Secondary structure and small RNA-seq evidence for dme-mir-990

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:12782713-12782828 -	TGGGAAAC-----------TGGCGA----ATCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGCTTCGGTGCC-ATTT-----------------------------------------CACCC------------CGAGCACCAAGAGCATCAGACT
droSim1	chr2R:11518341-11518456 -	TGGGAAAC-----------TGGCGA----ATCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGCTTCGGTGCC-ATTT-----------------------------------------CACCC------------CGAGCACCAAGAGCATCAGACT
droSec1	super_1:10286785-10286900 -	TGGGAAAC-----------TGGCGA----ATCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGCTTCGGTGCC-ATTT-----------------------------------------CACCC------------CGAGCACCAAGAGTATCAGACT
droYak2	chr2R:16191830-16191945 +	TGGGAAAC-----------TGGCGA----ATCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGTTTCGGTGCC-ATTT-----------------------------------------CACCC------------CGAACAGCAAGACCATCAGACT
droEre2	scaffold_4845:13064860-13064974 +	TGGGTAAC-----------TGGCGA----GTCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGTTTCGGTGCC-ATTT-----------------------------------------CACCC------------CCAGCACCAAGAGCACC-GACT
droAna3	scaffold_13266:13815719-13815830 +	TGGGAAAT-----------TGTCGA----AGCCA------------CTTTGC-GACATTCCCCGTTCTGCGTTGGCCCAAGGTGCACGTGGGGCCGACGA----------CTCTCCGCTTCCGGACCCATTG--------------------------------------------------------------CCGAAAATACATTCTTCA
dp4	chr3:6727705-6727891 -	TGGGAAAC-----------TGGCGA----GGCG-AGGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGGTTAC--GCCTGAAGCTCCAATTCGGTTACGGT------TTCGGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGACA
droPer1	super_2:6950668-6950854 -	TGGGAAAC-----------TGGCGA----GGCG-AGGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGGTTAC--GCCTGAAGCTCCAATTCGGTTACGGT------TTCGGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGACA
droWil1	scaffold_180700:6478759-6478837 -	TGGGAAATACATCTTCGTTTGGCTTTAGTTTCTC------------TTCTGCGGACATTCAATGTTCTGCGTTTGCCCCAAGCGCACGTGG-------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12875:2573949-2574010 +	TGGGAAAC-----------TG-CGA----AGCTG------------CTTTGC-GACATTCGACTTGCTGCGTTCGTCGCCGACGCACGTGG-------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:22657688-22657749 -	TGGGAAAC------------GGCGA----AGCTT------------CTGTGC-GACATTCAACGTTCTGCGTTCGTCGCCGACGCACGTGG-------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15112:4702153-4702224 +	TGGGAATT-----------TTGCGA----AGCTGCTGCTGTGGCT--GCTGC-GACATTCAACGTTCTGCGTTGGCCGCCGACGCACGTG--------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:12782713-12782828 -	TGGGAAACTGGCGAATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGCTTCGGTGCCATTTCACCCCGAGCACCAAGAGCATCAGACT
droSim1	chr2R:11518341-11518456 -	TGGGAAACTGGCGAATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGCTTCGGTGCCATTTCACCCCGAGCACCAAGAGCATCAGACT
droSec1	super_1:10286785-10286900 -	TGGGAAACTGGCGAATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGCTTCGGTGCCATTTCACCCCGAGCACCAAGAGTATCAGACT
droYak2	chr2R:16191830-16191945 +	TGGGAAACTGGCGAATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGTTTCGGTGCCATTTCACCCCGAACAGCAAGACCATCAGACT
droEre2	scaffold_4845:13064860-13064974 +	TGGGTAACTGGCGAGTCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGTTTCGGTGCCATTTCACCCCCAGCACCAAGAGCACC-GACT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGGGAAACTGGCGA-----------ATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCA------------------------GCTTTCAGCTTCGG------------------------------TG------CCATTTCACCCCGAGCACCAAGAGCATCAGACT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................................ATTCACCGTTCTGAGTTGGCCC..............................................................................................................................	22	1	12.00	12	12

dp4

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

Secondary Structure

dm3

-29.0	-28.9	-28.7	-28.7	-28.6	-28.5

droSim1

-29.0	-28.9	-28.7	-28.7	-28.6	-28.5

droSec1

-29.0	-28.9	-28.7	-28.7	-28.6	-28.5

droYak2

-25.4	-25.1	-25.0	-24.7	-24.6	-24.6

droEre2

-26.1	-26.0	-25.9	-25.8	-25.8	-25.7

droAna3

-21.0	-20.8	-20.1	-20.1	-20.1	-20.0

dp4

-46.7	-46.4	-46.4	-46.1	-46.1	-46.1

droPer1

-46.7	-46.4	-46.4	-46.1	-46.1	-46.1

droWil1

-11.5	-11.5	-10.7	-10.7

droVir3

-12.2	-11.5	-11.5	-11.2

droMoj3

-11.4	-10.7	-10.4

droGri2

-18.1	-18.1	-18.0	-18.0	-17.6	-17.5

Generated: 01/05/2013 at 05:36 PM