Secondary structure and small RNA-seq evidence for dme-mir-992

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:16472804-16472925 -	ACAAAT--------CT-----AGACATGATTTTCCCAAGTGCCTGGTATCAGCAAAGTGT-----TATTTTTTATGTTT-------------------------------------------------ATGTAAAGTACACGTTTCTGGTACTAAGTACTTCGAGAAAGTT---------------ACCTGCGTAGGATATCAA
droSim1	chr2R:15134498-15134613 -	AGGAAT--------CT-----AGACATGATTTTCGCAAGTGCCTGGTTTCAGAGAGGTGT-----AATTTTT---G----------------------------------------------------TTGTATAGTACCCTTTTTTGGAACCAAGCCCTTTGAGAAACTT---------------ACCTGCGGGGTATATCAA
droSec1	super_1:14027523-14027641 -	AGGAAT--------CT-----AGACATGATTTTCGGAAGTGCCTGGTATCAGATAGGTGT-----AATTTTT---GTGT-------------------------------------------------TTGTATAGTACACGTTTCTGGAACCAAGCCCTTTGAGAAACTT---------------ACCTGCGGGGTATATCAA
droYak2	chr2R:12723658-12723777 +	AGGACT--------CT--T--GGATCTGATTTTCCCAAGTGCTTAGTATCAGCAAGGTGT-----AATTTTT---GTTT-------------------------------------------------GGTTAAAGTACACGTTACTGGTACTACGTACTTCGAGAAACCT---------------AACTACGGAGGATACAAA
droEre2	scaffold_4845:10619147-10619257 -	AGAAC--------------------CTGATTTTCCCAAGTGCATAGTATCAGCAAGGTGT-----AATTTTT---ATTT-------------------------------------------------GGGTAAAGTACACGTTACTGGTACTAGGTACTTTGAGAAACAT---------------GACTACGGAGAATACCA-
droAna3	scaffold_13266:4131420-4131545 +	TAAAAT--------TCATTGTAAACCATACTTTTTAAG--GAGCAGTATCCACAATTTAA---------------GTTT-------------------------------------------------TTTCGTGGT----ATTTGCGGCATTGCCAACTTTAAGAAAAGTTCAAAGGGCGCTGTTACAAGCTATTACTATTAC
dp4	chr3:8679002-8679138 +	GTCGTT--------CT-----CCATCTCTTTCTCGCGTC-GCGTCGCTTAAACTATGTATGTATGCATTTTGTACATACGGTTAAATTCAAATGTA-------------ATCGGTTCCCAAACGCTCGTTTCATGTTTTCATTTTCTCGAATTTTCACG----------------------------------------TTTAG
droPer1	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:3840730-3840836 +	GCATT---------AT-----AGAAAACA--------AACGATTGTT----------------------------------------TACTGGCCATTTTGCTAATCTTTT-----------------TGGTAATCTAATC-TTTACGGTATCAAAATTAGTTAGAAAA-T---------------ACTTAATAATTATATTA-
droVir3	scaffold_13042:3503607-3503688 -	ATAAAAGGCAATTCCT--T--AGAATT--TTTCTTCAATTAATTAATTCT--------GT-----TATGTTTTATATT-------------------------------------------------------------TAATTTCCAATAATAAGTTCTTC------------------------------------------
droMoj3	scaffold_6680:4944926-4945004 -	GTTTAT--------AT---------ATG-------AAAATATTTGATATATGCAA------------TTTAT--------------ACAAAGAACTTTTTGCTA-------------------------------------------------------TTCTAAAAAATA---------------AA------CGAACATCCA
droGri2	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:16472804-16472925 -	ACAAATCT-AGACATGATTTTCCCAAGTGCCTGGTATCAGCAAAGTGTTATTTTTTATGTTTATGTAAAGTACACGTTTCTGGTACTAAGTACTTCGAGAAAGTTACCTGCGTAGGATATCAA
droSim1	chr2R:15134498-15134613 -	AGGAATCT-AGACATGATTTTCGCAAGTGCCTGGTTTCAGAGAGGTGTAATTTTT---GTT---GTATAGTACCCTTTTTTGGAACCAAGCCCTTTGAGAAACTTACCTGCGGGGTATATCAA
droSec1	super_1:14027523-14027641 -	AGGAATCT-AGACATGATTTTCGGAAGTGCCTGGTATCAGATAGGTGTAATTTTT---GTGTTTGTATAGTACACGTTTCTGGAACCAAGCCCTTTGAGAAACTTACCTGCGGGGTATATCAA
droYak2	chr2R:12723658-12723777 +	AGGACTCTTGGATCTGATTTTCCCAAGTGCTTAGTATCAGCAAGGTGTAATTTTT---GTTTGGTTAAAGTACACGTTACTGGTACTACGTACTTCGAGAAACCTAACTACGGAGGATACAAA
droEre2	scaffold_4845:10619147-10619257 -	AGA--------ACCTGATTTTCCCAAGTGCATAGTATCAGCAAGGTGTAATTTTT---ATTTGGGTAAAGTACACGTTACTGGTACTAGGTACTTTGAGAAACATGACTACGGAGAATACCA-

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AGGAATCTAGACATGATTTTCGCAAGTGCCTGGTTTCAGAGAGGTGT-----------------------------------------------AATTTTTGT------TGTATAGTACCCTTTTTTGGAACCAAGCCCTTTGAGAAACTTACCTGCGGGGTATATCAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
......................................................................................................................CCCTTTTTTGGAACCAAGCCCT.............................	22	1	3.00	3	3
...........................GCCTGGTTTCAGAGAGGTGT-----------------------------------------------A..........................................................................	21	1	2.00	2	2
...........................GCCTGGTTTCAGAGAGGTGT-----------------------------------------------...........................................................................	20	1	1.00	1	1
......................................................................................................................CCCTTTTTTGGAACCAAGCCC..............................	21	1	1.00	1	1

dp4

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

Secondary Structure

dm3

dG=-20.5, p-value=0.009901	dG=-20.5, p-value=0.009901	dG=-20.5, p-value=0.009901	dG=-20.5, p-value=0.009901	dG=-20.3, p-value=0.009901

droSim1

dG=-19.4, p-value=0.009901	dG=-18.6, p-value=0.009901	dG=-18.6, p-value=0.009901	dG=-18.5, p-value=0.009901	dG=-18.4, p-value=0.009901

droSec1

dG=-17.6, p-value=0.009901	dG=-17.0, p-value=0.009901	dG=-16.9, p-value=0.009901

droYak2

dG=-23.2, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.3, p-value=0.009901

droEre2

dG=-23.9, p-value=0.009901	dG=-23.4, p-value=0.009901

droAna3

dG=-10.5, p-value=0.009901	dG=-9.8, p-value=0.009901	dG=-8.1, p-value=0.009901

dp4

dG=-10.7, p-value=0.009901	dG=-10.7, p-value=0.009901	dG=-10.7, p-value=0.009901	dG=-10.7, p-value=0.009901	dG=-10.6, p-value=0.009901	dG=-8.9, p-value=0.009901

droPer1

No secondary structure predictions returned

droWil1

dG=-7.0, p-value=0.009901	dG=-6.8, p-value=0.009901	dG=-6.6, p-value=0.009901	dG=-6.4, p-value=0.009901

droVir3

dG=-0.3, p-value=0.009901	dG=-0.2, p-value=0.009901	dG=0.0, p-value=0.009901	dG=0.2, p-value=0.009901	dG=0.3, p-value=0.009901

droMoj3

dG=-1.8, p-value=0.009901	dG=-1.5, p-value=0.009901	dG=-1.2, p-value=0.009901	dG=-0.9, p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 07:28 PM