Secondary structure and small RNA-seq evidence for dme-mir-375

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:857527-857647 +	CATCCGAAACCC-------------------------------CTTCCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT-----------C---ATCCCGAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTGG--T
droSim1	chr2L_random:38968-39087 +	CATCCGAATCC--------------------------------CTCCCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT-----------C---ATCCCGAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTGG--T
droSec1	super_14:828161-828280 +	CATCCGAATCC--------------------------------CTCCCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT-----------C---ATCCCGAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTGG--T
droYak2	chr2L:841557-841670 +	CATCCGAGTC------------------------------------CCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT----------------GCCTAGTAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTGG--T
droEre2	scaffold_4929:914698-914811 +	CACCACC------------------------------------ATCCCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT----------------GCCTAGTAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTCG--A
droAna3	scaffold_12916:2746986-2747121 +	CCACGGAAA------------------AGACACCCCACGGAAA-CGAGGGGCAGCGAATTACTTGGGCCAAGGGAATTCAAACTGTG---AT-----------CGCAATGCTAGAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-TTGCAAACGCCACGTGG--T
dp4	chr4_group3:5649077-5649230 +	CATCCAAGGCCTGTGCCTGTGTCTGAGAGCCCACCCACCCGAA---TAGGGCAGCGAATTACTTGGGCCAGGGGAATTCAAACTGTG---AT-----------CGCAATGCAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCTC-AAGTAAACGCCACGTGGGTT
droPer1	super_1:7140235-7140385 +	CATCCAAGGCCTGTGCCTGTGCTTGAGAGCCCACCCACCCGAA---TAAGGCAGCGAATTACTTGGGCCAGGGGAATGCAAACTGTG---AT-----------CGCAATGCAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCTC-AAGTAAACGCCACGTGG---
droWil1	scaffold_180772:2278802-2278947 -	AATTTAAAACCGTTTTCCATTTC-------------ATTT---TTTGGGGGCAGCGAATTACTTGGGCCAAGGGAATTCAAACTGTG---AAT-----TATTTCAAAATGCAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCGTACAATTGCGACACGTGG--T
droVir3	scaffold_12963:19405390-19405507 +	CATTCAAAGT------------------------------------TCGGGCAGCAAATTACTTGGGCCAAGGGAATGCAAACTGTC---AA-----------CGCATTGCAATAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCCA-AC-ATAACGCCACGTGG--T
droMoj3	scaffold_6500:23808221-23808350 -	TGTTCAGTGTATGCTC---------------------------CTGCAGGGCTGCGAATTACTTGGGCCAAGGGAATGCAAACTGTTCGAAA-----------AGCATTGCAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCCG-A-TAAAACGCCACGTGG--T
droGri2	scaffold_15252:7270330-7270448 +	C-----------------------------------------------GGGCAGCGAATTACTTGGGCCAAGTGGATGTAAACTGTG---AAAGCGCATTTTGCATATAACAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCCG-A-TATAACGCCACGTGG--G

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:857527-857647 +	CATCCGAAACCC-------------------------------CTTCCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT-----------C---ATCCCGAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTGG--T
droSim1	chr2L_random:38968-39087 +	CATCCGAATCC--------------------------------CTCCCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT-----------C---ATCCCGAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTGG--T
droSec1	super_14:828161-828280 +	CATCCGAATCC--------------------------------CTCCCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT-----------C---ATCCCGAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTGG--T
droYak2	chr2L:841557-841670 +	CATCCGAGTC------------------------------------CCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT----------------GCCTAGTAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTGG--T
droEre2	scaffold_4929:914698-914811 +	CACCACC------------------------------------ATCCCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTG---AT----------------GCCTAGTAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-ACTAAAGCGCCACGTCG--A
droAna3	scaffold_12916:2746986-2747121 +	CCACGGAAA------------------AGACACCCCACGGAAA-CGAGGGGCAGCGAATTACTTGGGCCAAGGGAATTCAAACTGTG---AT-----------CGCAATGCTAGAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCG-TTGCAAACGCCACGTGG--T
dp4	chr4_group3:5649077-5649230 +	CATCCAAGGCCTGTGCCTGTGTCTGAGAGCCCACCCACCCGAA---TAGGGCAGCGAATTACTTGGGCCAGGGGAATTCAAACTGTG---AT-----------CGCAATGCAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCTC-AAGTAAACGCCACGTGGGTT
droPer1	super_1:7140235-7140385 +	CATCCAAGGCCTGTGCCTGTGCTTGAGAGCCCACCCACCCGAA---TAAGGCAGCGAATTACTTGGGCCAGGGGAATGCAAACTGTG---AT-----------CGCAATGCAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCTC-AAGTAAACGCCACGTGG---
droWil1	scaffold_180772:2278802-2278947 -	AATTTAAAACCGTTTTCCATTTC-------------ATTT---TTTGGGGGCAGCGAATTACTTGGGCCAAGGGAATTCAAACTGTG---AAT-----TATTTCAAAATGCAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCGTACAATTGCGACACGTGG--T
droVir3	scaffold_12963:19405390-19405507 +	CATTCAAAGT------------------------------------TCGGGCAGCAAATTACTTGGGCCAAGGGAATGCAAACTGTC---AA-----------CGCATTGCAATAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCCA-AC-ATAACGCCACGTGG--T
droMoj3	scaffold_6500:23808221-23808350 -	TGTTCAGTGTATGCTC---------------------------CTGCAGGGCTGCGAATTACTTGGGCCAAGGGAATGCAAACTGTTCGAAA-----------AGCATTGCAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCCG-A-TAAAACGCCACGTGG--T
droGri2	scaffold_15252:7270330-7270448 +	C-----------------------------------------------GGGCAGCGAATTACTTGGGCCAAGTGGATGTAAACTGTG---AAAGCGCATTTTGCATATAACAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCCG-A-TATAACGCCACGTGG--G

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CATCCG-----------------------------------AATCCCTCCCGGGCAGCGAATTACTTGGGCCAAGGGAATGCAAACTGTGATC---ATCCCGAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGTCCGACTAAAGCGCCACGTGG--T	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..........................................................................................................TTTGTTCGTTTGGCTTAAGTTA................................	22	1	432.00	432	432
...............................................................ACTTGGGCCAAGGGAATGCAAACT.........................................................................	24	1	370.00	370	370
..........................................................................................................TTTGTTCGTTTGGCTTAAGTT.................................	21	1	147.00	147	147
...............................................................ACTTGGGCCAAGGGAATGCAAAC..........................................................................	23	1	17.00	17	17
...............................................................ACTTGGGCCAAGGGAATGCAAA...........................................................................	22	1	7.00	7	7
..........................................................................................................TTTGTTCGTTTGGCTTAAGT..................................	20	1	7.00	7	7
...........................................................................................................TTGTTCGTTTGGCTTAAGTTA................................	21	1	5.00	5	5
..........................................................................................................TTTGTTCGTTTGGCTTAAG...................................	19	1	5.00	5	5
...............................................................ACTTGGGCCAAGGGAATGCA.............................................................................	20	1	5.00	5	5
...............................................................ACTTGGGCCAAGGGAATGCAA............................................................................	21	1	3.00	3	3
..............................................................TACTTGGGCCAAGGGAATGCAAACT.........................................................................	25	1	3.00	3	3
...........................................................................................................TTGTTCGTTTGGCTTAAGTT.................................	20	1	2.00	2	2
...............................................................ACTTGGGCCAAGGGAATG...............................................................................	18	1	2.00	2	2
..............................................................TACTTGGGCCAAGGGAATGCAAAC..........................................................................	24	1	1.00	1	1
..............................................................TACTTGGGCCAAGGGAATGCAAA...........................................................................	23	1	1.00	1	1
...............................................................ACTTGGGCCAAGGGAATGC..............................................................................	19	1	1.00	1	1
.................................................................TTGGGCCAAGGGAATGCAAACT.........................................................................	22	1	1.00	1	1
.................................................................TTGGGCCAAGGGAATGCAA............................................................................	19	1	1.00	1	1
..............................................................TACTTGGGCCAAGGGAATGCAA............................................................................	22	1	1.00	1	1
..........................................................................................................TTTGTTCGTTTGGCTTAAGTTAT...............................	23	1	1.00	1	1

dp4

CATCCAAGGCCTGTGCCTGTGTCTGAGAGCCCACCCACCCGAAT------AGGGCAGCGAATTACTTGGGCCAGGGGAATTCAAACTGTGATCGCAATGCAAAAAGTTTGTTCGTTTGGCTTAAGTTATTTTCATGCCTCAAGTAAACGCCACGTGGGTT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..........................................................................................................TTTGTTCGTTTGGCTTAAGTTA................................	22	1	1242.00	1242	780	462
..........................................................................................................TTTGTTCGTTTGGCTTAAGTT.................................	21	1	787.00	787	243	544
..........................................................................................................TTTGTTCGTTTGGCTTAAGT..................................	20	1	88.00	88	20	68
..........................................................................................................TTTGTTCGTTTGGCTTAAG...................................	19	1	42.00	42	12	30
...............................................................ACTTGGGCCAGGGGAATTCAAACT.........................................................................	24	1	30.00	30	30	0
..........................................................................................................TTTGTTCGTTTGGCTTAAGTTAT...............................	23	1	10.00	10	2	8
...........................................................................................................TTGTTCGTTTGGCTTAAGTTA................................	21	1	9.00	9	3	6
...........................................................................................................TTGTTCGTTTGGCTTAAGTT.................................	20	1	3.00	3	0	3
.......................................................................................GTGATCGCAATGCAAAAAG......................................................	19	1	2.00	2	2	0
..........................................................................................................TTTGTTCGTTTGGCTTAAGTTATT..............................	24	1	2.00	2	0	2
...............................................................ACTTGGGCCAGGGGAATTCAAAC..........................................................................	23	1	2.00	2	2	0
............................................................................................................TGTTCGTTTGGCTTAAGTTA................................	20	1	1.00	1	1	0
.............................................................................................................GTTCGTTTGGCTTAAGTTA................................	19	1	1.00	1	1	0
.........................................................................................................GTTTGTTCGTTTGGCTTAAGTTA................................	23	1	1.00	1	1	0