Secondary structure and small RNA-seq evidence for dme-mir-980

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:174190-174317 -	GCGTG-------------------TGAAATACGAAGTTGATTGTATGTCAGTTTTTCATTTGGCCTGGCTAGCTTACTCCT--TTTTAAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTCGAC-----------TCCCGAATA---ATA
droSim1	chrX:118257-118384 -	GCGTG-------------------TGAAATACGAAGTTGATTGTATGTCAGTTTTTCATTTGGCGTGGCTAGCTCACTACT--TTTTTAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTCAAC-----------TGCCAAATA---ATA
droSec1	super_10:47183-47310 -	GCGTG-------------------TGAAATACGAAGTTGATTGTATGTCAGTTTTTCATTTGGCGTGGCTAGCTCACTACT--TTTTTAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTCAAC-----------TGCCAAATA---ATA
droYak2	chrX:117050-117182 -	GCGTG-------------------TGAGATGTGAAGTTGATTGTATGTCAGTTTTTCATTTGGCGTGCCTAGCTTAGCTTT--TTTTAAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTCGACTCGA------CTGCCAAATG---ATA
droEre2	scaffold_4644:121637-121764 -	GCGTG-------------------TGAAATGTGAAGTTGATTGTATGTCAGTTTTTCATTTGGCGTGCCTAGCTTACCTCT--TTTTAAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGTAGTTCGAC-----------TGCAAAATT---ATA
droAna3	scaffold_13117:4815182-4815314 -	AAGTGATAAGAAATGTCC-----------TAGGAAGTAATTTGTATGTCAGCCTCTCATTTGGCCTGCCTAGCTGACTTT---AAATTAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTGATTGCGATTCAAC-----------TTGC--AGA---ATA
dp4	chrXL_group1e:4097625-4097758 -	CCGCC-------------------ACAAAAGAGAAACAAATTGAATGTGAGTCTCTCACATGGCTGGTCTAGCTGACTTG---TTTCTAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTTTTTGTAGCCCAACGTAA-------AGCCGAAAATCGTAA
droPer1	super_17:1039174-1039307 -	CCGCC-------------------ACAAAAGAGAAACAAATTGTATGTGAGTCTCTCACATGGCTGGTCTAGCTGACTTG---TTTCTAATACTGCTAGCTGCCTTGTGAAGGGCTTACGTGTTTTTGTAGCCCAACGTAA-------AGCCGAAAATCGTAA
droWil1	scaffold_181096:8731771-8731891 +	---------------------------------------ATTGTGTGTGAGTCTTTCACTGGGCGTGCTTAGCTAGAAATTTATTTACCATATTGCTAGCTGCCTTGTGAAGTGCTTACGTGTAATTGTTGAACAACAAAAAAAAATCAGAAAAAGC---ATA
droVir3	scaffold_10277:1011-1148 -	GGGCTATAAAATTTGGACCAAATGTGA------GAGCGCATTGCATGTGAGTCCCTCATTTGGCAGGTTTAGCTGCTTTT---AATACGATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTGATTGTTAAACAAC-----------T--TAAACA---ACA
droMoj3	scaffold_6473:11075547-11075659 +	TTATT-------------------T---ATATGAACCGCATTGCATGTGAGTCCCTCATTTGGTGCGCTTAGCTGTTTTTC--AATTTGATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTGTTTGTAATACAAC--------------------------
droGri2	scaffold_14853:6339037-6339158 +	GATTA-------------------TGAG------AGCGCATTACATGTGAGTCCCTCATTTGGCGGACTTAGCTGCTTTTC--AATTTGATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTGATTGTAAATCAAC-----------TGAGGAAAA---ATA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:174190-174317 -	GCGTG-------------------TGAAATACGAAGTTGATTGTATGTCAGTTTTTCATTTGGCCTGGCTAGCTTACTCCT--TTTTAAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTCGAC-----------TCCCGAATA---ATA
droSim1	chrX:118257-118384 -	GCGTG-------------------TGAAATACGAAGTTGATTGTATGTCAGTTTTTCATTTGGCGTGGCTAGCTCACTACT--TTTTTAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTCAAC-----------TGCCAAATA---ATA
droSec1	super_10:47183-47310 -	GCGTG-------------------TGAAATACGAAGTTGATTGTATGTCAGTTTTTCATTTGGCGTGGCTAGCTCACTACT--TTTTTAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTCAAC-----------TGCCAAATA---ATA
droYak2	chrX:117050-117182 -	GCGTG-------------------TGAGATGTGAAGTTGATTGTATGTCAGTTTTTCATTTGGCGTGCCTAGCTTAGCTTT--TTTTAAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTCGACTCGA------CTGCCAAATG---ATA
droEre2	scaffold_4644:121637-121764 -	GCGTG-------------------TGAAATGTGAAGTTGATTGTATGTCAGTTTTTCATTTGGCGTGCCTAGCTTACCTCT--TTTTAAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGTAGTTCGAC-----------TGCAAAATT---ATA
droAna3	scaffold_13117:4815182-4815314 -	AAGTGATAAGAAATGTCC-----------TAGGAAGTAATTTGTATGTCAGCCTCTCATTTGGCCTGCCTAGCTGACTTT---AAATTAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTGATTGCGATTCAAC-----------TTGC--AGA---ATA
dp4	chrXL_group1e:4097625-4097758 -	CCGCC-------------------ACAAAAGAGAAACAAATTGAATGTGAGTCTCTCACATGGCTGGTCTAGCTGACTTG---TTTCTAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTTTTTGTAGCCCAACGTAA-------AGCCGAAAATCGTAA
droPer1	super_17:1039174-1039307 -	CCGCC-------------------ACAAAAGAGAAACAAATTGTATGTGAGTCTCTCACATGGCTGGTCTAGCTGACTTG---TTTCTAATACTGCTAGCTGCCTTGTGAAGGGCTTACGTGTTTTTGTAGCCCAACGTAA-------AGCCGAAAATCGTAA
droWil1	scaffold_181096:8731771-8731891 +	---------------------------------------ATTGTGTGTGAGTCTTTCACTGGGCGTGCTTAGCTAGAAATTTATTTACCATATTGCTAGCTGCCTTGTGAAGTGCTTACGTGTAATTGTTGAACAACAAAAAAAAATCAGAAAAAGC---ATA
droVir3	scaffold_10277:1011-1148 -	GGGCTATAAAATTTGGACCAAATGTGA------GAGCGCATTGCATGTGAGTCCCTCATTTGGCAGGTTTAGCTGCTTTT---AATACGATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTGATTGTTAAACAAC-----------T--TAAACA---ACA
droMoj3	scaffold_6473:11075547-11075659 +	TTATT-------------------T---ATATGAACCGCATTGCATGTGAGTCCCTCATTTGGTGCGCTTAGCTGTTTTTC--AATTTGATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTGTTTGTAATACAAC--------------------------
droGri2	scaffold_14853:6339037-6339158 +	GATTA-------------------TGAG------AGCGCATTACATGTGAGTCCCTCATTTGGCGGACTTAGCTGCTTTTC--AATTTGATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTGATTGTAAATCAAC-----------TGAGGAAAA---ATA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GCGTGTGAAATACGAAGTTGATTGTATGTCAGTTTTTCATTTGGCGTGGCTAGCTCACTACTTTTTTAATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTAATTGCAGTTCAAC----TGCCAAATAAT---A	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...........................................................................TAGCTGCCTTGTGAAGGGCTT.......................................	21	1	497.00	497	497
...........................................................................TAGCTGCCTTGTGAAGGGCTTA......................................	22	1	67.00	67	67
..............................AGTTTTTCATTTGGCGTGGCTAGC.................................................................................	24	1	43.00	43	43
..............................AGTTTTTCATTTGGCGTGGCTAG..................................................................................	23	1	2.00	2	2
..............................AGTTTTTCATTTGGCGTGGC.....................................................................................	20	1	1.00	1	1
............................................................................AGCTGCCTTGTGAAGGGCTT.......................................	20	1	1.00	1	1

dp4

CCGCCACAAAAGAGAAACAAATTGAATGTGAGTCTCTCACATGGCTGGTCTAGCTGACTTGTTTCT-AATATTGCTAGCTGCCTTGTGAAGGGCTTACGTGTTTTTGTAGCCCAACGTAAAGCCGAAAATCGTAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...........................................................................TAGCTGCCTTGTGAAGGGCTT.......................................	21	1	4314.00	4314	505	3809
...........................................................................TAGCTGCCTTGTGAAGGGCTTA......................................	22	1	885.00	885	87	798
...........................................................................TAGCTGCCTTGTGAAGGGCT........................................	20	1	165.00	165	4	161
..............................AGTCTCTCACATGGCTGGTCTAGC.................................................................................	24	1	19.00	19	14	5
...........................................................................TAGCTGCCTTGTGAAGGGC.........................................	19	1	12.00	12	0	12
............................................................................AGCTGCCTTGTGAAGGGCTT.......................................	20	1	11.00	11	0	11
...........................................................................TAGCTGCCTTGTGAAGGGCTTAC.....................................	23	1	8.00	8	0	8
...........................................................................TAGCTGCCTTGTGAAGGG..........................................	18	1	7.00	7	1	6
..............................AGTCTCTCACATGGCTGGTCTAG..................................................................................	23	1	5.00	5	3	2
..........................................................................CTAGCTGCCTTGTGAAGGGCTT.......................................	22	1	4.00	4	0	4
.............................................................................GCTGCCTTGTGAAGGGCTT.......................................	19	1	3.00	3	2	1
..........................................................................CTAGCTGCCTTGTGAAGGGCTTA......................................	23	1	3.00	3	0	3
..............................AGTCTCTCACATGGCTGGTCT....................................................................................	21	1	1.00	1	0	1

Secondary Structure

dm3

-31.7	-31.4	-31.1	-30.9	-30.8

droSim1

-31.7	-31.4	-31.1	-31.0	-30.9	-30.8

droSec1

-31.7	-31.4	-31.1	-31.0	-30.9	-30.8

droYak2

-28.8	-28.5	-28.2	-28.0	-27.9	-27.9

droEre2

-28.8	-28.4	-27.9	-27.9

droAna3

-31.6	-30.6

dp4

-35.4	-34.6	-34.4	-34.4

droPer1

-35.2	-34.6	-34.4	-34.4	-34.2

droWil1

-27.8	-27.8	-27.7	-27.7	-27.4	-27.4

droVir3

-39.2	-38.9	-38.8	-38.5	-38.4

droMoj3

-33.9	-33.9	-33.7	-33.7	-33.5	-33.5

droGri2

-39.4	-39.1	-39.1	-39.0	-38.9	-38.8

Generated: 01/05/2013 at 05:34 PM