Secondary structure and small RNA-seq evidence for dme-mir-190

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:8564884-8565013 +	ACTT------------------------------------------GCCCTT-----------------------CAAAA---------C-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTTCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGCCAATCTACTAAAACA-------
droSim1	chr3L:8005898-8006027 +	ACTT------------------------------------------GCCCTT-----------------------CAAAA---------C-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTATCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGCCAATCTACTAAAACA-------
droSec1	super_0:844136-844265 +	ACTT------------------------------------------GCCCTT-----------------------CAAAA---------T-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTTCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGCCAATCTACTAAAACA-------
droYak2	chr3L:3348658-3348787 -	ACTA------------------------------------------GCCCTT-----------------------CAAAA---------C-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTTCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGCCAATCTACTAAAACA-------
droEre2	scaffold_4784:5482466-5482595 -	ACTA------------------------------------------GCCCTT-----------------------CAAAT---------C-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTTCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTAGCCTTCGCCAATCTACTAAAACA-------
droAna3	scaffold_13337:8074872-8075002 -	ACTC------------------------------------------GCCTCT-----------------------CCAAA---------CACA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACTCTCGCCAATCTACTAAAATA-------
dp4	chrXR_group3a:147689-147845 -	ACTA------------------------------------------GT---TAACCCTAACTCTCATCTGCCCACAAA--CCAACCCAAC-GA-------ACTAA-----------TTGGGGATTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAGAGTTCACCCAGGAATCAAACATATTATTACTGTGATACCCGGAAATCTACTAAACCC-------
droPer1	super_23:151050-151206 -	ACTA------------------------------------------GT---TAACCCTAACTCTCATCTGCCCACAAA--CCAACCCAAC-GA-------ACTAA-----------TTGGGGATTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAGAGTTCACCCAGGAATCAAACATATTATTACTGTGATACCCGGAAATCTACTAAACCC-------
droWil1	scaffold_180949:5214317-5214457 +	ACTT------------------------------------------GCCCT-----------CTCATCTGCCCACAAAAA---------C-GA-------ACTAA-----------TTGATGGTCCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGATCGTCGG-AATCTACTAAAAAC-------
droVir3	scaffold_13049:6215347-6215479 +	AC-------------------------------------------------------------------------CAAAT---------C-AA-------ACTACCCCCCACTCATCTAATGATTCCAGTAAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGATTGTTGAAACTCTACTAAACCA-------
droMoj3	scaffold_6680:4536880-4537026 +	AGCC------------------------------------------AC---------------------------CAAAATCAACCAAAC-TACCTATCCACTAC------CTCATCTAACGATTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGATCGCTTAAACTCTACTAAAA-A-------
droGri2	scaffold_15072:36258-36427 +	ACTACCAATAAAATAAAAATCCAACCAATCAACCAACCAACCAACTACCCA------------------------------------------------------------CTCATCTAATGATTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGATTGTTGAAACTCTACTAAAAACAAATCAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:8564884-8565013 +	ACTT------------------------------------------GCCCTT-----------------------CAAAA---------C-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTTCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGCCAATCTACTAAAACA-------
droSim1	chr3L:8005898-8006027 +	ACTT------------------------------------------GCCCTT-----------------------CAAAA---------C-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTATCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGCCAATCTACTAAAACA-------
droSec1	super_0:844136-844265 +	ACTT------------------------------------------GCCCTT-----------------------CAAAA---------T-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTTCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGCCAATCTACTAAAACA-------
droYak2	chr3L:3348658-3348787 -	ACTA------------------------------------------GCCCTT-----------------------CAAAA---------C-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTTCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGCCAATCTACTAAAACA-------
droEre2	scaffold_4784:5482466-5482595 -	ACTA------------------------------------------GCCCTT-----------------------CAAAT---------C-GA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTTCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTAGCCTTCGCCAATCTACTAAAACA-------
droAna3	scaffold_13337:8074872-8075002 -	ACTC------------------------------------------GCCTCT-----------------------CCAAA---------CACA-------ACTAA-----------TTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACTCTCGCCAATCTACTAAAATA-------
dp4	chrXR_group3a:147689-147845 -	ACTA------------------------------------------GT---TAACCCTAACTCTCATCTGCCCACAAA--CCAACCCAAC-GA-------ACTAA-----------TTGGGGATTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAGAGTTCACCCAGGAATCAAACATATTATTACTGTGATACCCGGAAATCTACTAAACCC-------
droPer1	super_23:151050-151206 -	ACTA------------------------------------------GT---TAACCCTAACTCTCATCTGCCCACAAA--CCAACCCAAC-GA-------ACTAA-----------TTGGGGATTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAGAGTTCACCCAGGAATCAAACATATTATTACTGTGATACCCGGAAATCTACTAAACCC-------
droWil1	scaffold_180949:5214317-5214457 +	ACTT------------------------------------------GCCCT-----------CTCATCTGCCCACAAAAA---------C-GA-------ACTAA-----------TTGATGGTCCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGATCGTCGG-AATCTACTAAAAAC-------
droVir3	scaffold_13049:6215347-6215479 +	AC-------------------------------------------------------------------------CAAAT---------C-AA-------ACTACCCCCCACTCATCTAATGATTCCAGTAAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGATTGTTGAAACTCTACTAAACCA-------
droMoj3	scaffold_6680:4536880-4537026 +	AGCC------------------------------------------AC---------------------------CAAAATCAACCAAAC-TACCTATCCACTAC------CTCATCTAACGATTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGATCGCTTAAACTCTACTAAAA-A-------
droGri2	scaffold_15072:36258-36427 +	ACTACCAATAAAATAAAAATCCAACCAATCAACCAACCAACCAACTACCCA------------------------------------------------------------CTCATCTAATGATTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGATTGTTGAAACTCTACTAAAAACAAATCAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ACTTGC---------------------------CCTTCAAAACGAACTAATTGATGGTTCCAGTGAGATATGTTTGATATTCTTGGTTGTATCATTCAAAAGTTCACCCAGGAATCAAACATATTATTACTGTGACCCTCGCCAATCTACTAAAACA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..........................................................................................................CCCAGGAATCAAACATATTATTA............................	23	1	416.00	416	416
.................................................................AGATATGTTTGATATTCTTGGTTG....................................................................	24	1	218.00	218	218
..........................................................................................................CCCAGGAATCAAACATATTATT.............................	22	1	161.00	161	161
.................................................................AGATATGTTTGATATTCTTGGTTGT...................................................................	25	1	18.00	18	18
.................................................................AGATATGTTTGATATTCTTGGT......................................................................	22	1	14.00	14	14
..........................................................................................................CCCAGGAATCAAACATATTA...............................	20	1	11.00	11	11
.................................................................AGATATGTTTGATATTCTTG........................................................................	20	1	10.00	10	10
.......................................................................GTTTGATATTCTTGGTTG....................................................................	18	1	9.00	9	9
.................................................................AGATATGTTTGATATTCTTGGTT.....................................................................	23	1	8.00	8	8
...........................................................................................................CCAGGAATCAAACATATTATT.............................	21	1	6.00	6	6
.................................................................AGATATGTTTGATATTCTTGG.......................................................................	21	1	4.00	4	4
..........................................................................................................CCCAGGAATCAAACATATTAT..............................	21	1	4.00	4	4
...........................................................................................................CCAGGAATCAAACATATTATTA............................	22	1	3.00	3	3
..........................................................................................................CCCAGGAATCAAACATATT................................	19	1	2.00	2	2
.......................................................................................................TCACCCAGGAATCAAACATATT................................	22	1	2.00	2	2
.....................................................................ATGTTTGATATTCTTGGTTG....................................................................	20	1	2.00	2	2
...................................................................ATATGTTTGATATTCTTGGTTG....................................................................	22	1	1.00	1	1
....................................................................TATGTTTGATATTCTTGGTT.....................................................................	20	1	1.00	1	1
........................................................................................................CACCCAGGAATCAAACATATTA...............................	22	1	1.00	1	1
..................................................................GATATGTTTGATATTCTTGGTTG....................................................................	23	1	1.00	1	1
......................................................................TGTTTGATATTCTTGGTT.....................................................................	18	1	1.00	1	1
............................................................................................................CAGGAATCAAACATATTATTA............................	21	1	1.00	1	1

dp4

ACTAGTTAACCCTAACTCTCATCTGCCCACAAACCAACCCAACGAACTAATTGGGGATTCCAGTGAGATATGTTTGATATTCTTGGTTGTTACATTCAAGAGTTCACCCAGGAATCAAACATATTATTACTGTGATACCCGGAAATCTACTAAACCC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..........................................................................................................CCCAGGAATCAAACATATTATTA............................	23	1	210.00	210	205	5
.................................................................AGATATGTTTGATATTCTTGGTTG....................................................................	24	1	127.00	127	109	18
..........................................................................................................CCCAGGAATCAAACATATTATT.............................	22	1	114.00	114	110	4
.................................................................AGATATGTTTGATATTCTTG........................................................................	20	1	37.00	37	11	26
.................................................................AGATATGTTTGATATTCTTGG.......................................................................	21	1	28.00	28	8	20
.................................................................AGATATGTTTGATATTCTTGGTTGT...................................................................	25	1	25.00	25	19	6
.................................................................AGATATGTTTGATATTCTTGGT......................................................................	22	1	19.00	19	5	14
.......................................................................GTTTGATATTCTTGGTTG....................................................................	18	1	10.00	10	9	1
.................................................................AGATATGTTTGATATTCTTGGTT.....................................................................	23	1	10.00	10	5	5
..........................................................................................................CCCAGGAATCAAACATATTAT..............................	21	1	8.00	8	3	5
..........................................................................................................CCCAGGAATCAAACATATTA...............................	20	1	7.00	7	4	3
..........................................................................................................CCCAGGAATCAAACATATT................................	19	1	3.00	3	1	2
...........................................................................................................CCAGGAATCAAACATATTATT.............................	21	1	3.00	3	2	1
...........................................................................................................CCAGGAATCAAACATATTATTA............................	22	1	2.00	2	2	0
.....................................................................ATGTTTGATATTCTTGGTTG....................................................................	20	1	2.00	2	2	0
....................................................................TATGTTTGATATTCTTGGTTG....................................................................	21	1	1.00	1	1	0
......................................................................TGTTTGATATTCTTGGTTG....................................................................	19	1	1.00	1	1	0
..................................................................GATATGTTTGATATTCTTGGTTGT...................................................................	24	1	1.00	1	1	0
.................................................................AGATATGTTTGATATTCTT.........................................................................	19	1	1.00	1	1	0