Secondary structure and small RNA-seq evidence for dme-mir-308

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12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:10103292-10103384 -	AACACG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAATCCAAATCACAGGATTATACTGTGAGATGACCAGCGTG---CCA
droSim1	chr2R:8866656-8866748 -	CACACG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCGTG---CCA
droSec1	super_1:7611688-7611779 -	CA--CG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCGTG---CCA
droYak2	chr2R:10041132-10041224 -	CACACG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCCTTTTGCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCGTG---CCA
droEre2	scaffold_4845:15739235-15739330 +	CACACG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAAATCAAATCACAGGATTATACTGTGAGATGACCAGCGTGCCGCCA
droAna3	scaffold_13266:5819955-5820045 +	CA--TG--TCTCGTCGCCTCGCAGTATATTTTTGTGTTTTGTTTGG-TTTGAAACTCAAATCACAGGATTATACTGTGAGATGCCAAGCGTG---TCA
dp4	chr3:16336992-16337078 -	--------TCTTGACGCCTCGCAGTATATTTTTGTGTTTTGTTGTG-TCTGAAACGCAAATCACAGGATTATACTGTGAGATGCTGGGCGTG---CTA
droPer1	super_4:426256-426345 +	G---CG--TCTTGACGCCTCGCAGTATATTTTTGTGTTTTGTTGTG-TCTGAAACGCAAATCACAGGATTATACTGTGAGATGCTGGGCGTG---CTA
droWil1	scaffold_180700:1860929-1861010 +	AGACTA--TTCTTGCGTCTCGCAGTATATTTTTGTGTTTTGTTCAATTTGTCAACTCAAATCACAGGATTATACTGTGAGCTGC--------------
droVir3	scaffold_12875:17605293-17605383 +	AACGCA--T-TCGATGTCTCGCAGTATACTTTTGTGTTTTGTTTAT-TTTGAAAATCAAATCACAGGATTATACTGTGAGTTATCGGCTGTA---GCA
droMoj3	scaffold_6496:11229058-11229148 +	AACACA--T-TCGATGTCTCGCAGTATATTTTTGTGTTTTGTTTAT-TATAAAAATCAAATCACAGGATTATACTGTGAGTTATCGGCTGAA---ACA
droGri2	scaffold_15245:14076242-14076330 -	CCCACCACTGTCGATGTCTCGCAGTATATTTTTGTGTTTTGTTTATTTTTGAAAATCAAATCACAGGATTATACTGTGAGTTATC------G---CCA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:10103292-10103384 -	AACACG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAATCCAAATCACAGGATTATACTGTGAGATGACCAGCGTG---CCA
droSim1	chr2R:8866656-8866748 -	CACACG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCGTG---CCA
droSec1	super_1:7611688-7611779 -	CA--CG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCGTG---CCA
droYak2	chr2R:10041132-10041224 -	CACACG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCCTTTTGCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCGTG---CCA
droEre2	scaffold_4845:15739235-15739330 +	CACACG--TCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAAATCAAATCACAGGATTATACTGTGAGATGACCAGCGTGCCGCCA
droAna3	scaffold_13266:5819955-5820045 +	CA--TG--TCTCGTCGCCTCGCAGTATATTTTTGTGTTTTGTTTGG-TTTGAAACTCAAATCACAGGATTATACTGTGAGATGCCAAGCGTG---TCA
dp4	chr3:16336992-16337078 -	--------TCTTGACGCCTCGCAGTATATTTTTGTGTTTTGTTGTG-TCTGAAACGCAAATCACAGGATTATACTGTGAGATGCTGGGCGTG---CTA
droPer1	super_4:426256-426345 +	G---CG--TCTTGACGCCTCGCAGTATATTTTTGTGTTTTGTTGTG-TCTGAAACGCAAATCACAGGATTATACTGTGAGATGCTGGGCGTG---CTA
droWil1	scaffold_180700:1860929-1861010 +	AGACTA--TTCTTGCGTCTCGCAGTATATTTTTGTGTTTTGTTCAATTTGTCAACTCAAATCACAGGATTATACTGTGAGCTGC--------------
droVir3	scaffold_12875:17605293-17605383 +	AACGCA--T-TCGATGTCTCGCAGTATACTTTTGTGTTTTGTTTAT-TTTGAAAATCAAATCACAGGATTATACTGTGAGTTATCGGCTGTA---GCA
droMoj3	scaffold_6496:11229058-11229148 +	AACACA--T-TCGATGTCTCGCAGTATATTTTTGTGTTTTGTTTAT-TATAAAAATCAAATCACAGGATTATACTGTGAGTTATCGGCTGAA---ACA
droGri2	scaffold_15245:14076242-14076330 -	CCCACCACTGTCGATGTCTCGCAGTATATTTTTGTGTTTTGTTTATTTTTGAAAATCAAATCACAGGATTATACTGTGAGTTATC------G---CCA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CACACGTCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTTGCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCGTGCCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.................CGCAGTATATTTTTGTGTTTTG......................................................	22	1	732.00	732	732
........................................................AATCACAGGATTATACTGTGA................	21	1	107.00	107	107
.................CGCAGTATATTTTTGTGTTTT.......................................................	21	1	40.00	40	40
........................................................AATCACAGGATTATACTGT..................	19	1	18.00	18	18
..................GCAGTATATTTTTGTGTTTTG......................................................	21	1	11.00	11	11
........................................................AATCACAGGATTATACTGTGAG...............	22	1	9.00	9	9
.................CGCAGTATATTTTTGTGTTT........................................................	20	1	5.00	5	5
.................CGCAGTATATTTTTGTGT..........................................................	18	1	2.00	2	2
........................................................AATCACAGGATTATACTGTG.................	20	1	2.00	2	2
.....................GTATATTTTTGTGTTTTG......................................................	18	1	1.00	1	1
.................CGCAGTATATTTTTGTGTT.........................................................	19	1	1.00	1	1
................TCGCAGTATATTTTTGTGTTTT.......................................................	22	1	1.00	1	1
...................CAGTATATTTTTGTGTTTTG......................................................	20	1	1.00	1	1
........................................................AATCACAGGATTATACTG...................	18	1	1.00	1	1

dp4

------TCTTGACGCCTCGCAGTATATTTTTGTGTTTTGTTGTGT-CTGAAACGCAAATCACAGGATTATACTGTGAGATGCTGGGCGTGCTA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.................CGCAGTATATTTTTGTGTTTTG......................................................	22	1	932.00	932	460	472
........................................................AATCACAGGATTATACTGTGA................	21	1	124.00	124	65	59
........................................................AATCACAGGATTATACTGT..................	19	1	82.00	82	38	44
.................CGCAGTATATTTTTGTGTTTT.......................................................	21	1	44.00	44	20	24
........................................................AATCACAGGATTATACTGTG.................	20	1	11.00	11	0	11
.................CGCAGTATATTTTTGTGTTT........................................................	20	1	9.00	9	4	5
.................CGCAGTATATTTTTGTGTT.........................................................	19	1	9.00	9	7	2
..................GCAGTATATTTTTGTGTTTTG......................................................	21	1	9.00	9	6	3
........................................................AATCACAGGATTATACTGTGAG...............	22	1	9.00	9	4	5
.................CGCAGTATATTTTTGTGTTTTGT.....................................................	23	1	4.00	4	2	2
.................CGCAGTATATTTTTGTGTTTTGTTG...................................................	25	1	2.00	2	1	1
........................................................AATCACAGGATTATACTG...................	18	1	2.00	2	1	1
...................CAGTATATTTTTGTGTTTTG......................................................	20	1	1.00	1	1	0
.......................................................AAATCACAGGATTATACTGT..................	20	1	1.00	1	1	0
.................CGCAGTATATTTTTGTGT..........................................................	18	1	1.00	1	0	1
................TCGCAGTATATTTTTGTGTTTTG......................................................	23	1	1.00	1	0	1
..................GCAGTATATTTTTGTGTT.........................................................	18	1	1.00	1	0	1
..................GCAGTATATTTTTGTGTTTT.......................................................	20	1	1.00	1	0	1
.......................................................AAATCACAGGATTATACTGTGA................	22	1	1.00	1	1	0
.......................................................AAATCACAGGATTATACTG...................	19	1	1.00	1	0	1

Secondary Structure

dm3

-23.5	-23.3	-22.8	-22.5

droSim1

-24.1	-23.9

droSec1

-24.1	-23.9

droYak2

-23.9

droEre2

-24.7	-24.3	-24.1	-24.0	-23.9

droAna3

-24.8	-24.3	-24.2	-24.0	-23.9	-23.9

dp4

-27.0	-27.0	-26.5

droPer1

-27.0	-27.0	-26.5

droWil1

-23.9

droVir3

-23.6	-23.2	-23.2

droMoj3

-24.3	-23.9	-23.9

droGri2

-24.4	-24.3	-23.9	-23.4

Generated: 01/05/2013 at 05:16 PM