Secondary structure and small RNA-seq evidence for dme-mir-100

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:18471419-18471548 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droSim1	chr2L:18160327-18160456 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droSec1	super_7:2092721-2092850 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droYak2	chr2R:4988205-4988334 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droEre2	scaffold_4845:5800004-5800133 -	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droAna3	scaffold_12916:2378756-2378885 +	ATACTCACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTTTATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATCGAA
dp4	chr4_group3:3634738-3634867 +	ATACTTATATATGGACCATTAACAGAAACCCGTAATTCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------TT-ATCACA
droPer1	super_1:5115309-5115438 +	ATACTTATATATGGACCATTAACAGAAACCCGTAATTCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------TT-ATCACA
droWil1	scaffold_180708:11622810-11622939 +	ATAGTCACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGGCCAACAAAAT---------------------CGAAT--CG
droVir3	scaffold_12963:18449830-18449980 +	ATACTCAAATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAGACATATAAAATATATTAACAAAA-ATGACA
droMoj3	scaffold_6500:6185704-6185833 -	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACTTGGTTTTTGG-CAACAAA-G---------------------CA-AAGCAA
droGri2	scaffold_15252:6427650-6427777 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTTTATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAA-----------------------G-ACTACA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:18471419-18471548 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droSim1	chr2L:18160327-18160456 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droSec1	super_7:2092721-2092850 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droYak2	chr2R:4988205-4988334 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droEre2	scaffold_4845:5800004-5800133 -	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATGACA
droAna3	scaffold_12916:2378756-2378885 +	ATACTCACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTTTATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------CA-ATCGAA
dp4	chr4_group3:3634738-3634867 +	ATACTTATATATGGACCATTAACAGAAACCCGTAATTCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------TT-ATCACA
droPer1	super_1:5115309-5115438 +	ATACTTATATATGGACCATTAACAGAAACCCGTAATTCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAT---------------------TT-ATCACA
droWil1	scaffold_180708:11622810-11622939 +	ATAGTCACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGGCCAACAAAAT---------------------CGAAT--CG
droVir3	scaffold_12963:18449830-18449980 +	ATACTCAAATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAAGACATATAAAATATATTAACAAAA-ATGACA
droMoj3	scaffold_6500:6185704-6185833 -	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACTTGGTTTTTGG-CAACAAA-G---------------------CA-AAGCAA
droGri2	scaffold_15252:6427650-6427777 +	ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTTTATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACT-GGTTTTTGG-CAACAAAA-----------------------G-ACTACA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATACTTACATATGGACCATTAACAGAAACCCGTAAATCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACTGGTTTTTGGCAACAAAATCAATGACA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..........................AACCCGTAAATCCGAACTTGTG..................................................................................	22	1	1.00	1	1
.................................................................CAAGACCGGCATTATGGGAGTC...........................................	22	1	1.00	1	1

dp4

ATACTTATATATGGACCATTAACAGAAACCCGTAATTCCGAACTTGTGCTGTTTTATATCTGTTACAAGACCGGCATTATGGGAGTCTGTCAATGCAAACAACTGGTTTTTGGCAACAAAATTTATCACA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..........................AACCCGTAATTCCGAACTTGT...................................................................................	21	1	295.00	295	0	295
..........................AACCCGTAATTCCGAACTTGTG..................................................................................	22	1	94.00	94	0	94
.................................................................CAAGACCGGCATTATGGGAGTC...........................................	22	1	32.00	32	0	32
.................................................................CAAGACCGGCATTATGGGAGT............................................	21	1	17.00	17	0	17
...........................ACCCGTAATTCCGAACTTGT...................................................................................	20	1	9.00	9	0	9
.................................................................CAAGACCGGCATTATGGGAG.............................................	20	1	8.00	8	0	8
...........................ACCCGTAATTCCGAACTTGTG..................................................................................	21	1	8.00	8	0	8
............................................................TGTTACAAGACCGGCATTATGGG...............................................	23	1	6.00	6	0	6
.........................AAACCCGTAATTCCGAACTTGT...................................................................................	22	1	5.00	5	0	5
..........................AACCCGTAATTCCGAACTTG....................................................................................	20	1	4.00	4	0	4
.....................................................................ACCGGCATTATGGGAGTCTGT........................................	21	1	1.00	1	0	1
................................................................ACAAGACCGGCATTATGGGAG.............................................	21	1	1.00	1	0	1
....................................................................GACCGGCATTATGGGAGTCTGT........................................	22	1	1.00	1	0	1
...........................ACCCGTAATTCCGAACTTGTGC.................................................................................	22	1	1.00	1	0	1
.................................................................CAAGACCGGCATTATGGG...............................................	18	1	1.00	1	0	1
.................................................................CAAGACCGGCATTATGGGA..............................................	19	1	1.00	1	0	1
............................................................TGTTACAAGACCGGCATTATG.................................................	21	1	1.00	1	0	1
............................................................TGTTACAAGACCGGCATTATGG................................................	22	1	1.00	1	0	1

Secondary Structure

dm3

-27.1	-27.0	-26.4	-26.4	-26.3	-26.2

droSim1

-27.1	-27.0	-26.4	-26.4	-26.3	-26.2

droSec1

-27.1	-27.0	-26.4	-26.4	-26.3	-26.2

droYak2

-27.1	-27.0	-26.4	-26.4	-26.3	-26.2

droEre2

-27.1	-27.0	-26.4	-26.4	-26.3	-26.2

droAna3

-27.1	-27.0	-26.4	-26.4	-26.3	-26.2

dp4

-28.9	-28.8	-28.2	-28.2	-28.1	-28.0

droPer1

-28.9	-28.8	-28.2	-28.2	-28.1	-28.0

droWil1

-29.4	-29.3	-28.6	-28.6	-28.5	-28.5

droVir3

-27.1	-27.0	-26.4	-26.4	-26.3	-26.2

droMoj3

-27.4	-27.3	-27.1	-26.7	-26.6	-26.5

droGri2

-27.1	-27.0	-26.4	-26.4	-26.3	-26.2

Generated: 01/05/2013 at 05:04 PM