Secondary structure and small RNA-seq evidence for dme-mir-2a-2

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:19569475-19569576 -	TGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droSim1	chr2L:19257527-19257628 -	CGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droSec1	super_7:3183838-3183939 -	CGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droYak2	chr2R:6066549-6066650 -	CGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droEre2	scaffold_4845:4720188-4720289 +	CGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droAna3	scaffold_12916:12013971-12014072 +	GGC---ACGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAAACA
dp4	chr4_group5:1153071-1153173 +	TAT--TATGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAAAACA
droPer1	super_5:5560564-5560666 +	TAT--TATGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAAACA
droWil1	scaffold_180708:4285049-4285146 +	--------GATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAAAACA
droVir3	scaffold_12723:2960501-2960597 -	--------GATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCGACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAAAACA
droMoj3	scaffold_6500:6908893-6908997 +	AGAAATTTGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCGACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAAAACA
droGri2	scaffold_15126:521944-522043 +	TT-----TGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCGACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAGAACA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:19569475-19569576 -	TGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droSim1	chr2L:19257527-19257628 -	CGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droSec1	super_7:3183838-3183939 -	CGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droYak2	chr2R:6066549-6066650 -	CGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droEre2	scaffold_4845:4720188-4720289 +	CGT---ACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA
droAna3	scaffold_12916:12013971-12014072 +	GGC---ACGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAAACA
dp4	chr4_group5:1153071-1153173 +	TAT--TATGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAAAACA
droPer1	super_5:5560564-5560666 +	TAT--TATGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAAACA
droWil1	scaffold_180708:4285049-4285146 +	--------GATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAAAACA
droVir3	scaffold_12723:2960501-2960597 -	--------GATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCGACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAAAACA
droMoj3	scaffold_6500:6908893-6908997 +	AGAAATTTGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCGACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAAAACA
droGri2	scaffold_15126:521944-522043 +	TT-----TGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCGACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAGAACA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CG-TACGATGTTGATTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGGAGACA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.............................................................TCACAGCCAGCTTTGATGAGCTA...................	23	1	137884.00	137884	137884
.............................................................TCACAGCCAGCTTTGATGAGCT....................	22	2	43346.00	86692	86692
...........................................................TATCACAGCCAGCTTTGATGAGCTA...................	25	1	5845.00	5845	5845
.............................................................TCACAGCCAGCTTTGATGAGC.....................	21	2	1467.50	2935	2935
.............................................................TCACAGCCAGCTTTGATGAG......................	20	2	1140.50	2281	2281
...............................................................ACAGCCAGCTTTGATGAGCTA...................	21	1	984.00	984	984
...............................................................ACAGCCAGCTTTGATGAGCT....................	20	2	802.50	1605	1605
.............................................................TCACAGCCAGCTTTGATGAGCTAG..................	24	1	716.00	716	716
............................................................ATCACAGCCAGCTTTGATGAGCTA...................	24	1	483.00	483	483
......................GCCTCATCAAGTGGTTGTGATA...........................................................	22	1	379.00	379	379
..............................................................CACAGCCAGCTTTGATGAGCTA...................	22	1	207.00	207	207
...........................................................TATCACAGCCAGCTTTGATGA.......................	21	2	172.00	344	344
.......................CCTCATCAAGTGGTTGTGATA...........................................................	21	1	114.00	114	114
.............................................................TCACAGCCAGCTTTGATGA.......................	19	2	106.50	213	213
...............................................................ACAGCCAGCTTTGATGAGC.....................	19	2	92.00	184	184
...............................................................ACAGCCAGCTTTGATGAG......................	18	2	64.50	129	129
.................................................................AGCCAGCTTTGATGAGCTA...................	19	1	59.00	59	59
......................GCCTCATCAAGTGGTTGTGAT............................................................	21	1	54.00	54	54
..............................................................CACAGCCAGCTTTGATGAGCT....................	21	2	47.50	95	95
..................................................................GCCAGCTTTGATGAGCTA...................	18	1	31.00	31	31
............................................................ATCACAGCCAGCTTTGATGAGC.....................	22	2	25.50	51	51
......................GCCTCATCAAGTGGTTGTGA.............................................................	20	1	21.00	21	21
...........................................................TATCACAGCCAGCTTTGATGAGCTAG..................	26	1	20.00	20	20
.......................CCTCATCAAGTGGTTGTGAT............................................................	20	1	19.00	19	19
.......................CCTCATCAAGTGGTTGTGATATG.........................................................	23	1	15.00	15	15
......................GCCTCATCAAGTGGTTGTGATATG.........................................................	24	1	13.00	13	13
.................................................................AGCCAGCTTTGATGAGCTAG..................	20	1	12.00	12	12
.......................CCTCATCAAGTGGTTGTGA.............................................................	19	1	12.00	12	12
................................................................CAGCCAGCTTTGATGAGCTA...................	20	1	10.00	10	10
..............................................................CACAGCCAGCTTTGATGAGCTAG..................	23	1	9.00	9	9
.....................AGCCTCATCAAGTGGTTGTGATA...........................................................	23	1	9.00	9	9

dp4

TATTATGATGTTGCTTATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGATAATCAACGGAAAACA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.............................................................TCACAGCCAGCTTTGATGAGCTA...................	23	1	176645.00	176645	160664	15981
.............................................................TCACAGCCAGCTTTGATGAGCT....................	22	2	68435.50	136871	99137	37734
...........................................................TATCACAGCCAGCTTTGATGAGCT....................	24	2	14554.00	29108	0	29108
.............................................................TCACAGCCAGCTTTGATGAGC.....................	21	2	12612.00	25224	21191	4033
...........................................................TATCACAGCCAGCTTTGATGAGCTA...................	25	1	8892.00	8892	8276	616
...........................................................TATCACAGCCAGCTTTGATGAG......................	22	2	7992.00	15984	15984	0
.............................................................TCACAGCCAGCTTTGATGAG......................	20	2	4456.00	8912	5287	3625
...........................................................TATCACAGCCAGCTTTGATGAGC.....................	23	2	2927.50	5855	0	5855
.............................................................TCACAGCCAGCTTTGATGAGCTAG..................	24	1	2158.00	2158	2130	28
.......................CCTCATCAAGTGGTTGTGATA...........................................................	21	1	1462.00	1462	714	748
...............................................................ACAGCCAGCTTTGATGAGCTA...................	21	1	1457.00	1457	1346	111
......................GCCTCATCAAGTGGTTGTGATA...........................................................	22	1	698.00	698	680	18
.......................CCTCATCAAGTGGTTGTGAT............................................................	20	1	611.00	611	81	530
...........................................................TATCACAGCCAGCTTTGATGA.......................	21	2	487.00	974	0	974
............................................................ATCACAGCCAGCTTTGATGAGCTA...................	24	1	469.00	469	426	43
............................................................ATCACAGCCAGCTTTGATGAGCT....................	23	2	328.50	657	657	0
...............................................................ACAGCCAGCTTTGATGAGC.....................	19	2	307.00	614	614	0
..............................................................CACAGCCAGCTTTGATGAGCTA...................	22	1	250.00	250	231	19
.......................CCTCATCAAGTGGTTGTGA.............................................................	19	1	232.00	232	25	207
.............................................................TCACAGCCAGCTTTGATGA.......................	19	2	158.50	317	317	0
.................................................................AGCCAGCTTTGATGAGCTA...................	19	1	133.00	133	115	18
...........................................................TATCACAGCCAGCTTTGATG........................	20	3	76.33	229	229	0
...........................................................TATCACAGCCAGCTTTGAT.........................	19	3	72.67	218	0	218
...........................................................TATCACAGCCAGCTTTGATGAGCTAG..................	26	1	71.00	71	71	0
..................................................................GCCAGCTTTGATGAGCTA...................	18	1	65.00	65	57	8
...............................................................ACAGCCAGCTTTGATGAG......................	18	2	61.50	123	0	123
.......................CCTCATCAAGTGGTTGTGATATG.........................................................	23	1	55.00	55	53	2
.................................................................AGCCAGCTTTGATGAGCTAG..................	20	1	46.00	46	44	2
..............................................................CACAGCCAGCTTTGATGAGCT....................	21	2	45.00	90	90	0
......................GCCTCATCAAGTGGTTGTGAT............................................................	21	1	41.00	41	38	3
.....................AGCCTCATCAAGTGGTTGTGATA...........................................................	23	1	38.00	38	37	1
..............................................................CACAGCCAGCTTTGATGAGC.....................	20	2	33.50	67	61	6
................................................................CAGCCAGCTTTGATGAGCTA...................	20	1	31.00	31	17	14
..................................................................GCCAGCTTTGATGAGCTAG..................	19	1	31.00	31	29	2
...................................................................CCAGCTTTGATGAGCTAG..................	18	1	29.00	29	26	3
..............................................................CACAGCCAGCTTTGATGAGCTAG..................	23	1	26.00	26	26	0