Secondary structure and small RNA-seq evidence for dme-mir-2282

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:3412130-3412266 -	TGGGGCAGTGGAGCT-----G-----------------------------------------------------CCTGCAT---AACGC---------TGTGGCTTTCCGCTTCTATTTTTCGTTCACTGCCTTGTGC----TTCGTT--------------------------------------------------------------------------GGAAAATCGGTGAGCTAAAAATAGAATTCGGTTGCCACGCTTCAAGGGAAATGAGGAAAATTA
droSim1	zdo07f06.g1:327-468 +	TGGGGCAGTGGAGCT-----G-----------------------------------------------------CCTGCAT---AAGGC---------TGTGGCTTTCCGCTTCTATTTTTCGTTCACTGCCTTGTGCTTGCTTCGTT--------------------------------------------------------------------------GGAAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCAAGGGAAATGAGGAAAATTA
droSec1	super_2:3404661-3404801 -	TGGGGCAGTGGAGCT-----G-----------------------------------------------------CCTGCAT---AAGGC---------TGTGGCTTTCCGCTTCTATTTTTCGTTCACTGCCTTGTGCTTGCTTCGTT--------------------------------------------------------------------------GGAAAAGCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCAAGGGAAATGAGGAAAATTA
droYak2	chr3L:3959855-3959989 -	TGGGGCAGTGGGGCT-----G-----------------------------------------------------CAT--AT---AAGGC---------TGTGGCTTTCCGCTTCTATTTTGTGCTCACTGTCTTGTGC----GGCGTT--------------------------------------------------------------------------GGAAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGTGGAAAATGAGGAAAATTA
droEre2	scaffold_4784:6102142-6102274 -	TGGGGCAGTGGAGCT-----G---------------------------------------------------------CAT---AAGGC---------TGTGGCTTTCCGCTTCTATTTTGTGTTCACTGTCCTGCGT----TTCGTT--------------------------------------------------------------------------GGAAAATCGGTGAGCCAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAATGCGGAAAATTA
droAna3	scaffold_13337:10031066-10031241 +	TGGGGGCAGGTGGTG-----GCAGGAGGTGGCCGGAGGTGGTGGTAGGTGGGTGGGGGTGGTGTATGTAGGGGGCCTGTA------------------TGTGGCTTTCCGCTTCTACC--------ATTTTTTTTTGT-------------------------------------------------------TG----------------GAGGGTTCAGTGGAAATTCGGCGAGCTAAAAATATAATTCGGTTGCCACGCTTC---GGAAA----GAGAATTA
dp4	chrXR_group8:5510827-5511013 -	TGTGTGTGTGTGTCT-----GT-----------------------GTGTGTGTGTGTGT-GTGTGTGTGT----GTGGCAGGGTGACAGCACTCTCTCTAAGGCTTTCCGCTTTTCGT------TCTCTTTT---TGT-TG-T-TGTTGTTCTTTCTTTCGTTTTGGTGGAAATTTTC----------GTTGTATCTAAAAATAGACTTTTTGGGGTTCAAAGGAAATTT-------------------------------------------TGTGGGACAAAA
droPer1	super_7263:1394-1409 +	TACGGGTGTGAGACT-----G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180955:1135974-1136099 -	TATGGCGATATTTTGTAGGTT-----------------------------------------------------TTGGC-A---ATGGT---------TGTGGCTTTCCGCTTCTATTCAGT----------------------CGCA------------------CGAAAAATTTTCTCGGTTTTTTCCCAT-----------------------------------------GTCTAAAAATAGATTT------ACACCC---AAAGTA---GAAAAACATAA
droVir3	scaffold_13049:19660195-19660299 +	G------------------------------------------------------------------------------------------------------TTCTGCGCTAGCTTGTTCGGTTTGGTAACATGAGC----TTCATT--------------------------------------------------------------------------AGTGTATGCAATAATGGCAAACATTTTTTGCCTGCCAGGCCTCGGCGAGGACGATGACGACGA
droMoj3	scaffold_6496:15371578-15371721 +	TGCAACATTGATGAA-----A-----------------------------------------------------TATGCATAATGAAAATGTGCCCTCA-GAGTTATCCACG------------------------------------------------------------ATTTTTCTACTTTTTTTTTATACCCTGAAC---------CCATTTTCAATGGGAAATCAGGGTATA------ATGGTTTTGTTGAAATGTATG---TAACA----GGGAGAAG
droGri2	scaffold_15203:7704730-7704834 +	CAGAATAATAGAATG-----T-----------------------------------------------------ACTCACT---TCAGC---------TATGGCATACAGATTTGCTTTATT-TGCTTTTCGTTGTAC-------------------------------------------------------------------------------------------------------------TTTCTGTTTTCTCAATGTACATGAAAAAGACTGAATTT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:3412130-3412266 -	TGGGGCAGTGGAGCTGCCTGCATAACGCTGTGGCTTTCCGCTTCTATTTTTCGTTCACTGCCTTGTGC----TTCGTTGGAAAATCGGTGAGCTAAAAATAGAATTCGGTTGCCACGCTTCAAGGGAAATGAGGAAAATTA
droSim1	zdo07f06.g1:327-468 +	TGGGGCAGTGGAGCTGCCTGCATAAGGCTGTGGCTTTCCGCTTCTATTTTTCGTTCACTGCCTTGTGCTTGCTTCGTTGGAAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCAAGGGAAATGAGGAAAATTA
droSec1	super_2:3404661-3404801 -	TGGGGCAGTGGAGCTGCCTGCATAAGGCTGTGGCTTTCCGCTTCTATTTTTCGTTCACTGCCTTGTGCTTGCTTCGTTGGAAAAGCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCAAGGGAAATGAGGAAAATTA
droYak2	chr3L:3959855-3959989 -	TGGGGCAGTGGGGCTGCAT--ATAAGGCTGTGGCTTTCCGCTTCTATTTTGTGCTCACTGTCTTGTGC----GGCGTTGGAAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGTGGAAAATGAGGAAAATTA
droEre2	scaffold_4784:6102142-6102274 -	TGGGGCAGTGGAGCTG----CATAAGGCTGTGGCTTTCCGCTTCTATTTTGTGTTCACTGTCCTGCGT----TTCGTTGGAAAATCGGTGAGCCAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAATGCGGAAAATTA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGGGGCAGTGGAGCTGCC------------------------------------TGCA-TAAGGCTGTGGCTTTCCGCTTCTATTTTTCGTTCACTGCC--------TTGTGCTTG------CTTCGTTGGAAAA--TCGGTG-AGCTAAAAATAGATTTCGGTTGCCACGCTTCAAGGGAAAT---GAGGAAAATTA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

TGTGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGCAGGGTGACAGCACTCTCTCTAAGGCTTTCCGCTTT------TCGTTCTCTTTTTGTTGTTGTTGTTCTTTCTTTCGTTTTGGTGGAAATTTTCGTTGTATCTAAAAATAGACTTT-----TTGGGGTTCAAAGGAAATTTTGTGGGACAAAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................TGTGTGTGTGTGTGTGTGTGTGTG..............................................................................................................................................................	24	5	4.20	21	0	21
...................GTGTGTGTGTGTGTGTGTGTGTGTG..........................................................................................................................................................	25	3	2.33	7	0	7
.......................GTGTGTGTGTGTGTGTGTGTGGC........................................................................................................................................................	23	1	2.00	2	0	2
.....................GTGTGTGTGTGTGTGTGTGTGTGG.........................................................................................................................................................	24	1	2.00	2	0	2
................TGTGTGTGTGTGTGTGTGTGTGTGTG............................................................................................................................................................	26	3	1.67	5	0	5
..............TGTGTGTGTGTGTGTGTGTGTGTGT...............................................................................................................................................................	25	4	1.25	5	0	5
..................TGTGTGTGTGTGTGTGTGTGTGTGTGG.........................................................................................................................................................	27	1	1.00	1	0	1
........................TGTGTGTGTGTGTGTGTGTGGC........................................................................................................................................................	22	1	1.00	1	0	1
...................GTGTGTGTGTGTGTGTGTGTGTGTGG.........................................................................................................................................................	26	1	1.00	1	0	1
.........................GTGTGTGTGTGTGTGTGTGG.........................................................................................................................................................	20	1	1.00	1	0	1
.............CTGTGTGTGTGTGTGTGTGTGTGTG................................................................................................................................................................	25	1	1.00	1	0	1
................TGTGTGTGTGTGTGTGTGTGTG................................................................................................................................................................	22	9	0.44	4	0	4
.......................GTGTGTGTGTGTGTGTGTG............................................................................................................................................................	19	14	0.07	1	0	1

Secondary Structure

dm3

-34.9	-34.8	-34.6	-34.5	-34.5	-34.3

droSim1

-36.1	-35.9	-35.7	-35.4	-35.4	-35.4

droSec1

-39.7	-39.5	-39.4	-39.4	-39.2	-39.1

droYak2

-37.7	-37.7	-37.6	-37.6	-37.5	-37.4

droEre2

-38.2	-37.6	-37.6	-37.6	-37.6	-37.6

droAna3

-46.3	-46.2	-45.6	-45.5	-45.5	-45.5

dp4

-22.9	-22.9	-22.5	-22.5	-22.5	-22.5

droPer1

0.0

droWil1

-14.2	-14.2	-13.9	-13.6	-13.6	-13.5

droVir3

-22.1	-21.9	-21.8	-21.8	-21.6	-21.6

droMoj3

-28.8	-28.7	-28.6	-28.5	-28.4	-28.3

droGri2

-8.2	-8.1	-8.1	-8.0	-7.9	-7.8

Generated: 01/05/2013 at 05:10 PM