Secondary structure and small RNA-seq evidence for dme-mir-969

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:18018375-18018498 +	TTCGG---------------TGAATCC--CCAAGTCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGA--TGGAC----TACTGC-----AATTCGAAA--T
droSim1	chrU:15519348-15519471 +	TTCGG---------------GGAATCC--CCAAGTCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGA--TGGAC----TACTGC-----AATTCAAAA--T
droSec1	super_8:326574-326685 +	TTCGA---------------GGAATCC--CCAAGTCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGA--TGGAC----TACT-------------------
droYak2	chrX:16642309-16642432 +	TTCGG---------------GGTATCC--CCAAACCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTTGTGGGA--TGGTC----TACCGC-----AATTCGAAA--G
droEre2	scaffold_4690:8346009-8346128 +	TTTGG---------------GAAGTTC--CCAAATCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGA--TGGAT----TACTGC---------CGAAA--G
droAna3	scaffold_13335:1607974-1608101 -	TGTGT--TTATTTTTTTT--GGAA-------AATATTCTGTTTTACGTGCGAGTTCCACTAAGCAAGTTTTGAGAATTT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTCCGTGGGG--CAGAT----AATGTC-----AG--CAGTA--T
dp4	chrXL_group3a:1977519-1977620 -	TTCCT---------------GGAAGCCATCTAGGAGCCTGTTCTACGTGCGAGTTCCACCATGCAAGTTTTGAGC--GTATATGAATCCAAAAACTTGACACGTTGAGCTCGTGCGTGG------------------------------------
droPer1	super_11:2701270-2701398 +	TTCCT---------------GGAAGCCATCTAGGAGCCTGTTCTACGTGCGAGTTCCACCATGCAAGTTTTGAGC--GTATATGAATCCAAAAACTTGACACGTTGAGCTCGTGCGTGGTG--CAGCCAAATCATCGC-----AGCGCATCC--A
droWil1	scaffold_181096:12029390-12029503 +	TTTAT-----------------------------ATCCTGTCCTACGCATGAGTTCCACTAAGCAAGTTTTGGGCATAT-TTCAAAAACAAAAACTTGACACGTTGAGCTCGTCTGTGTGA--CAGAA----C-GAACAAC--AAATGAAGA--A
droVir3	scaffold_12928:1264092-1264205 -	TTCAA---------------GAGCAGC--TCGCGCTTCTGCCCTACGCACGAGTTCCACTAATCAAGTTTTGAGCGGAT-TCGAAAGTCGAAAACTTGACACGTTGAGCTCGTCCGTGGGG--CGGCA----TTC---------------AA--G
droMoj3	scaffold_6473:13724290-13724417 +	TCCTTATCCATAC-------CATATCC--ACATTTGGCTGTCCTACGAGCGAGTTCCACTAATCAAGTTTTGAGT--GT-TCGAAAATCAAAAACTTGACACGTTGAGCTCGTCTGTGTGG--CA--C----AAGTTC-----AA--CAAAAGCA
droGri2	scaffold_15203:8445730-8445869 +	TTCGGT-TTGTTCTTTTACAGCAGTGCATCCGGGTGTCTGCCACACTTACGAGTTCCACTATTCAAGTTTTGAGC--GTATTTGAAATCAAAAACTTGACACGTTGAGCTCGTGTGTGCGTTGCGG------AAA-TCAACTTA---CTCAA--A

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:18018375-18018498 +	TTCGG---------------TGAATCC--CCAAGTCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGA--TGGAC----TACTGC-----AATTCGAAA--T
droSim1	chrU:15519348-15519471 +	TTCGG---------------GGAATCC--CCAAGTCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGA--TGGAC----TACTGC-----AATTCAAAA--T
droSec1	super_8:326574-326685 +	TTCGA---------------GGAATCC--CCAAGTCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGA--TGGAC----TACT-------------------
droYak2	chrX:16642309-16642432 +	TTCGG---------------GGTATCC--CCAAACCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTTGTGGGA--TGGTC----TACCGC-----AATTCGAAA--G
droEre2	scaffold_4690:8346009-8346128 +	TTTGG---------------GAAGTTC--CCAAATCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGA--TGGAT----TACTGC---------CGAAA--G
droAna3	scaffold_13335:1607974-1608101 -	TGTGT--TTATTTTTTTT--GGAA-------AATATTCTGTTTTACGTGCGAGTTCCACTAAGCAAGTTTTGAGAATTT-TTTAAAAACAAAAACTTGACACGTTGAGCTCGTCCGTGGGG--CAGAT----AATGTC-----AG--CAGTA--T
dp4	chrXL_group3a:1977519-1977620 -	TTCCT---------------GGAAGCCATCTAGGAGCCTGTTCTACGTGCGAGTTCCACCATGCAAGTTTTGAGC--GTATATGAATCCAAAAACTTGACACGTTGAGCTCGTGCGTGG------------------------------------
droPer1	super_11:2701270-2701398 +	TTCCT---------------GGAAGCCATCTAGGAGCCTGTTCTACGTGCGAGTTCCACCATGCAAGTTTTGAGC--GTATATGAATCCAAAAACTTGACACGTTGAGCTCGTGCGTGGTG--CAGCCAAATCATCGC-----AGCGCATCC--A
droWil1	scaffold_181096:12029390-12029503 +	TTTAT-----------------------------ATCCTGTCCTACGCATGAGTTCCACTAAGCAAGTTTTGGGCATAT-TTCAAAAACAAAAACTTGACACGTTGAGCTCGTCTGTGTGA--CAGAA----C-GAACAAC--AAATGAAGA--A
droVir3	scaffold_12928:1264092-1264205 -	TTCAA---------------GAGCAGC--TCGCGCTTCTGCCCTACGCACGAGTTCCACTAATCAAGTTTTGAGCGGAT-TCGAAAGTCGAAAACTTGACACGTTGAGCTCGTCCGTGGGG--CGGCA----TTC---------------AA--G
droMoj3	scaffold_6473:13724290-13724417 +	TCCTTATCCATAC-------CATATCC--ACATTTGGCTGTCCTACGAGCGAGTTCCACTAATCAAGTTTTGAGT--GT-TCGAAAATCAAAAACTTGACACGTTGAGCTCGTCTGTGTGG--CA--C----AAGTTC-----AA--CAAAAGCA
droGri2	scaffold_15203:8445730-8445869 +	TTCGGT-TTGTTCTTTTACAGCAGTGCATCCGGGTGTCTGCCACACTTACGAGTTCCACTATTCAAGTTTTGAGC--GTATTTGAAATCAAAAACTTGACACGTTGAGCTCGTGTGTGCGTTGCGG------AAA-TCAACTTA---CTCAA--A

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTCGGGGAATCC--CCAAGTCTCTGTCCTACGTCCGAGTTCCACTAAGCAAGTTTTGAGATCGTTT-TAAAAACAAAAACTTGACACGTTGAGCTCGTTCGTGGGATGGACTACTGCAATTCAAAAT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.............................................................................AACTTGACACGTTGAGCTCGT.............................	21	1	4.00	4	4
...................................GAGTTCCACTAAGCAAGTTTT.......................................................................	21	1	1.00	1	1
.............................................................................AACTTGACACGTTGAGCTCGTT............................	22	1	1.00	1	1

dp4

TTCCTGGAAGCCATCTAGGAGCCTGTTCTACGTGCGAGTTCCACCATGCAAGTTTTGAG--CGTATATGAATCCAAAAACTTGACACGTTGAGCTCGTGCGTGG-----------------------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.............................................................................AACTTGACACGTTGAGCTCGT.............................	21	1	57.00	57	2	55
...................................GAGTTCCACCATGCAAGTTTT.......................................................................	21	1	20.00	20	0	20
............................................................................AAACTTGACACGTTGAGCTC...............................	20	1	10.00	10	0	10
............................................................................AAACTTGACACGTTGAGCTCG..............................	21	1	7.00	7	0	7
.............................................................................AACTTGACACGTTGAGCTCG..............................	20	1	5.00	5	1	4
............................................................................AAACTTGACACGTTGAGCTCGT.............................	22	1	4.00	4	1	3
.............................................................................AACTTGACACGTTGAGCTCGTG............................	22	1	2.00	2	1	1
............................................................................AAACTTGACACGTTGAGCT................................	19	1	1.00	1	0	1
...........................................................................AAAACTTGACACGTTGAGCTCGT.............................	23	1	1.00	1	0	1
.............................................................................AACTTGACACGTTGAGCTC...............................	19	1	1.00	1	0	1
...................................GAGTTCCACCATGCAAGTTT........................................................................	20	1	1.00	1	0	1

Secondary Structure

dm3

-35.4	-35.3	-35.2

droSim1

-35.4	-35.3	-35.2

droSec1

-35.4	-35.3	-35.2

droYak2

-30.9	-30.2

droEre2

-35.1

droAna3

-33.8

dp4

-28.9	-28.7	-28.2	-28.0	-27.9

droPer1

-36.1	-36.0	-36.0	-35.9	-35.8	-35.8

droWil1

-28.0	-27.5	-27.5	-27.5	-27.5

droVir3

-43.8

droMoj3

-29.0	-28.6	-28.6	-28.6	-28.6	-28.6

droGri2

-31.4	-31.4	-31.4	-31.4	-31.4	-30.7

Generated: 01/05/2013 at 05:33 PM