Secondary structure and small RNA-seq evidence for dme-mir-978-as

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:19455254-19455375 -	CCTTCG----CT-----------------GCTGCCGTTTGCG--TTCACACAACTGCAATTTACGGCACTGGACACGATTTTCGA-TTG----C-AACGTAAGCCAGTGGCGTAGATTGCAGATTG------TGCCGCCAACCAAGAT---ATTGTACTT
droSim1	chrX_random:5079001-5079113 -	CCTTCG----CT-----------------GCTGCCGTTTGCG--TCCACACAACTGCAATATACGGCACTGGACACGATTCTCGA-CCA----C-AACGTAAGCCAGTGGCGTAGATTGCAGATTG------TGCCGCCAATC------------TACTT
droSec1	super_8:1737859-1737971 -	CCTTCG----CT-----------------GCTGCCGTTTGCG--TCCACACAACTGCAATTTACGGGACTGGACACGATTCTCGA-CTA----C-AACGTAAGCCAGTGGCGTAGATTGCAGATTG------TGCCGCCAATC------------TACTT
droYak2	chrX:11883747-11883862 +	TCTCCG----C--------------------TGCCCTTTGCG--TCCACACAACTGCAATCAACGGCACTGGACACGATTTCCGA-GTA----C-AACGTAAGCCAGCGGCGTAGAGTGCTGGCTG------TGCCGCCCACCT------GGATGCACTT
droEre2	scaffold_4690:9691187-9691301 -	CCTCCG----C--------------------TGCCCTTTGCG--TCCACACAATTGCAATCAACGGCACTGGACACGATTTTCGA-GTA----C-AACGTAAGCCAGCGGCGTAGAATGCTGGTTG------TGCCGCCCACT-------GGATGCACTT
droAna3	scaffold_13417:2460507-2460635 +	CAACTATCGGTC-----------------GCTGTAATTCGCG--TCTACACAACTGCAATCAACGTCACTGGACACGGATATCAA-CCA----C-CACGTAAGCCAGCAGCGTCGAATGCTGTCTG------TGCCGCCGAGCTTGCCCTGTCCGCACTC
dp4	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	super_14:1991206-1991216 +	TAGTTG----TT-----------------GTT--------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7961115-7961220 -	AAATCG----CC-----------------GCTAATCATTG------TACACAACTGCAATCAACGTCACTGGACACGGATATCGT-TTGTTTTT-AACGTAAGCCAGCGTCGTCGAATGCTGCCTG------TGTTGCCAA-------------------
droVir3	scaffold_13042:902659-902773 +	TTCTTG----TTTGAATCAAT------ACGTTGAGATATGCA--TCAGGACAGCTCTACTCAACGGCAATGGAACCGAGTGC----GTCAAAGAGCTCGT-TCCCAAAAGCGTAGAGTACGGC-TGTGCCTG---------------------------T
droMoj3	scaffold_6328:2897048-2897148 +	GTTGTG----AT-----------------G--------TGCAAACGGGGGCAGCTCTACTCAACGGCTATGGAACCGAGTGGCTTTGTATGATTGCTCGT-TCCCAAAAGCGTAGAGTACGGC-TGTACCCG----------------------------
droGri2	scaffold_15081:2040911-2041055 +	TTATTG----ATTGATTCGATTCAGTTACGTTGCGATTTGCA--TTGGGACAGCTTTACTCAGCGGCATTGAAACTAGGAGA----ATCATGTTCCTTAC-TTCCAAAAGCGCTGAATACGGC-TGGACCTGTGTTGGTTATCGAACT---GCCGTACTT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:19455254-19455375 -	CCTTCG------------------CTGCTGCCGTTTGCG--TTCACACAACTGCAATTTACGGCACTGGACACGATTTTCGA-TTG----C-AACGTAAGCCAGTGGCGTAGATTGCAGATTG------TGCCGCCAACCAAGAT---ATTGTACTT
droSim1	chrX_random:5079001-5079113 -	CCTTCG------------------CTGCTGCCGTTTGCG--TCCACACAACTGCAATATACGGCACTGGACACGATTCTCGA-CCA----C-AACGTAAGCCAGTGGCGTAGATTGCAGATTG------TGCCGCCAATC------------TACTT
droSec1	super_8:1737859-1737971 -	CCTTCG------------------CTGCTGCCGTTTGCG--TCCACACAACTGCAATTTACGGGACTGGACACGATTCTCGA-CTA----C-AACGTAAGCCAGTGGCGTAGATTGCAGATTG------TGCCGCCAATC------------TACTT
droYak2	chrX:11883747-11883862 +	TCTCC---------------------GCTGCCCTTTGCG--TCCACACAACTGCAATCAACGGCACTGGACACGATTTCCGA-GTA----C-AACGTAAGCCAGCGGCGTAGAGTGCTGGCTG------TGCCGCCCACCT------GGATGCACTT
droEre2	scaffold_4690:9691187-9691301 -	CCTCC---------------------GCTGCCCTTTGCG--TCCACACAATTGCAATCAACGGCACTGGACACGATTTTCGA-GTA----C-AACGTAAGCCAGCGGCGTAGAATGCTGGTTG------TGCCGCCCACT-------GGATGCACTT
droAna3	scaffold_13417:2460507-2460635 +	CAACTAT-CGG-------------TCGCTGTAATTCGCG--TCTACACAACTGCAATCAACGTCACTGGACACGGATATCAA-CCA----C-CACGTAAGCCAGCAGCGTCGAATGCTGTCTG------TGCCGCCGAGCTTGCCCTGTCCGCACTC
droWil1	scaffold_181096:7961115-7961220 -	AAATCG------------------CCGCTAATCATTG------TACACAACTGCAATCAACGTCACTGGACACGGATATCGT-TTGTTTTT-AACGTAAGCCAGCGTCGTCGAATGCTGCCTG------TGTTGCCAA-------------------
droVir3	scaffold_13042:902659-902773 +	TTCTTGTTTGAATCAAT------A-CGTTGAGATATGCA--TCAGGACAGCTCTACTCAACGGCAATGGAACCGAGTGC----GTCAAAGAGCTCGT-TCCCAAAAGCGTAGAGTACGGC-TGTGCCTG---------------------------T
droMoj3	scaffold_6328:2897048-2897148 +	GTTGTG------------------AT--------GTGCAAACGGGGGCAGCTCTACTCAACGGCTATGGAACCGAGTGGCTTTGTATGATTGCTCGT-TCCCAAAAGCGTAGAGTACGGC-TGTACCCG----------------------------
droGri2	scaffold_15081:2040911-2041055 +	TTATTGATTGATTCGATTCAGTTA-CGTTGCGATTTGCA--TTGGGACAGCTTTACTCAGCGGCATTGAAACTAGGAGA----ATCATGTTCCTTAC-TTCCAAAAGCGCTGAATACGGC-TGGACCTGTGTTGGTTATCGAACT---GCCGTACTT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CCTTCGCTGCTGCCGTTTGCGTCCACACAACTGCAATATACGGCACTGGACACGATTCTCGACCACAACGTAAGCCAGTGGCGTAGATTGCAGATTGTGCCGCCAATC---------TACTT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
......................................................................TAAGCCAGTGGCGTAGATTGCA..............................	22	2	1.00	2	2

dp4

--------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-37.8	-37.0

droSim1

-34.0	-33.5	-33.2

droSec1

-31.9	-31.1

droYak2

-25.8	-25.6	-25.5	-25.4	-25.3	-25.3

droEre2

-24.0	-23.8	-23.4	-23.1	-23.1	-23.0

droAna3

-23.4	-23.3	-22.9	-22.9	-22.8	-22.8

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

-18.7	-18.7	-18.3	-18.0	-18.0	-17.9

droVir3

-34.1	-34.1

droMoj3

-36.2	-36.2	-36.2	-36.2	-36.2	-36.2

droGri2

-31.9	-31.5	-31.2	-31.2	-31.2	-31.1

Generated: 01/05/2013 at 05:34 PM