Secondary structure and small RNA-seq evidence for dme-mir-986

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:4332472-4332601 +	TAGCCACGCAG--AGGA---------CACACCTG-------AAATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGAATCTACTCAGCGGCGAGGCTATTCAAGTAAGGTTATTTTGGGC----CAGCGACTTTA--CGACC
droSim1	chr2R:2956848-2956977 +	TAGCCACGCAG--AGGA---------CACACCTG-------AAATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGAATCTACTCAGCGGCGAGGCTATTCCAGTAAGGTTGTTTTGGGC----CAGCGACTTTA--TGACC
droSec1	super_1:1974074-1974203 +	TAGCCACGCAG--AGGA---------CACACCTG-------AAATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGAATCTACTCAGCGGCGAGGCTATTCCAGTAAGGTTGTTTTGGGC----CAGCGACTTTA--TGACC
droYak2	chr2L:16988548-16988677 +	TAGAAACGCAG--AGGA---------CACACCTA-------AAATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGTATCTACTCAGCGGCGAAGCTATTCCAGTAAGGTTATTTTGGGC----CAGCGACTTTA--CGACC
droEre2	scaffold_4929:18305702-18305825 -	TAGATACG--------A---------GATACCTA-------AGATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGAATCTACTCAGCGGCAAGGCTATTCCAGTAAGGTTATTTTGGGC----CAGCGACTCAA--CGACC
droAna3	scaffold_13266:1670175-1670300 -	TGGTTTC-CTG--AGGA---------TACGTCCA-------AAATGACTCATCTCGAATAGCGTTGTGACTGATGGTATTTAAATAT------AAATCCGAGACAATGCTATTCTTGTAAAGTCATCTTGACC----AAGCAACTTTTTCTAATC
dp4	chr3:2308599-2308727 +	TATCTCCTGAATCGGAG---------TACGACTG-------AAACAACCCGTCTCGAATAGCGTTGTGACTGAT-GA--CTGCATTTGTAATTTTCTCAGCGGCAGTGCTATTCCAGTTGGGTTGTTTGCGGCCAAACAACAACTATA-------
droPer1	super_2:2480065-2480185 +	GAATCG--------GAG---------TACGACTG-------AAACAACCCGTCTCGAATAGCGTTGTGACTGAT-GA--CTGCATTTGTAATTTTCTCAGCGGCAGTGCTATTCCAGTTGGGTTGTTTGCGGCCAAACAACAACTATA-------
droWil1	scaffold_180700:3161017-3161152 -	TTACTACACAA--AGTGAACAGTTC-GATGACTT-------AAATGCCCAATCTCGAATAGCGTTGTAACTGAT-GA--TTGT-GATATGAGAGAGTCAGCCACTATGCTATACGAGGTGGGGCATTTGTGGGT---AAACAACCAAA--TTACG
droVir3	scaffold_12875:9403376-9403510 +	AAACTATAAAG--TG--TTTTAATGGTTCACTTAAATGGCTAATTGTCTTCTCTCGAATAGCATTATGGCTGAT-GACAAT---TCTGGAATAACATCAGTTGAAATGCCATTCGGGTTAAGGCACTTGAGAAATGGCAGCGA------------
droMoj3	scaffold_6496:17707880-17708014 -	TGTTGGCGAAC------TTTCAATGGCTCATTTAACTGGCTAATTGCCTTCTCTCGAATTGCATTATGGCCGAT-GACACAATTC-TGCAAAATCATCAGTTGGAATGCCATTCGGGTCAAGGCATTTACGAATCGCCAACGA------------
droGri2	scaffold_15245:2671305-2671410 +	TTGAATGGCT-------------------------------TATTGCCTTTTCTCGAATTGCATTGTGACTGAT-GAAAAT----TTAGAAATTCATCAGTTAAAATGCCATTCGAGTTAAGGCACTTATGCA-----------TTAA--CAACC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:4332472-4332601 +	TAGCCACGCAG--AGGA---------CACACCTG-------AAATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGAATCTACTCAGCGGCGAGGCTATTCAAGTAAGGTTATTTTGGGC----CAGCGACTTTA--CGACC
droSim1	chr2R:2956848-2956977 +	TAGCCACGCAG--AGGA---------CACACCTG-------AAATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGAATCTACTCAGCGGCGAGGCTATTCCAGTAAGGTTGTTTTGGGC----CAGCGACTTTA--TGACC
droSec1	super_1:1974074-1974203 +	TAGCCACGCAG--AGGA---------CACACCTG-------AAATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGAATCTACTCAGCGGCGAGGCTATTCCAGTAAGGTTGTTTTGGGC----CAGCGACTTTA--TGACC
droYak2	chr2L:16988548-16988677 +	TAGAAACGCAG--AGGA---------CACACCTA-------AAATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGTATCTACTCAGCGGCGAAGCTATTCCAGTAAGGTTATTTTGGGC----CAGCGACTTTA--CGACC
droEre2	scaffold_4929:18305702-18305825 -	TAGATACG--------A---------GATACCTA-------AGATTACCCATCTCGAATAGCGTTGTGACTGA-GGTAACTGCGCATCGAATCTACTCAGCGGCAAGGCTATTCCAGTAAGGTTATTTTGGGC----CAGCGACTCAA--CGACC
droAna3	scaffold_13266:1670175-1670300 -	TGGTTTC-CTG--AGGA---------TACGTCCA-------AAATGACTCATCTCGAATAGCGTTGTGACTGATGGTATTTAAATAT------AAATCCGAGACAATGCTATTCTTGTAAAGTCATCTTGACC----AAGCAACTTTTTCTAATC
dp4	chr3:2308599-2308727 +	TATCTCCTGAATCGGAG---------TACGACTG-------AAACAACCCGTCTCGAATAGCGTTGTGACTGAT-GA--CTGCATTTGTAATTTTCTCAGCGGCAGTGCTATTCCAGTTGGGTTGTTTGCGGCCAAACAACAACTATA-------
droPer1	super_2:2480065-2480185 +	GAATCG--------GAG---------TACGACTG-------AAACAACCCGTCTCGAATAGCGTTGTGACTGAT-GA--CTGCATTTGTAATTTTCTCAGCGGCAGTGCTATTCCAGTTGGGTTGTTTGCGGCCAAACAACAACTATA-------
droWil1	scaffold_180700:3161017-3161152 -	TTACTACACAA--AGTGAACAGTTC-GATGACTT-------AAATGCCCAATCTCGAATAGCGTTGTAACTGAT-GA--TTGT-GATATGAGAGAGTCAGCCACTATGCTATACGAGGTGGGGCATTTGTGGGT---AAACAACCAAA--TTACG
droVir3	scaffold_12875:9403376-9403510 +	AAACTATAAAG--TG--TTTTAATGGTTCACTTAAATGGCTAATTGTCTTCTCTCGAATAGCATTATGGCTGAT-GACAAT---TCTGGAATAACATCAGTTGAAATGCCATTCGGGTTAAGGCACTTGAGAAATGGCAGCGA------------
droMoj3	scaffold_6496:17707880-17708014 -	TGTTGGCGAAC------TTTCAATGGCTCATTTAACTGGCTAATTGCCTTCTCTCGAATTGCATTATGGCCGAT-GACACAATTC-TGCAAAATCATCAGTTGGAATGCCATTCGGGTCAAGGCATTTACGAATCGCCAACGA------------
droGri2	scaffold_15245:2671305-2671410 +	TTGAATGGCT-------------------------------TATTGCCTTTTCTCGAATTGCATTGTGACTGAT-GAAAAT----TTAGAAATTCATCAGTTAAAATGCCATTCGAGTTAAGGCACTTATGCA-----------TTAA--CAACC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TAGCCAC----GCAGAGGACACACCTGAAATTACCCATCTCGAATAGCGTTGTGACTGAGGTAACTGCGCATCGAATCTACTCAGCGGCGAGGCTATTCCAGTAAGGTTGTTTTGGGCCA----GCGACTTTATGACC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.....................................TCTCGAATAGCGTTGTGACTGA...............................................................................	22	2	222.00	444	444
.....................................TCTCGAATAGCGTTGTGACTG................................................................................	21	2	35.00	70	70
.....................................TCTCGAATAGCGTTGTGACT.................................................................................	20	2	5.50	11	11
.....................................TCTCGAATAGCGTTGTGACTGAG..............................................................................	23	2	1.50	3	3
...................................................................................AGCGGCGAGGCTATTCCAGTA..................................	21	2	0.50	1	1

dp4

TATCTCCTGAATCGGAGT--ACGACTGAAACAACCCGTCTCGAATAGCGTTGTGACTGA--TGACTGCATTTGTAATTTTCTCAGCGGCAGTGCTATTCCAGTTGGGTTGTTTGCGGCCAAACAACAACTATA-----	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.....................................TCTCGAATAGCGTTGTGACTGA--.............................................................................	22	2	198.50	397	0	397
.....................................TCTCGAATAGCGTTGTGACTG................................................................................	21	2	170.00	340	139	201
.....................................TCTCGAATAGCGTTGTGACTGA--TG...........................................................................	24	2	28.00	56	37	19
........................................CGAATAGCGTTGTGACTGA--TGA..........................................................................	22	2	13.50	27	27	0
.....................................TCTCGAATAGCGTTGTGACTGA--TGA..........................................................................	25	2	9.00	18	18	0
................................................................................CTCAGCGGCAGTGCTATTCCAG....................................	22	2	5.00	10	0	10
.....................................TCTCGAATAGCGTTGTGACTGA--T............................................................................	23	2	5.00	10	4	6
.......................................TCGAATAGCGTTGTGACTGA--.............................................................................	20	2	2.00	4	4	0
.......................................TCGAATAGCGTTGTGACTG................................................................................	19	2	1.00	2	0	2
................................................................................CTCAGCGGCAGTGCTATTCCA.....................................	21	2	0.50	1	1	0
.........................................GAATAGCGTTGTGACTGA--.............................................................................	18	2	0.50	1	0	1
......................................CTCGAATAGCGTTGTGACT.................................................................................	19	2	0.50	1	0	1
.............................................................TGACTGCATTTGTAATTTTCTC.......................................................	22	2	0.50	1	1	0
.....................................TCTCGAATAGCGTTGTGACTGA--TGAC.........................................................................	26	2	0.50	1	1	0

Secondary Structure

dm3

-35.4	-35.3	-34.5	-34.5

droSim1

-35.5	-35.4	-34.6	-34.6

droSec1

-35.5	-35.4	-34.6	-34.6

droYak2

-36.1	-36.1	-36.1	-35.2

droEre2

-36.7	-36.6	-35.8	-35.8

droAna3

-25.6	-25.6	-25.5	-25.5	-25.4	-25.4

dp4

-37.8	-37.8	-37.6	-37.2	-37.2	-37.0

droPer1

-37.8	-37.8	-37.6	-37.2	-37.2	-37.0

droWil1

-37.6	-37.2	-37.1	-37.0	-36.8	-36.7

droVir3

-30.3	-30.1	-30.0	-30.0	-29.9	-29.8

droMoj3

-32.2	-31.8	-31.4	-31.4

droGri2

-38.7	-37.9	-37.9	-37.8

Generated: 01/05/2013 at 05:35 PM