Secondary structure and small RNA-seq evidence for dme-mir-219

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:17308091-17308220 +	AAATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droSim1	chr3L:16646167-16646296 +	AAATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droSec1	super_0:9359464-9359593 +	AAATAAATATTTGGTTAATTCAATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droYak2	chr3L:16762572-16762701 -	AAATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droEre2	scaffold_4784:16541302-16541431 -	AAATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droAna3	scaffold_13337:8265335-8265463 +	CAAAATAT-TTTGGTTAATTCAATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGAAT-TCAAATACTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATACGAATACAACGAAGAGAACCAT--TTC
dp4	chrXR_group6:9338098-9338227 -	ATCAAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TCCAATACTCAAGGGTTGTGACTGGACATCGCGGCTCGAAATAAGAATACAACCCAGCAACCAAA--ATC
droPer1	super_35:387455-387584 +	ATCAAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TCCAATACTCAAGGGTTGTGACTGGACATCGCGGCTCGAAATAAGAATACAACCCATCAACCAAA--ATC
droWil1	scaffold_180955:2086476-2086593 +	A---AAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATT-TCAAATACTCAAGGGTTGCATCTGGGCATCGCGGCTCGAAATAAGAATACA---------CCCAA--TAA
droVir3	scaffold_13049:5991414-5991542 -	GTATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATT-TCAAATACTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATGAGAATCCAACCCA-CAACCAAA--CAA
droMoj3	scaffold_6680:4316890-4317021 -	AAACATATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATTTTTAAATACTCAAGGGTTGCATCTGGGCATCGCGGCTCGAAATGAGAATCCAACACAAA-GCCAAAATATA
droGri2	scaffold_15110:13121815-13121944 +	TAACAAACATTTGGTGAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATT-TCAAAAACTCAAGGGTTGCATCTGGGCATCGCGGCTCGAAATGAGAATACAACACAAAAATCAAA--ACA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:17308091-17308220 +	AAATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droSim1	chr3L:16646167-16646296 +	AAATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droSec1	super_0:9359464-9359593 +	AAATAAATATTTGGTTAATTCAATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droYak2	chr3L:16762572-16762701 -	AAATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droEre2	scaffold_4784:16541302-16541431 -	AAATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAA--TCA
droAna3	scaffold_13337:8265335-8265463 +	CAAAATAT-TTTGGTTAATTCAATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGAAT-TCAAATACTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATACGAATACAACGAAGAGAACCAT--TTC
dp4	chrXR_group6:9338098-9338227 -	ATCAAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TCCAATACTCAAGGGTTGTGACTGGACATCGCGGCTCGAAATAAGAATACAACCCAGCAACCAAA--ATC
droPer1	super_35:387455-387584 +	ATCAAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATA-TCCAATACTCAAGGGTTGTGACTGGACATCGCGGCTCGAAATAAGAATACAACCCATCAACCAAA--ATC
droWil1	scaffold_180955:2086476-2086593 +	A---AAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATT-TCAAATACTCAAGGGTTGCATCTGGGCATCGCGGCTCGAAATAAGAATACA---------CCCAA--TAA
droVir3	scaffold_13049:5991414-5991542 -	GTATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATT-TCAAATACTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATGAGAATCCAACCCA-CAACCAAA--CAA
droMoj3	scaffold_6680:4316890-4317021 -	AAACATATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATTTTTAAATACTCAAGGGTTGCATCTGGGCATCGCGGCTCGAAATGAGAATCCAACACAAA-GCCAAAATATA
droGri2	scaffold_15110:13121815-13121944 +	TAACAAACATTTGGTGAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATT-TCAAAAACTCAAGGGTTGCATCTGGGCATCGCGGCTCGAAATGAGAATACAACACAAAAATCAAA--ACA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAATAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATATTCAATATTCAAGGGTTGCGACTGGGCATCGCGGCTCGAAATAAGAATACAACTCGGCAACCAAATCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................................................................AGGGTTGCGACTGGGCATCGCG...................................	22	1	28.00	28	28
.................................TGATTGTCCAAACGCAATTCTTG..........................................................................	23	1	2.00	2	2
.........................................................................AGGGTTGCGACTGGGCATCGC....................................	21	1	1.00	1	1

dp4

ATCAAAATATTTGGTTAATTCGATTTTTAGCTATGATTGTCCAAACGCAATTCTTGTTGATATCCAATACTCAAGGGTTGTGACTGGACATCGCGGCTCGAAATAAGAATACAACCCAGCAACCAAAATC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.........................................................................AGGGTTGTGACTGGACATCGCG...................................	22	1	38.00	38	20	18
.................................TGATTGTCCAAACGCAATTCTTG..........................................................................	23	1	17.00	17	4	13
.................................TGATTGTCCAAACGCAATTCT............................................................................	21	1	12.00	12	0	12
.........................................................................AGGGTTGTGACTGGACATCGC....................................	21	1	7.00	7	4	3
.................................TGATTGTCCAAACGCAATTCTT...........................................................................	22	1	7.00	7	0	7
.................................TGATTGTCCAAACGCAATTC.............................................................................	20	1	7.00	7	0	7
.................................TGATTGTCCAAACGCAATTCTTGT.........................................................................	24	1	4.00	4	0	4
........................................................................AAGGGTTGTGACTGGACATCGC....................................	22	1	3.00	3	3	0
.....................................TGTCCAAACGCAATTCTTG..........................................................................	19	1	1.00	1	1	0
.........................................................................AGGGTTGTGACTGGACATCG.....................................	20	1	1.00	1	0	1

Secondary Structure

dm3

-34.3	-34.3	-34.1	-34.1	-33.5	-33.5

droSim1

-34.3	-34.3	-34.1	-34.1	-33.5	-33.5

droSec1

-33.2	-33.2	-33.0	-33.0	-32.4	-32.4

droYak2

-34.3	-34.3	-34.1	-34.1	-33.5	-33.5

droEre2

-34.3	-34.3	-34.1	-34.1	-33.5	-33.5

droAna3

-32.3	-32.3	-32.0	-32.0

dp4

-32.1	-32.1	-32.1	-32.1	-32.0	-32.0

droPer1

-32.1	-32.1	-32.1	-32.1	-32.0	-32.0

droWil1

-30.4	-30.4	-30.3	-30.3	-30.0	-30.0

droVir3

-33.7	-33.7	-33.6	-33.6	-33.3	-33.3

droMoj3

-31.1	-31.1	-30.4	-30.4	-30.4	-30.4

droGri2

-30.3	-30.3	-30.0	-30.0	-29.3	-29.3

Generated: 01/05/2013 at 05:09 PM