Secondary structure and small RNA-seq evidence for dme-mir-281-2

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:8057643-8057764 -	CTTTCAG----ATC-CTCCGCGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----AGACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT--TAT
droSim1	zdp42d09.g1:294-416 +	CTTTCAG----ATC-CTCCGCGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----AGACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT--TAT
droSec1	super_1:5602746-5602867 -	CTTTCAG----ATC-CTCCGCGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----AGACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT--TAT
droYak2	chr2R:8893539-8893660 +	CTTTCAG----ATC-CCCCACGAATAGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----ATACCAATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAGGCGACGAT--TAG
droEre2	scaffold_4845:17736400-17736520 +	CTTTCAG----ATC-CTCCACGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----ATACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT--TA-
droAna3	scaffold_13266:2568922-2569043 +	CCGCAAG---GATA-CTCCACGAATAGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-AA--AACACGGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT-----
dp4	chr3:418209-418322 -	TAT---A----ATA-CTGAACGAATAGTGAAATAAAGAGAGCTATCCGTCGACAGTCAAGTT-A----A-TCAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAAGCGCCGA------
droPer1	super_2:605106-605226 -	TTTTCTGTATAATA-CTGAACGAATAGTGAAATAAAGAGAGCTATCCGTCGACAGTCAAGTT-A----A-TCAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAAGCGCCGA------
droWil1	scaffold_181141:3242068-3242181 +	T------------------CCGAATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCCAGTTTAATACATCCGAATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAATCGACGGT--TTT
droVir3	scaffold_12875:19830099-19830219 +	CTAACCA----AAC-T--TGCGAATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCAAGCT-A-----TACAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAAGCGACGACTTTAT
droMoj3	scaffold_6496:6376053-6376173 -	CCCTCAG----T----TCTGCGAATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A---TATACATATTTTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAATCGACGAT-ATAT
droGri2	scaffold_15245:18178374-18178494 +	GTTTCAC----AACAAATTACGAATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A---TATACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAAGCGACGAT-----

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:8057643-8057764 -	CTTTCAG----ATC-CTCCGCGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----AGACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT--TAT
droSim1	zdp42d09.g1:294-416 +	CTTTCAG----ATC-CTCCGCGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----AGACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT--TAT
droSec1	super_1:5602746-5602867 -	CTTTCAG----ATC-CTCCGCGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----AGACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT--TAT
droYak2	chr2R:8893539-8893660 +	CTTTCAG----ATC-CCCCACGAATAGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----ATACCAATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAGGCGACGAT--TAG
droEre2	scaffold_4845:17736400-17736520 +	CTTTCAG----ATC-CTCCACGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A----ATACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT--TA-
droAna3	scaffold_13266:2568922-2569043 +	CCGCAAG---GATA-CTCCACGAATAGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-AA--AACACGGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGAT-----
dp4	chr3:418209-418322 -	TAT---A----ATA-CTGAACGAATAGTGAAATAAAGAGAGCTATCCGTCGACAGTCAAGTT-A----A-TCAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAAGCGCCGA------
droPer1	super_2:605106-605226 -	TTTTCTGTATAATA-CTGAACGAATAGTGAAATAAAGAGAGCTATCCGTCGACAGTCAAGTT-A----A-TCAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAAGCGCCGA------
droWil1	scaffold_181141:3242068-3242181 +	T------------------CCGAATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCCAGTTTAATACATCCGAATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAATCGACGGT--TTT
droVir3	scaffold_12875:19830099-19830219 +	CTAACCA----AAC-T--TGCGAATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCAAGCT-A-----TACAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAAGCGACGACTTTAT
droMoj3	scaffold_6496:6376053-6376173 -	CCCTCAG----T----TCTGCGAATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A---TATACATATTTTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAATCGACGAT-ATAT
droGri2	scaffold_15245:18178374-18178494 +	GTTTCAC----AACAAATTACGAATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT-A---TATACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAAGCGACGAT-----

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTTTCAGATCCTCCGCGAATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTTAAGACCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAAAGGCGACGATTAT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.............................AAGAGAGCTATCCGTCGACAGTC......................................................................	23	1	1098.00	1098	1098
.............................AAGAGAGCTATCCGTCGACAGT.......................................................................	22	1	233.00	233	233
..........................................................................TGTCATGGAATTGCTCTCTTTGT.........................	23	2	199.50	399	399
.............................AAGAGAGCTATCCGTCGACAG........................................................................	21	1	38.00	38	38
.............................AAGAGAGCTATCCGTCGACAGTCA.....................................................................	24	1	25.00	25	25
..............................AGAGAGCTATCCGTCGACAGTC......................................................................	22	1	4.00	4	4
.........................................................................CTGTCATGGAATTGCTCTCTTT...........................	22	2	4.00	8	8
.............................AAGAGAGCTATCCGTCGACA.........................................................................	20	1	4.00	4	4
..........................................................................TGTCATGGAATTGCTCTCTTTGTA........................	24	2	3.00	6	6
.............................AAGAGAGCTATCCGTCGACAGTCAA....................................................................	25	1	2.00	2	2
...........................................................................GTCATGGAATTGCTCTCTTTG..........................	21	2	1.00	2	2
.............................AAGAGAGCTATCCGTCGAC..........................................................................	19	1	1.00	1	1
...........................TGAAGAGAGCTATCCGTCGACA.........................................................................	22	1	1.00	1	1
....................................................................TAATACTGTCATGGAATTGCTCTCTTTG..........................	28	1	1.00	1	1
............................................................................TCATGGAATTGCTCTCTTTGTA........................	22	2	0.50	1	1
..............................................................................ATGGAATTGCTCTCTTTG..........................	18	2	0.50	1	1

dp4

T---ATAATACTGAACGAATAGTGAAATAAAGAGAGCTATCCGTCGACAGTCAAGTTAA-TCAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAAAAGCGCCGA----	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.............................AAGAGAGCTATCCGTCGACAGTC......................................................................	23	1	2264.00	2264	838	1426
.............................AAGAGAGCTATCCGTCGACAGT.......................................................................	22	1	1303.00	1303	305	998
..........................................................................TGTCATGGAATTGCTCTCTTTGT.........................	23	2	950.00	1900	577	1323
..........................................................................TGTCATGGAATTGCTCTCTTTG..........................	22	2	938.50	1877	330	1547
.............................AAGAGAGCTATCCGTCGACAG........................................................................	21	1	327.00	327	25	302
.............................AAGAGAGCTATCCGTCGACA.........................................................................	20	1	153.00	153	2	151
.........................................................................CTGTCATGGAATTGCTCTCTTT...........................	22	2	71.00	142	10	132
...........................................................................GTCATGGAATTGCTCTCTTTGT.........................	22	2	22.00	44	15	29
.............................AAGAGAGCTATCCGTCGACAGTCA.....................................................................	24	1	21.00	21	2	19
.........................................................................CTGTCATGGAATTGCTCTCTTTGT.........................	24	2	20.00	40	0	40
..........................................................................TGTCATGGAATTGCTCTCTT............................	20	2	11.50	23	0	23
.............................AAGAGAGCTATCCGTCGAC..........................................................................	19	1	11.00	11	1	10
............................AAAGAGAGCTATCCGTCGACAGT.......................................................................	23	1	9.00	9	6	3
..............................AGAGAGCTATCCGTCGACAGTC......................................................................	22	1	7.00	7	5	2
.............................AAGAGAGCTATCCGTCGA...........................................................................	18	1	3.00	3	0	3
............................AAAGAGAGCTATCCGTCGACAG........................................................................	22	1	3.00	3	1	2
..........................................................................TGTCATGGAATTGCTCTCTTT...........................	21	2	2.50	5	5	0
..........................................................................TGTCATGGAATTGCTCTCTTTGTA........................	24	2	2.50	5	0	5

Secondary Structure

dm3

-31.4	-31.4	-31.4	-31.4	-31.0	-31.0

droSim1

-31.4	-31.4	-31.4	-31.4	-31.0	-31.0

droSec1

-31.4	-31.4	-31.4	-31.4	-31.0	-31.0

droYak2

-31.4	-30.8	-30.8	-30.5	-30.5

droEre2

-31.6	-31.6	-31.4	-31.4	-31.0	-31.0

droAna3

-31.6	-30.8	-30.7	-30.6

dp4

-32.0	-31.8	-31.5	-31.5	-31.1	-31.0

droPer1

-32.0	-31.8	-31.5	-31.5	-31.1	-31.0

droWil1

-33.0	-32.1

droVir3

-32.0	-31.8	-31.5	-31.2	-31.1

droMoj3

-31.3	-31.0	-30.7	-30.4

droGri2

-34.3	-33.4

Generated: 01/05/2013 at 05:13 PM