Secondary structure and small RNA-seq evidence for dme-mir-87

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:9950403-9950531 -	CCAAAGT---------CCTTT--GGCAACACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATTATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGAATTT
droSim1	chr2L:9739846-9739974 -	CTTAAGT---------CCTTT--GGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATCATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGGATTT
droSec1	super_3:5397127-5397255 -	ACCAAGT---------CCTTT--GGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATCATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGGATTT
droYak2	chr2L:12640967-12641095 -	TCCAAGT---------CCTTT--GGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTATGGTCTTCG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTTAGCATTCATC----GGAGGATTT
droEre2	scaffold_4929:10570531-10570659 -	CACGAGT---------CCTTT--GGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTGCC-ATTATGGCCTACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTTAGCATTCATC----GGACGATTT
droAna3	scaffold_12916:13789760-13789886 -	TG--AAT---------CCTTTCAAGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACC-GATATGGCACAGA-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC----AAAAGAT--
dp4	chr4_group3:220105-220226 +	TCCTAC----------CGTGT--GCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCC-ATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC----AC-------
droPer1	super_1:1694906-1695025 +	TCCTAC----------CGTGT--GCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCC-ATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC-------------
droWil1	scaffold_180708:12250833-12250971 -	CCA--ATCAAAATTAACATTT-GGCCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACCAATTGTGATCTTCATTTCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTGACGGTAACATC----GTTGGAATA
droVir3	scaffold_12723:3996238-3996344 +	CTA---T---------CCCTT-GGCCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTGAGACATCTAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGT-------------------------
droMoj3	scaffold_6500:14729857-14729979 -	-----AT---------CCTTA--GCCGGCATCTTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTGTCACATCCAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTAGCGGTCTCATC----AAAGCA---
droGri2	scaffold_15252:3661296-3661426 -	TT---AT---------CCTTG--ACCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACC-ATTGTGACATCCAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTAGCGGCTTCATCACTTGGTGGATAG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:9950403-9950531 -	CCAAAGT---------CCTTT--GGCAACACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATTATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGAATTT
droSim1	chr2L:9739846-9739974 -	CTTAAGT---------CCTTT--GGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATCATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGGATTT
droSec1	super_3:5397127-5397255 -	ACCAAGT---------CCTTT--GGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATCATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGGATTT
droYak2	chr2L:12640967-12641095 -	TCCAAGT---------CCTTT--GGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTATGGTCTTCG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTTAGCATTCATC----GGAGGATTT
droEre2	scaffold_4929:10570531-10570659 -	CACGAGT---------CCTTT--GGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTGCC-ATTATGGCCTACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTTAGCATTCATC----GGACGATTT
droAna3	scaffold_12916:13789760-13789886 -	TG--AAT---------CCTTTCAAGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACC-GATATGGCACAGA-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC----AAAAGAT--
dp4	chr4_group3:220105-220226 +	TCCTAC----------CGTGT--GCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCC-ATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC----AC-------
droPer1	super_1:1694906-1695025 +	TCCTAC----------CGTGT--GCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCC-ATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC-------------
droWil1	scaffold_180708:12250833-12250971 -	CCA--ATCAAAATTAACATTT-GGCCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACCAATTGTGATCTTCATTTCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTGACGGTAACATC----GTTGGAATA
droVir3	scaffold_12723:3996238-3996344 +	CTA---T---------CCCTT-GGCCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTGAGACATCTAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGT-------------------------
droMoj3	scaffold_6500:14729857-14729979 -	-----AT---------CCTTA--GCCGGCATCTTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTGTCACATCCAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTAGCGGTCTCATC----AAAGCA---
droGri2	scaffold_15252:3661296-3661426 -	TT---AT---------CCTTG--ACCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACC-ATTGTGACATCCAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTAGCGGCTTCATCACTTGGTGGATAG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTTAAGTCCTTTGGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCCATCATGGCCAACGATC-CGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATCGGAGGATTT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................................................................TTGAGCAAAATTTCAGGTGTGTGA..............................	24	1	5937.00	5937	5937
............................................................................TTGAGCAAAATTTCAGGTGTGTG...............................	23	1	1222.00	1222	1222
.............................................................................TGAGCAAAATTTCAGGTGTGTGA..............................	23	1	931.00	931	931
.............................................................................TGAGCAAAATTTCAGGTGTGTG...............................	22	1	92.00	92	92
............................................................................TTGAGCAAAATTTCAGGTGTGT................................	22	1	76.00	76	76
............................................................................TTGAGCAAAATTTCAGGTGTG.................................	21	1	17.00	17	17
...........................TCGCGCCTGTATCTTGCTGAACC................................................................................	23	1	13.00	13	13
...........................TCGCGCCTGTATCTTGCTGAAC.................................................................................	22	1	8.00	8	8
..............................................................................GAGCAAAATTTCAGGTGTGTGA..............................	22	1	6.00	6	6
............................................................................TTGAGCAAAATTTCAGGTGTGTGAG.............................	25	1	3.00	3	3
.............................................................................TGAGCAAAATTTCAGGTGTGTGAG.............................	24	1	3.00	3	3

dp4

TCCTAC-CGTGTGCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCCATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTCAC-------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................................................................TTGAGCAAAATTTCAGGTGTGTGA..............................	24	1	3515.00	3515	2998	517
............................................................................TTGAGCAAAATTTCAGGTGTGTG...............................	23	1	749.00	749	536	213
.............................................................................TGAGCAAAATTTCAGGTGTGTGA..............................	23	1	664.00	664	571	93
............................................................................TTGAGCAAAATTTCAGGTGTGT................................	22	1	375.00	375	140	235
............................................................................TTGAGCAAAATTTCAGGTGTG.................................	21	1	237.00	237	133	104
.............................................................................TGAGCAAAATTTCAGGTGTGTG...............................	22	1	79.00	79	49	30
.............................................................................TGAGCAAAATTTCAGGTGTGT................................	21	1	22.00	22	2	20
............................................................................TTGAGCAAAATTTCAGGTGT..................................	20	1	21.00	21	10	11
...........................TCGCGCCTGTATCTTGCTGAACC................................................................................	23	1	8.00	8	7	1
...........................TCGCGCCTGTATCTTGCTGAAC.................................................................................	22	1	6.00	6	3	3
.............................................................................TGAGCAAAATTTCAGGTGTG.................................	20	1	5.00	5	1	4
.............................................................................TGAGCAAAATTTCAGGTGTGTGAG.............................	24	1	5.00	5	4	1
...........................................................................GTTGAGCAAAATTTCAGGTGTGTG...............................	24	1	3.00	3	3	0

Secondary Structure

dm3

-41.2	-41.1	-40.8	-40.7	-40.7	-40.6

droSim1

-41.1	-41.0	-41.0	-40.9	-40.7	-40.6

droSec1

-41.1	-41.0	-41.0	-40.9	-40.7	-40.6

droYak2

-32.9	-32.8	-32.8	-32.7	-31.9

droEre2

-35.3	-35.2	-35.2	-35.1	-34.9	-34.8

droAna3

-31.8	-31.7	-31.7	-31.6	-31.6	-31.5

dp4

-33.8	-33.7	-33.5	-33.4	-33.4	-33.3

droPer1

-33.8	-33.7	-33.5	-33.4	-33.4	-33.3

droWil1

-31.8	-31.8	-31.7	-31.7	-31.2	-31.1

droVir3

-31.5	-31.4	-30.8	-30.7	-30.7	-30.6

droMoj3

-30.0	-29.9	-29.4	-29.4	-29.3	-29.3

droGri2

-32.0	-31.9	-31.7	-31.6	-31.1	-31.0

Generated: 01/05/2013 at 05:30 PM