Secondary structure and small RNA-seq evidence for dme-mir-314

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:11766097-11766216 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAACTTACCTAGTTGAGGAAA-----ACTCCC-ATG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droSim1	chr3L:11131600-11131719 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AGTCCC-GTG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droSec1	super_0:3951120-3951239 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AGTCCC-GTG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droYak2	chr3L:11794902-11795021 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AACCCC-ATG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droEre2	scaffold_4784:11743709-11743828 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAG-----AATCCC-ATG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droAna3	scaffold_13337:6019503-6019620 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AATC-A--GT-TTGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
dp4	chrXR_group8:4342117-4342235 -	TGGTCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----ACTC-CGA-A-ATGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAAATCGCATT
droPer1	super_29:576219-576337 -	TGGTCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----ACTC-CGA-A-ATGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAAATCGCATT
droWil1	scaffold_180949:2570151-2570270 -	TAGTTCGTACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AATTCA-ATG-TTGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droVir3	scaffold_13049:23988146-23988266 +	TGGTTCGTGCTCTTATCGTAACTTGTGTGGCTT-GAATGTACCTGGTTGAGGAAC----GAATTCA-ACGTTTGGATTTTGTTGCCTTTGGTATTCGAGCCAATAAGTTCGGCCACCGGTTCACATT
droMoj3	scaffold_6680:18619757-18619881 +	TAGGTCGGGCTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTCGTCGAGCGAAAAGCGAATTCA-TTG-TTGGATTTTGTTGCTCTTGGTATTCGAGCCAATAAGTTCGGCAACCAGTTCGCATT
droGri2	scaffold_15110:9705224-9705329 -	TATTTCCAGCTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTGGCTAAGGAAA--------------G-TTGGATTTCC------TAGGTATTCGAGCCAATAAGTTCGGCAGCGGGTTCGCATT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:11766097-11766216 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAACTTACCTAGTTGAGGAAA-----ACTCCC-ATG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droSim1	chr3L:11131600-11131719 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AGTCCC-GTG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droSec1	super_0:3951120-3951239 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AGTCCC-GTG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droYak2	chr3L:11794902-11795021 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AACCCC-ATG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droEre2	scaffold_4784:11743709-11743828 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAG-----AATCCC-ATG-TCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droAna3	scaffold_13337:6019503-6019620 +	TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AATC-A--GT-TTGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
dp4	chrXR_group8:4342117-4342235 -	TGGTCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----ACTC-CGA-A-ATGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAAATCGCATT
droPer1	super_29:576219-576337 -	TGGTCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----ACTC-CGA-A-ATGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAAATCGCATT
droWil1	scaffold_180949:2570151-2570270 -	TAGTTCGTACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAA-----AATTCA-ATG-TTGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT
droVir3	scaffold_13049:23988146-23988266 +	TGGTTCGTGCTCTTATCGTAACTTGTGTGGCTT-GAATGTACCTGGTTGAGGAAC----GAATTCA-ACGTTTGGATTTTGTTGCCTTTGGTATTCGAGCCAATAAGTTCGGCCACCGGTTCACATT
droMoj3	scaffold_6680:18619757-18619881 +	TAGGTCGGGCTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTCGTCGAGCGAAAAGCGAATTCA-TTG-TTGGATTTTGTTGCTCTTGGTATTCGAGCCAATAAGTTCGGCAACCAGTTCGCATT
droGri2	scaffold_15110:9705224-9705329 -	TATTTCCAGCTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTGGCTAAGGAAA--------------G-TTGGATTTCC------TAGGTATTCGAGCCAATAAGTTCGGCAGCGGGTTCGCATT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGGCCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAAAGTCCCGTGTCGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
....................................................................................TATTCGAGCCAATAAGTTCGG...............	21	1	553.00	553	553
....................................................................................TATTCGAGCCAATAAGTTCGGC..............	22	1	85.00	85	85
....................................................................................TATTCGAGCCAATAAGTTCG................	20	1	21.00	21	21
.................GTAACTTGTGTGGCTTCGAATGTACC.............................................................................	26	1	17.00	17	17
....................................ATGTACCTAGTTGAGGAAAA................................................................	20	1	5.00	5	5
.............................................................................................CAATAAGTTCGGCCACGA.........	18	1	4.00	4	4
........................................................................TGTTACCTCTGGTATTCGAGC...........................	21	1	4.00	4	4
..................................GAATGTACCTAGTTGAGGAAAA................................................................	22	1	3.00	3	3
....................................................................................TATTCGAGCCAATAAGTT..................	18	1	2.00	2	2
...................................AATGTACCTAGTTGAGGAAAAGT..............................................................	23	1	2.00	2	2
......................................GTACCTAGTTGAGGAAAA................................................................	18	1	2.00	2	2
....................................................................................TATTCGAGCCAATAAGTTC.................	19	1	2.00	2	2
........................................................GTCCCGTGTCGGATTTTGTTACCTCTGG....................................	28	1	1.00	1	1
.................GTAACTTGTGTGGCTTCGAATGTACCT............................................................................	27	1	1.00	1	1
....................................ATGTACCTAGTTGAGGAAAAGT..............................................................	22	1	1.00	1	1
.....................................................................................ATTCGAGCCAATAAGTTCGGC..............	21	1	1.00	1	1
.................................CGAATGTACCTAGTTGAGGAAAA................................................................	23	1	1.00	1	1
...........................................TAGTTGAGGAAAAGTCCCG..........................................................	19	1	1.00	1	1
........................................................GTCCCGTGTCGGATTTTGTTACCTCTGGT...................................	29	1	1.00	1	1
....................................................................ATTTTGTTACCTCTGGTATTCGAGC...........................	25	1	1.00	1	1
............................................AGTTGAGGAAAAGTCCCGTGTCGG....................................................	24	1	1.00	1	1
.................GTAACTTGTGTGGCTTCGA....................................................................................	19	1	1.00	1	1
...........................................TAGTTGAGGAAAAGTCCCGTGTCGGAT..................................................	27	1	1.00	1	1
.........................................................................GTTACCTCTGGTATTCGAGC...........................	20	1	1.00	1	1
........................................................................TGTTACCTCTGGTATTCGAGCCA.........................	23	1	1.00	1	1
.................GTAACTTGTGTGGCTTCGAAT..................................................................................	21	1	1.00	1	1
...................AACTTGTGTGGCTTCGAATGTACC.............................................................................	24	1	1.00	1	1
.................GTAACTTGTGTGGCTTCGAATGTA...............................................................................	24	1	1.00	1	1
...................................AATGTACCTAGTTGAGGAAAA................................................................	21	1	1.00	1	1
....................................................................................TATTCGAGCCAATAAGTTCGGCC.............	23	1	1.00	1	1
.....................................TGTACCTAGTTGAGGAAAAGTC.............................................................	22	1	1.00	1	1
..............................................................TGTCGGATTTTGTTACCTCTGG....................................	22	1	1.00	1	1
..........................................................CCCGTGTCGGATTTTGTTAC..........................................	20	1	1.00	1	1
............................................................................ACCTCTGGTATTCGAGCCA.........................	19	1	1.00	1	1
.................GTAACTTGTGTGGCTTCGAATGT................................................................................	23	1	1.00	1	1
.................GTAACTTGTGTGGCTTCGAATGTAC..............................................................................	25	1	1.00	1	1
..........................GTGGCTTCGAATGTACCTAGTT........................................................................	22	1	1.00	1	1
.................GTAACTTGTGTGGCTTCGAA...................................................................................	20	1	1.00	1	1

dp4

TGGTCCGCACTCTTATCGTAACTTGTGTGGCTTCGAATGTACCTAGTTGAGGAAAACTCCGA-AATGGATTTTGTTACCTCTGGTATTCGAGCCAATAAGTTCGGCCACGAAATCGCATT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
....................................................................................TATTCGAGCCAATAAGTTCGG...............	21	1	1790.00	1790	565	1225
....................................................................................TATTCGAGCCAATAAGTTCG................	20	1	251.00	251	17	234
....................................................................................TATTCGAGCCAATAAGTTCGGC..............	22	1	130.00	130	89	41
.................GTAACTTGTGTGGCTTCGAATGTACC.............................................................................	26	1	21.00	21	18	3
....................................................................................TATTCGAGCCAATAAGTT..................	18	1	12.00	12	12	0
....................................................................................TATTCGAGCCAATAAGTTC.................	19	1	10.00	10	1	9
....................................ATGTACCTAGTTGAGGAA..................................................................	18	1	6.00	6	6	0
........................................................................TGTTACCTCTGGTATTCGAGC...........................	21	1	5.00	5	5	0
.......................................................................TTGTTACCTCTGGTATTCGAGC...........................	22	1	4.00	4	4	0
..................TAACTTGTGTGGCTTCGAATGTACC.............................................................................	25	1	4.00	4	4	0
.................GTAACTTGTGTGGCTTCGA....................................................................................	19	1	3.00	3	3	0
....................................ATGTACCTAGTTGAGGAAAACT..............................................................	22	1	3.00	3	3	0
.................GTAACTTGTGTGGCTTCGAAT..................................................................................	21	1	3.00	3	3	0
.............................................................................................CAATAAGTTCGGCCACGA.........	18	1	3.00	3	3	0
.................GTAACTTGTGTGGCTTCGAATGTAC..............................................................................	25	1	3.00	3	3	0
...................................AATGTACCTAGTTGAGGAA..................................................................	19	1	2.00	2	2	0
......................TTGTGTGGCTTCGAATGTACC.............................................................................	21	1	2.00	2	2	0
.................................CGAATGTACCTAGTTGAGGAA..................................................................	21	1	2.00	2	2	0
..........................................................CCGA-AATGGATTTTGTTACCTCTGGT...................................	26	1	2.00	2	2	0
..................................GAATGTACCTAGTTGAGGAA..................................................................	20	1	2.00	2	2	0
..................................GAATGTACCTAGTTGAGGA...................................................................	19	1	2.00	2	2	0
......................................GTACCTAGTTGAGGAAAA................................................................	18	1	2.00	2	2	0
...................................AATGTACCTAGTTGAGGAAAACTCC............................................................	25	1	1.00	1	1	0
..............ATCGTAACTTGTGTGGCTTCGAAT..................................................................................	24	1	1.00	1	1	0
............................................................................ACCTCTGGTATTCGAGCCAATAA.....................	23	1	1.00	1	1	0
...........................................................................TACCTCTGGTATTCGAGCCAATAA.....................	24	1	1.00	1	1	0
...........................................................................TACCTCTGGTATTCGAGCC..........................	19	1	1.00	1	1	0
........................GTGTGGCTTCGAATGTAC..............................................................................	18	1	1.00	1	1	0
......................................................................TTTGTTACCTCTGGTATTCGAGC...........................	23	1	1.00	1	1	0
...........................................................CGA-AATGGATTTTGTTACCTCTGGT...................................	25	1	1.00	1	1	0
..............................................................................................AATAAGTTCGGCCACGAAAT......	20	1	1.00	1	1	0
......................TTGTGTGGCTTCGAATGT................................................................................	18	1	1.00	1	1	0
.................GTAACTTGTGTGGCTTCGAATGTA...............................................................................	24	1	1.00	1	1	0
.....................................................................................ATTCGAGCCAATAAGTTCGG...............	20	1	1.00	1	0	1
...........................................................................................GCCAATAAGTTCGGCCACGAAATCGCATT	29	1	1.00	1	1	0
.................GTAACTTGTGTGGCTTCG.....................................................................................	18	1	1.00	1	1	0
.....................................TGTACCTAGTTGAGGAAAACTCC............................................................	23	1	1.00	1	1	0
........................................ACCTAGTTGAGGAAAACTCCGA-.........................................................	22	1	1.00	1	1	0
.......................TGTGTGGCTTCGAATGTAC..............................................................................	19	1	1.00	1	1	0
.......................TGTGTGGCTTCGAATGTACCTAGTT........................................................................	25	1	1.00	1	1	0
.........................................................TCCGA-AATGGATTTTGTTACCTCTGGT...................................	27	1	1.00	1	1	0
.........................TGTGGCTTCGAATGTACC.............................................................................	18	1	1.00	1	1	0
......................................................................................................CGGCCACGAAATCGCATT	18	1	1.00	1	1	0
....................................ATGTACCTAGTTGAGGAAAACTC.............................................................	23	1	1.00	1	1	0
....................ACTTGTGTGGCTTCGAATGTACC.............................................................................	23	1	1.00	1	1	0
..............................................................................CTCTGGTATTCGAGCCAATAAGTTCGGC..............	28	1	1.00	1	1	0
......................TTGTGTGGCTTCGAATGTACCT............................................................................	22	1	1.00	1	1	0
........................GTGTGGCTTCGAATGTACC.............................................................................	19	1	1.00	1	1	0
.................GTAACTTGTGTGGCTTCGAA...................................................................................	20	1	1.00	1	1	0
...........................................TAGTTGAGGAAAACTCCGA-AATGGATT.................................................	27	1	1.00	1	1	0
.................GTAACTTGTGTGGCTTCGAATGTACCT............................................................................	27	1	1.00	1	1	0
.....................................................................................ATTCGAGCCAATAAGTTCGGCCACGA.........	26	1	1.00	1	1	0
..........................................................CCGA-AATGGATTTTGTTACC.........................................	20	1	1.00	1	1	0
....................ACTTGTGTGGCTTCGAATGTACCT............................................................................	24	1	1.00	1	1	0
........................GTGTGGCTTCGAATGTACCTAGTTGA......................................................................	26	1	1.00	1	1	0
............................................................................ACCTCTGGTATTCGAGCCAATA......................	22	1	1.00	1	1	0
........................................................................TGTTACCTCTGGTATTCGAGCCA.........................	23	1	1.00	1	1	0
...............................................TGAGGAAAACTCCGA-AATGGATTTT...............................................	25	1	1.00	1	1	0
......................................GTACCTAGTTGAGGAAAACT..............................................................	20	1	1.00	1	1	0
........................................................................TGTTACCTCTGGTATTCGAGCCAATAA.....................	27	1	1.00	1	1	0
..........................GTGGCTTCGAATGTACCTAGTTGAGG....................................................................	26	1	1.00	1	1	0
.........................................................................................GAGCCAATAAGTTCGGCCACGAAATCGC...	28	1	1.00	1	1	0
...................................AATGTACCTAGTTGAGGA...................................................................	18	1	1.00	1	1	0
...................................................................................GTATTCGAGCCAATAAGTTCGG...............	22	1	1.00	1	1	0
...........................................................CGA-AATGGATTTTGTTACCTCT......................................	22	1	1.00	1	1	0
............................................................GA-AATGGATTTTGTTACCTC.......................................	20	1	1.00	1	1	0
..........................................................CCGA-AATGGATTTTGTTAC..........................................	19	1	1.00	1	1	0
............................................................GA-AATGGATTTTGTTACCTCTGG....................................	23	1	1.00	1	1	0
.................................CGAATGTACCTAGTTGAGGA...................................................................	20	1	1.00	1	1	0
........................................................CTCCGA-AATGGATTTTGTTACCTCTGGT...................................	28	1	1.00	1	1	0
...................AACTTGTGTGGCTTCGAAT..................................................................................	19	1	1.00	1	1	0
............................................................................ACCTCTGGTATTCGAGCCAATAAGT...................	25	1	1.00	1	1	0
......................................GTACCTAGTTGAGGAAAACTCC............................................................	22	1	1.00	1	1	0
..............................CTTCGAATGTACCTAGTTGAG.....................................................................	21	1	1.00	1	1	0
.....................................TGTACCTAGTTGAGGAAAACT..............................................................	21	1	1.00	1	1	0
..................................GAATGTACCTAGTTGAGGAAAACT..............................................................	24	1	1.00	1	1	0
................................................................................CTGGTATTCGAGCCAATAAGTTCGGC..............	26	1	1.00	1	1	0