Secondary structure and small RNA-seq evidence for dme-mir-iab-8

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:12681982-12682079 -	GTTGTTAGTGCTCTCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droSim1	chr3R:8791202-8791299 +	GTTGCTCGTGCTATCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droSec1	super_12:1472230-1472327 +	GTTGCTCGTGCTATCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droYak2	chr3R:11708953-11709050 +	GTTGCTCGTGCTTTCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droEre2	scaffold_4770:8952402-8952499 +	GTTGCTCGTGCTTTCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droAna3	scaffold_13340:7215188-7215285 +	GTTGAAGGTGTTACCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAAAATCA
dp4	chr2:17671753-17671849 -	GTTGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTCGCACAGGTTC-
droPer1	super_0:11526559-11526655 -	GTTGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTCGCACAGGTTC-
droWil1	scaffold_181130:4905585-4905682 +	GTTGTTGGTGTTTCATCGTGTTACGTATACTGAAGGTATACCGGATAGCATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAGATTCA
droVir3	scaffold_12855:414691-414788 +	GTCGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAGGCTCT
droMoj3	scaffold_6540:1943729-1943826 -	GTTGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAGGCTCA
droGri2	scaffold_14906:12815109-12815201 -	GTTGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAG-----

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:12681982-12682079 -	GTTGTTAGTGCTCTCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droSim1	chr3R:8791202-8791299 +	GTTGCTCGTGCTATCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droSec1	super_12:1472230-1472327 +	GTTGCTCGTGCTATCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droYak2	chr3R:11708953-11709050 +	GTTGCTCGTGCTTTCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droEre2	scaffold_4770:8952402-8952499 +	GTTGCTCGTGCTTTCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG
droAna3	scaffold_13340:7215188-7215285 +	GTTGAAGGTGTTACCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAAAATCA
dp4	chr2:17671753-17671849 -	GTTGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTCGCACAGGTTC-
droPer1	super_0:11526559-11526655 -	GTTGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTCGCACAGGTTC-
droWil1	scaffold_181130:4905585-4905682 +	GTTGTTGGTGTTTCATCGTGTTACGTATACTGAAGGTATACCGGATAGCATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAGATTCA
droVir3	scaffold_12855:414691-414788 +	GTCGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAGGCTCT
droMoj3	scaffold_6540:1943729-1943826 -	GTTGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAGGCTCA
droGri2	scaffold_14906:12815109-12815201 -	GTTGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTTGCACAG-----

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GTTGCTCGTGCTATCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTTTACGAGGTCGCACAGAATCG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
....................TTACGTATACTGAAGGTATACC........................................................	22	2	13.50	27	27
....................TTACGTATACTGAAGGTATAC.........................................................	21	2	3.00	6	6
....................TTACGTATACTGAAGGTATACCGGA.....................................................	25	2	2.00	4	4
....................TTACGTATACTGAAGGTAT...........................................................	19	2	1.50	3	3
....................TTACGTATACTGAAGGTATACCGG......................................................	24	2	1.50	3	3
.TTGCTCGTGCTATCTCGTG..............................................................................	19	2	1.00	2	2
.............................................TAGGATACACTCAGGATACATTCAGT...........................	26	2	0.50	1	1
.........................................................AGGATACATTCAGTATACGTTTA..................	23	2	0.50	1	1

dp4

GTTGCTGGTGTTTCCTCGTGTTACGTATACTGAAGGTATACCGGATAGGATACACTCAGGATACATTCAGTATACGTATACGAAGTCGCACAGGTTC-	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
....................TTACGTATACTGAAGGTAT...........................................................	19	2	21.00	42	5	37
....................TTACGTATACTGAAGGTATA..........................................................	20	2	20.00	40	37	3
....................TTACGTATACTGAAGGTATAC.........................................................	21	2	3.00	6	0	6
....................TTACGTATACTGAAGGTATACC........................................................	22	2	2.50	5	0	5
....................TTACGTATACTGAAGGTATACCGG......................................................	24	2	2.00	4	3	1
.........................................................AGGATACATTCAGTATACGTATA..................	23	2	1.00	2	2	0
....................TTACGTATACTGAAGGTATACCGGA.....................................................	25	2	1.00	2	1	1
....................TTACGTATACTGAAGGTA............................................................	18	2	0.50	1	1	0
....................TTACGTATACTGAAGGTATACCG.......................................................	23	2	0.50	1	1	0

Secondary Structure

dm3

-26.3	-25.7	-25.7	-25.4	-25.3

droSim1

-26.3	-25.7	-25.7	-25.4	-25.3

droSec1

-26.3	-25.7	-25.7	-25.4	-25.3

droYak2

-26.3	-25.7	-25.7	-25.4	-25.3

droEre2

-26.3	-25.7	-25.7	-25.4	-25.3

droAna3

-28.2	-28.2	-27.6	-27.6	-27.6	-27.6

dp4

-28.2	-28.2	-27.6	-27.6	-27.6	-27.6

droPer1

-28.2	-28.2	-27.6	-27.6	-27.6	-27.6

droWil1

-27.6	-27.6	-27.2	-27.2	-27.0	-27.0

droVir3

-28.2	-28.2	-27.6	-27.6	-27.6	-27.6

droMoj3

-28.2	-28.2	-27.6	-27.6	-27.6	-27.6

droGri2

-28.2	-28.2	-27.6	-27.6	-27.6	-27.6

Generated: 01/05/2013 at 05:38 PM