTCGAGAAACACCCGTAAACACCGATCTC-----------
dp4	chrXR_group8:344159-344293 -	GGATA-TGGC-------------------T--AGCACGATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATCTAATAGAGC-AGCCCTC
droPer1	super_96:132292-132395 +	G-------------------------------------ATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATC-----------------
droWil1	scaffold_180698:7060886-7061014 +	TGAGTTTTGA--------------CTATGACT--ATCTAACGGTGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCCTTTACAACCGGTGTGAGATTCTTCTATTCTACTTTCGAAAAGCACCCGATAACAACAAA--------------
droVir3	scaffold_13049:17089392-17089522 +	TGTTT-TTTTA------ATGTTCTCTATAT--ATTTTGATCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTACAATTCA-ACCTAGTGTGAGATTCTTCTATTCTACTTTCGACAAACACCAGCTAGCGTC-----------------
droMoj3	scaffold_6680:22084806-22084935 +	GTGTT-TTCC--------------CTGTGATT--CTCAGTCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTACCATTTG-ACCGAGTGTGAGATTCTTCTATTCTACTTTCGACAAGCACCAGTCAGCGTCGTTTTCG----------
droGri2	scaffold_15110:15103971-15104124 -	GTGTG-TGCAGGTTTTATGGTTTTTGTTTT--ACTCTGATCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTAACATTCG-ACATGGTGTGAGATTCTTCTATTCTACTTTCGACAAACACCAGCTAGCGTCACATTCAGTTAAGTTTA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:22662374-22662495 -	GGATT-TTCC-------------------------ACGATCGGCGTGTCTATGGCAAGTAGAATAGCAGGCTTATCACATGTTTAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCACACCCG---------A
droSim1	chr3L:21947666-21947787 -	GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCACACCCG---------A
droSec1	super_11:2578674-2578788 -	GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCA----------------
droYak2	chr3L:23128644-23128763 -	GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTTAACTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCGAACCC-----------
droEre2	scaffold_4784:22312266-22312387 -	GGATT-GTCT-------------------------ACGATCGGCGTGGCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTTACATCAAACCCG---------A
droAna3	scaffold_13337:22380395-22380515 -	GAATA-TTCCA------------------------ACGACCGGTGGGTTTTTAGCAAGTAGAATAGCAGGCTTATCACAGGTTCC-TTTA-ACCCACTGTGAGATTCTTCTATTCTACTTTCGAGAAACACCCGTAAACACCGATCTC-----------
dp4	chrXR_group8:344159-344293 -	GGATA-TGGC-------------------T--AGCACGATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATCTAATAGAGC-AGCCCTC
droPer1	super_96:132292-132395 +	G-------------------------------------ATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATC-----------------
droWil1	scaffold_180698:7060886-7061014 +	TGAGTTTTGA--------------CTATGACT--ATCTAACGGTGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCCTTTACAACCGGTGTGAGATTCTTCTATTCTACTTTCGAAAAGCACCCGATAACAACAAA--------------
droVir3	scaffold_13049:17089392-17089522 +	TGTTT-TTTTA------ATGTTCTCTATAT--ATTTTGATCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTACAATTCA-ACCTAGTGTGAGATTCTTCTATTCTACTTTCGACAAACACCAGCTAGCGTC-----------------
droMoj3	scaffold_6680:22084806-22084935 +	GTGTT-TTCC--------------CTGTGATT--CTCAGTCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTACCATTTG-ACCGAGTGTGAGATTCTTCTATTCTACTTTCGACAAGCACCAGTCAGCGTCGTTTTCG----------
droGri2	scaffold_15110:15103971-15104124 -	GTGTG-TGCAGGTTTTATGGTTTTTGTTTT--ACTCTGATCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTAACATTCG-ACATGGTGTGAGATTCTTCTATTCTACTTTCGACAAACACCAGCTAGCGTCACATTCAGTTAAGTTTA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GGATT----TTCCACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCAATCTGCTGTGAGATTCTTCTATTCTACTTTCGACA-ACACCCGTTAACATCACA--------CCCGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..................................AGTAGAATAGCAGGCTTATCACA..............................................................................	23	1	2335.00	2335	2335
............................................................................TGAGATTCTTCTATTCTACTTT.....................................	22	1	564.00	564	564
..................................AGTAGAATAGCAGGCTTATCAC...............................................................................	22	1	510.00	510	510
....................................TAGAATAGCAGGCTTATCACA..............................................................................	21	1	172.00	172	172
....................................TAGAATAGCAGGCTTATCAC...............................................................................	20	1	70.00	70	70
............................................................................TGAGATTCTTCTATTCTACTT......................................	21	1	39.00	39	39
.........................................................TGTTCAATTCAATCTGCTG...........................................................	19	1	17.00	17	17
..................................AGTAGAATAGCAGGCTTATCA................................................................................	21	1	9.00	9	9
....................................TAGAATAGCAGGCTTATCACATG............................................................................	23	1	9.00	9	9
..................................AGTAGAATAGCAGGCTTATC.................................................................................	20	1	8.00	8	8
............................................................................TGAGATTCTTCTATTCTACT.......................................	20	1	7.00	7	7
.................................AAGTAGAATAGCAGGCTTATCAC...............................................................................	23	1	4.00	4	4
............................................................................TGAGATTCTTCTATTCTACTTTC....................................	23	1	2.00	2	2
..................................AGTAGAATAGCAGGCTTAT..................................................................................	19	1	2.00	2	2
...................................GTAGAATAGCAGGCTTATCACA..............................................................................	22	1	2.00	2	2
..........................................................................TGTGAGATTCTTCTATTCTACT.......................................	22	1	2.00	2	2
.............................................................................GAGATTCTTCTATTCTACTTT.....................................	21	1	1.00	1	1
.................................AAGTAGAATAGCAGGCTTATCACA..............................................................................	24	1	1.00	1	1
....................................................................ATCTGCTGTGAGATTCTTCT...............................................	20	1	1.00	1	1
......................................GAATAGCAGGCTTATCACA..............................................................................	19	1	1.00	1	1
..................................AGTAGAATAGCAGGCTTATCACAT.............................................................................	24	1	1.00	1	1

dp4

GGATATGGCTAGCACGATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCAATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATCTAATAGAGCAGCCCTC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..................................AGTAGAATAGCAGGCTTATCACA..............................................................................	23	1	1985.00	1985	1926	59
............................................................................TGAGATTCTTCTATTCTACTTT.....................................	22	1	1302.00	1302	1099	203
..................................AGTAGAATAGCAGGCTTATCAC...............................................................................	22	1	440.00	440	434	6
.........................................................TGTTCCATTCAATCCGCTG...........................................................	19	1	76.00	76	75	1
............................................................................TGAGATTCTTCTATTCTACTT......................................	21	1	69.00	69	45	24
..................................AGTAGAATAGCAGGCTTATCA................................................................................	21	1	60.00	60	40	20
..................................AGTAGAATAGCAGGCTTATC.................................................................................	20	1	31.00	31	28	3
....................................TAGAATAGCAGGCTTATCACA..............................................................................	21	1	29.00	29	29	0
............................................................................TGAGATTCTTCTATTCTACT.......................................	20	1	19.00	19	11	8
....................................TAGAATAGCAGGCTTATCAC...............................................................................	20	1	8.00	8	8	0
..................................AGTAGAATAGCAGGCTTAT..................................................................................	19	1	8.00	8	8	0
.............................................................................GAGATTCTTCTATTCTACTTT.....................................	21	1	6.00	6	6	0
....................................TAGAATAGCAGGCTTATCACATG............................................................................	23	1	4.00	4	4	0
............................................................................TGAGATTCTTCTATTCTAC........................................	19	1	4.00	4	4	0
..................................AGTAGAATAGCAGGCTTA...................................................................................	18	1	3.00	3	3	0
............................................................................TGAGATTCTTCTATTCTACTTTC....................................	23	1	3.00	3	3	0