Secondary structure and small RNA-seq evidence for dme-mir-3641

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:2065104-2065202 +	GGCGAACTTTTTAATGTGAGTGTCCTGTTT------------ACAGCTGGTATATTTT---------TCGAAA---AGCC----------CTCTAAAC---------TGG------------T---CACTTCCAC-TCTACAGATCTATAACTACATA
droSim1	chrX:1441441-1441539 +	GGCGAACTGTTCAATGTGAGTTTCCTACTT------------ACAGCTGGTATATTTC---------TCGAAC---AGTC----------CTCTAAAC---------TGG------------T---CCCTTCCGC-TCCGCAGATCTACAACTACATA
droSec1	super_10:1848730-1848828 +	GGCGAACTGTTCAATGTGAGTTTCCTACTT------------ACAGCTGGTATATTTC---------GCGAAC---AGTC----------CTCTAAAC---------TGG------------T---CCCTTCCGC-TCCGCAGATCTACAACTACATA
droYak2	chrX:6259202-6259289 -	GGCGAACTCTTCAATGTGAGTTTCCTATGT------------TTCGCATGTACATAT---------------------------------ATCTAAAT---------TGG------------T---TCCTTCTCC-TCTGCAGATCTACAACTACATA
droEre2	scaffold_4644:2028284-2028382 +	GGCGAACTGTTCAATGTGAGTATCCTGTGA------------TCCGCTTGTACTTATC---------TCGAGC---AGTT----------CTCTAAAC---------TGG------------T---CCCTGATCC-TCTGCAGATCTACAACTACATA
droAna3	scaffold_13117:1070684-1070773 -	GGCGAGCTCTTCAACGTAAGTTTCCCCGCT------------TAAAC------------GCCTAAGA-----T----TTT----------CCCTAAAC---------CGT------------T---GCTGTTCTG-TCTCTAGATCTACAACTATATC
dp4	chrXL_group1e:3790116-3790235 -	GGCGAGTTGTTCAACGTAAGTTCCAGCATT------------TCAGCCT---------CGAATTCGG-----C---AGTCACTTGATAC---------TCTCCCACCTCCCTCTCCCTCTGCCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droPer1	super_17:723995-724114 -	GGCGAGTTGTTCAACGTAAGTTCCAGCATT------------TCAGCCT---------CGAATTCGG-----C---AGTCACTTAATAC---------TCTCCCACCTCCCTCTCCCTCTGCCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droWil1	scaffold_181096:7421152-7421244 -	GGCGAGCTTTTCAACGTGAGTTACTCAGTC------------CA----A---------AGAAACTGG-----TTTTAGTTA--TGAT-----------TAACTC-----A------------C----TTTTTTTT-GTTATAGATTTACAACTATATA
droVir3	scaffold_12928:7113520-7113613 +	GGCGAGTTGTTCAACGTAAGTCGATGACCTCGCG--------T------------------ATGTGGGCGTAC---TTTC----------A------CTGACGC---CTG------------C---CTCTTTGTC-TATTCAGATTTACAACTACATT
droMoj3	scaffold_6328:2787435-2787524 +	GGGGAGTTGTTCAACGTAAATTCT--ATTC------------TCACTTAACACA----AGAATCAAA-----T----CTC---------------ATC---------TAA------------T---T-TTTCGCT-CGTTTAGATTTACAACTACATT
droGri2	scaffold_14853:3491672-3491772 -	GGAGAGTTGTTTAATGTAAGCTAA--ACTTCGCCCATCCTCTCCAGCTG-----------------------------TT---TGGTTAACTTTCAAC---------TGT------------TTGTC-CTCCATC-TCCTCAGATTTACAACTACATT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:2065104-2065202 +	GGCGAACTTTTTAATGTGAGTGTCCTGTTT------------ACAGCTGGTATATTTT---------TCGAAA---AGCC----------CTCTAAAC---------TGG------------T---CACTTCCAC-TCTACAGATCTATAACTACATA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GGCGAACTGTTCAATGTGAGTTTCCTACTTACAGCTGGTATATTTCTCGAA-----CAGTC-CTCTAAACTGGTC------CCTTCCGCT-------------------CCGCAGATCTACAACTACATA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

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

Secondary Structure

dm3

-13.6	-13.6	-12.9	-12.9	-12.7	-12.7

droSim1

-10.1	-9.6	-9.2

droSec1

-10.1	-9.6	-9.4	-9.2	-9.2

droYak2

-2.6	-2.5	-2.4	-2.0	-1.6

droEre2

-12.8	-12.5

droAna3

-2.5	-2.3	-2.1	-2.0	-2.0	-1.8

dp4

-7.97	-7.8	-7.37	-7.2

droPer1

-7.97	-7.37

droWil1

-11.6	-11.2	-10.6

droVir3

-12.5	-12.2

droMoj3

-0.6	-0.5	-0.4	0.0	0.1	0.2

droGri2

-6.5	-6.0	-5.9	-5.9	-5.6	-5.5

Generated: 01/05/2013 at 05:18 PM