Secondary structure and small RNA-seq evidence for dme-mir-9b

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:16698729-16698849 +	TGTTGCTCTT------------T-TGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTTTATGTATATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCATTAT---GTTTGAGTTGA
droSim1	vom21g07.g1:730-849 +	TGTTGCTCTT------------T-TGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTATA--AGTATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCATTAT---GCTTGAGTTGA
droSec1	super_7:345741-345859 +	TGTTGCTCTT------------T-TGTTTGCATATTATTTGGTCTTTGGTGATTTTAGCTGTATGGTGTATA--AGTATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCATTAT---GCTTGAGTTGA
droYak2	chr2R:4404225-4404345 -	GGTTGCTCTT------------T-TGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTGTTTATGTGTTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCATTAT---GCTTGAGTTGA
droEre2	scaffold_4845:19768375-19768493 +	AGTTGCTCTT------------T-TGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTGTA--TGTGTTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATTAT---GCTTGAGTTGA
droAna3	scaffold_12916:15864526-15864643 -	AGTTGCTCTT------------T-TGTTTGCACATTATTTGTTCTTTGGTGATTTTAGCTGTATGGTGTCT---CATATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATTTT---TTCTGAGTTGC
dp4	chr4_group3:8444179-8444302 +	AGTTGATCTT------------T-TGTTTGCACATTATTTGATCTTTGGTGATTTTAGCTGTATGGTGTATATCAAAGATCCATAGAGCTTTATCACCAAAACCCAAATGGTTTTTGCATTTTTTCGCTTGAGTTGC
droPer1	super_1:9895298-9895421 +	AGTTGATCTT------------T-TGTTTGCACATTATTTGATCTTTGGTGATTTTAGCTGTATGGTGTATATCAAAGATCCATAGAGCTTTATCACCAAAACCCAAATGGTTTTTGCATTTTTTCGCTTGAGTTGC
droWil1	scaffold_181132:873333-873452 -	ATTGATTTTG------------A-TTTTCGCATATTATTTGGTCTTTGGTGATTTTAGCTGTATGGTGTATGAGCATAATCCATAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATTTT---GCTTGAGTTG-
droVir3	scaffold_12963:12862857-12862965 -	TGTTGCCTTT------------TTATTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTGCG--CGTATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATT--------------GC
droMoj3	scaffold_6500:7202293-7202399 +	TG--GCTTTT------------T-ATTTTGCATATTATTTGTTCTTTGGTGATTTTAGCTGTATGGTGTGCG--CGTATTCCATAGAGCTTTATTACCAAAAACCAAATGGTCTTTGCATT--------------GC
droGri2	scaffold_14978:831270-831399 +	TGCTGCCCTTTGTTTGCCCTTTTGAGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTCTATGGTGTGCG--CATAATCCACAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATT-T---GCTTTCTTTT-

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:16698729-16698849 +	TGTTGCTCTT------------T-TGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTTTATGTATATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCATTAT---GTTTGAGTTGA
droSim1	vom21g07.g1:730-849 +	TGTTGCTCTT------------T-TGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTATA--AGTATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCATTAT---GCTTGAGTTGA
droSec1	super_7:345741-345859 +	TGTTGCTCTT------------T-TGTTTGCATATTATTTGGTCTTTGGTGATTTTAGCTGTATGGTGTATA--AGTATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCATTAT---GCTTGAGTTGA
droYak2	chr2R:4404225-4404345 -	GGTTGCTCTT------------T-TGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTGTTTATGTGTTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCATTAT---GCTTGAGTTGA
droEre2	scaffold_4845:19768375-19768493 +	AGTTGCTCTT------------T-TGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTGTA--TGTGTTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATTAT---GCTTGAGTTGA
droAna3	scaffold_12916:15864526-15864643 -	AGTTGCTCTT------------T-TGTTTGCACATTATTTGTTCTTTGGTGATTTTAGCTGTATGGTGTCT---CATATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATTTT---TTCTGAGTTGC
dp4	chr4_group3:8444179-8444302 +	AGTTGATCTT------------T-TGTTTGCACATTATTTGATCTTTGGTGATTTTAGCTGTATGGTGTATATCAAAGATCCATAGAGCTTTATCACCAAAACCCAAATGGTTTTTGCATTTTTTCGCTTGAGTTGC
droPer1	super_1:9895298-9895421 +	AGTTGATCTT------------T-TGTTTGCACATTATTTGATCTTTGGTGATTTTAGCTGTATGGTGTATATCAAAGATCCATAGAGCTTTATCACCAAAACCCAAATGGTTTTTGCATTTTTTCGCTTGAGTTGC
droWil1	scaffold_181132:873333-873452 -	ATTGATTTTG------------A-TTTTCGCATATTATTTGGTCTTTGGTGATTTTAGCTGTATGGTGTATGAGCATAATCCATAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATTTT---GCTTGAGTTG-
droVir3	scaffold_12963:12862857-12862965 -	TGTTGCCTTT------------TTATTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTGCG--CGTATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATT--------------GC
droMoj3	scaffold_6500:7202293-7202399 +	TG--GCTTTT------------T-ATTTTGCATATTATTTGTTCTTTGGTGATTTTAGCTGTATGGTGTGCG--CGTATTCCATAGAGCTTTATTACCAAAAACCAAATGGTCTTTGCATT--------------GC
droGri2	scaffold_14978:831270-831399 +	TGCTGCCCTTTGTTTGCCCTTTTGAGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTCTATGGTGTGCG--CATAATCCACAGAGCTTTATTACCAAAAACCAAATGGTTTTTGCATT-T---GCTTTCTTTT-

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGTTGCTCTTTTGTTTGCATATTATTTGCTCTTTGGTGATTTTAGCTGTATGGTGTATAAGT--ATTCCATAGAGCTTTATTACCAAAAACCAAATGGTTTCTGCATTAT---GCTTGAGTTGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.............................TCTTTGGTGATTTTAGCTGTATG........................................................................	23	1	5856.00	5856	5856
.............................TCTTTGGTGATTTTAGCTGTAT.........................................................................	22	1	2773.00	2773	2773
.............................TCTTTGGTGATTTTAGCTGTATGG.......................................................................	24	1	245.00	245	245
.............................TCTTTGGTGATTTTAGCTGTA..........................................................................	21	1	166.00	166	166
......................................................................TAGAGCTTTATTACCAAAAACC................................	22	1	80.00	80	80
.............................TCTTTGGTGATTTTAGCTGT...........................................................................	20	1	61.00	61	61
...............................TTTGGTGATTTTAGCTGTATG........................................................................	21	1	16.00	16	16
......................................................................TAGAGCTTTATTACCAAAAAC.................................	21	1	14.00	14	14
.............................TCTTTGGTGATTTTAGCTG............................................................................	19	1	12.00	12	12
............................CTCTTTGGTGATTTTAGCTGTATG........................................................................	24	1	10.00	10	10
.............................TCTTTGGTGATTTTAGCTGTATGGT......................................................................	25	1	8.00	8	8
..............................CTTTGGTGATTTTAGCTGTATG........................................................................	22	1	7.00	7	7
...............................TTTGGTGATTTTAGCTGTAT.........................................................................	20	1	6.00	6	6
............................CTCTTTGGTGATTTTAGCTGTAT.........................................................................	23	1	6.00	6	6
......................................................................TAGAGCTTTATTACCAAAAACCA...............................	23	1	4.00	4	4
..............................CTTTGGTGATTTTAGCTGTATGG.......................................................................	23	1	3.00	3	3
..............................CTTTGGTGATTTTAGCTGTAT.........................................................................	21	1	3.00	3	3
......................................................................TAGAGCTTTATTACCAAAAA..................................	20	1	2.00	2	2
.................................TGGTGATTTTAGCTGTAT.........................................................................	18	1	2.00	2	2
...............................TTTGGTGATTTTAGCTGTATGG.......................................................................	22	1	2.00	2	2
.......................................................................AGAGCTTTATTACCAAAAACC................................	21	1	1.00	1	1
.....................................................................ATAGAGCTTTATTACCAAAAACC................................	23	1	1.00	1	1

dp4

AGTTGATCTTTTGTTTGCACATTATTTGATCTTTGGTGATTTTAGCTGTATGGTGTATATCAAAGATCCATAGAGCTTTATCACCAAAACCCAAATGGTTTTTGCATTTTTTCGCTTGAGTTGC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.............................TCTTTGGTGATTTTAGCTGTATG........................................................................	23	1	10038.00	10038	8752	1286
.............................TCTTTGGTGATTTTAGCTGTAT.........................................................................	22	1	4862.00	4862	3232	1630
.............................TCTTTGGTGATTTTAGCTGTA..........................................................................	21	1	280.00	280	161	119
.............................TCTTTGGTGATTTTAGCTGTATGG.......................................................................	24	1	165.00	165	153	12
......................................................................TAGAGCTTTATCACCAAAACC.................................	21	1	130.00	130	93	37
......................................................................TAGAGCTTTATCACCAAAACCC................................	22	1	106.00	106	53	53
.............................TCTTTGGTGATTTTAGCTGT...........................................................................	20	1	104.00	104	45	59
..............................CTTTGGTGATTTTAGCTGTATGG.......................................................................	23	1	93.00	93	87	6
..............................CTTTGGTGATTTTAGCTGTATG........................................................................	22	1	44.00	44	44	0
...............................TTTGGTGATTTTAGCTGTATG........................................................................	21	1	24.00	24	21	3
.............................TCTTTGGTGATTTTAGCTG............................................................................	19	1	15.00	15	5	10
...............................TTTGGTGATTTTAGCTGTAT.........................................................................	20	1	10.00	10	9	1
......................................................................TAGAGCTTTATCACCAAAAC..................................	20	1	10.00	10	8	2
................................TTGGTGATTTTAGCTGTATG........................................................................	20	1	5.00	5	5	0
.............................TCTTTGGTGATTTTAGCTGTATGGT......................................................................	25	1	4.00	4	3	1
..............................CTTTGGTGATTTTAGCTGTAT.........................................................................	21	1	4.00	4	3	1
................................TTGGTGATTTTAGCTGTAT.........................................................................	19	1	3.00	3	3	0
.....................................................................ATAGAGCTTTATCACCAAAACC.................................	22	1	3.00	3	3	0
...............................TTTGGTGATTTTAGCTGTATGG.......................................................................	22	1	3.00	3	3	0
......................................................................TAGAGCTTTATCACCAAAA...................................	19	1	2.00	2	2	0
................................TTGGTGATTTTAGCTGTATGG.......................................................................	21	1	2.00	2	2	0
..............................CTTTGGTGATTTTAGCTGTATGGT......................................................................	24	1	2.00	2	2	0
.................................TGGTGATTTTAGCTGTATG........................................................................	19	1	2.00	2	2	0

Secondary Structure

dm3

dG=-22.4, p-value=0.009901	dG=-22.1, p-value=0.009901	dG=-21.8, p-value=0.009901

droSim1

dG=-22.8, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.2, p-value=0.009901	dG=-21.9, p-value=0.009901

droSec1

dG=-29.1, p-value=0.009901	dG=-28.8, p-value=0.009901	dG=-28.2, p-value=0.009901

droYak2

dG=-21.0, p-value=0.009901	dG=-20.7, p-value=0.009901	dG=-20.4, p-value=0.009901

droEre2

dG=-21.2, p-value=0.009901	dG=-20.9, p-value=0.009901	dG=-20.6, p-value=0.009901

droAna3

dG=-21.7, p-value=0.009901	dG=-21.7, p-value=0.009901	dG=-21.3, p-value=0.009901	dG=-21.3, p-value=0.009901	dG=-21.0, p-value=0.009901

dp4

dG=-23.2, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.6, p-value=0.009901

droPer1

dG=-23.2, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.6, p-value=0.009901

droWil1

dG=-29.1, p-value=0.009901	dG=-28.8, p-value=0.009901

droVir3

dG=-22.5, p-value=0.009901	dG=-22.2, p-value=0.009901	dG=-21.9, p-value=0.009901	dG=-21.9, p-value=0.009901	dG=-21.6, p-value=0.009901

droMoj3

dG=-22.9, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.3, p-value=0.009901	dG=-22.2, p-value=0.009901	dG=-21.9, p-value=0.009901

droGri2

dG=-20.7, p-value=0.009901	dG=-20.7, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.4, p-value=0.009901

Generated: 03/07/2013 at 07:29 PM