Secondary structure and small RNA-seq evidence for dme-mir-932

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:6902047-6902167 +	ATTT------CAAAAAGA----------GTATTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGTT----TCATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTCATCATCT---GCT--------------AGAGA
droSim1	chr2L:6697521-6697641 +	ATTT------CAAAAAAG----------GTATTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGTT----TAATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTCATCATCT---GCT--------------AGAGA
droSec1	super_3:2435750-2435870 +	ATTT------CAAAAAGG----------GTATTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGTT----TAATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTCATCATCT---GCT--------------AGAGA
droYak2	chr2L:6007719-6007838 -	ATTT------CAAAAAT-----------ATATTGGCTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGCT----TAATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTCCATCATCT---GCT--------------AGAGA
droEre2	scaffold_4929:15815527-15815649 +	ATTT------CAAGAAG-----------GTATTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTCTT----TACTTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTAATCATCTGGAGCT--------------AGAGA
droAna3	scaffold_12916:8482562-8482668 +	-------------------------------TTGGTTTCGAGACTTTCAATTCCGTAGTGCATTGCAGTGTTTT----TAAACTACAACTGCATGCTCTGCGGACTTGGCAGATTTGAAGACCAGGAGCAACT---TTT-------------AAGAAC
dp4	chr4_group5:397117-397229 +	----------------------------GCATTGGTGTCGTGGCTCTCAATTCCGTAGTGCATTGCAGTTTAATATAATTATCAACAACTGCAAGCGCTGTGGACTTGGCAGCTCCGATAGCCGCAAACA-CA---GCT--------------GCAGC
droPer1	super_5:4895121-4895233 +	----------------------------GCATTGGTGTCGTGGCTCTCAATTCCGTAGTGCATTGCAGTTTAATATAATTATCAACAACTGCAAGCGCTGTGGACTTGGCAGCTCCGATAGCCGCAAACA-CA---GCT--------------GCAGC
droWil1	scaffold_180772:6812317-6812450 -	ATTT------AATCCAAA----------TTCAAGGCATTGTAGCTATCAATTCCGTAGTGCATTGCAGTTGGTA----CTAGAAAATACTGCAAGCGCTGCGGACTTGCTAACTCTGATGACCATAAAAC-CA---CCTAAAAGCAATTCCTTAGATA
droVir3	scaffold_12963:14767730-14767833 -	--------------------------------TGGCAGCGAAACTCTCAATTCCGTAGTGCATTGCAGTTGATT----TTAGGAATTACTGCAAGCGCTGCAGAATTGGCAGCTCCGCTGACCGCAGACAACG---TAT----------------GGA
droMoj3	scaffold_6500:17707448-17707541 -	TAT--------------------------CAATGGCTGCGTAACTTTCAATTCCGTAGTGCATTGCAGTTGATT----TAAGGAATTACTGCAAGCGCTGCAGAATTGGCAGCTCCGTTGACC-----------------------------------
droGri2	scaffold_15126:4596325-4596461 +	ATTTGTGCGGCAGGAAAAGTTGGGAGTTGCAATGGCAATGTAACTTTCAATTCCGTAGTGCATTGCAGTTGATT----TAAGCAACTACTGCATGCCCTGCAGAATTGGCAGCTCTGTTGACCACATACAGCA---AAT--------------GGTGT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:6902047-6902167 +	ATTT------CAAAAAGA----------GTATTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGTT----TCATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTCATCATCT---GCT--------------AGAGA
droSim1	chr2L:6697521-6697641 +	ATTT------CAAAAAAG----------GTATTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGTT----TAATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTCATCATCT---GCT--------------AGAGA
droSec1	super_3:2435750-2435870 +	ATTT------CAAAAAGG----------GTATTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGTT----TAATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTCATCATCT---GCT--------------AGAGA
droYak2	chr2L:6007719-6007838 -	ATTT------CAAAAAT-----------ATATTGGCTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGCT----TAATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTCCATCATCT---GCT--------------AGAGA
droEre2	scaffold_4929:15815527-15815649 +	ATTT------CAAGAAG-----------GTATTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTCTT----TACTTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTAATCATCTGGAGCT--------------AGAGA
droAna3	scaffold_12916:8482562-8482668 +	-------------------------------TTGGTTTCGAGACTTTCAATTCCGTAGTGCATTGCAGTGTTTT----TAAACTACAACTGCATGCTCTGCGGACTTGGCAGATTTGAAGACCAGGAGCAACT---TTT-------------AAGAAC
dp4	chr4_group5:397117-397229 +	----------------------------GCATTGGTGTCGTGGCTCTCAATTCCGTAGTGCATTGCAGTTTAATATAATTATCAACAACTGCAAGCGCTGTGGACTTGGCAGCTCCGATAGCCGCAAACA-CA---GCT--------------GCAGC
droPer1	super_5:4895121-4895233 +	----------------------------GCATTGGTGTCGTGGCTCTCAATTCCGTAGTGCATTGCAGTTTAATATAATTATCAACAACTGCAAGCGCTGTGGACTTGGCAGCTCCGATAGCCGCAAACA-CA---GCT--------------GCAGC
droWil1	scaffold_180772:6812317-6812450 -	ATTT------AATCCAAA----------TTCAAGGCATTGTAGCTATCAATTCCGTAGTGCATTGCAGTTGGTA----CTAGAAAATACTGCAAGCGCTGCGGACTTGCTAACTCTGATGACCATAAAAC-CA---CCTAAAAGCAATTCCTTAGATA
droVir3	scaffold_12963:14767730-14767833 -	--------------------------------TGGCAGCGAAACTCTCAATTCCGTAGTGCATTGCAGTTGATT----TTAGGAATTACTGCAAGCGCTGCAGAATTGGCAGCTCCGCTGACCGCAGACAACG---TAT----------------GGA
droMoj3	scaffold_6500:17707448-17707541 -	TAT--------------------------CAATGGCTGCGTAACTTTCAATTCCGTAGTGCATTGCAGTTGATT----TAAGGAATTACTGCAAGCGCTGCAGAATTGGCAGCTCCGTTGACC-----------------------------------
droGri2	scaffold_15126:4596325-4596461 +	ATTTGTGCGGCAGGAAAAGTTGGGAGTTGCAATGGCAATGTAACTTTCAATTCCGTAGTGCATTGCAGTTGATT----TAAGCAACTACTGCATGCCCTGCAGAATTGGCAGCTCTGTTGACCACATACAGCA---AAT--------------GGTGT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATTTCAAAAAAGGTATTGGTTTTGAAGTTTTCAATTCCGTAGTGCATTGCAGTGTGTT----TAATTATTTACTGCAAGCGCTGCGGATTTGGCAACTTTGACGACCTTCATCATCTGCTAGAGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................TCAATTCCGTAGTGCATTGCAGT........................................................................	23	1	158.00	158	158
.........................................................................TGCAAGCGCTGCGGATTTGGCA..............................	22	1	31.00	31	31
.........................................................................TGCAAGCGCTGCGGATTTGGC...............................	21	1	8.00	8	8
..............................TCAATTCCGTAGTGCATTGCA..........................................................................	21	1	3.00	3	3
..............................TCAATTCCGTAGTGCATTGCAG.........................................................................	22	1	2.00	2	2
................................AATTCCGTAGTGCATTGCAGT........................................................................	21	1	1.00	1	1
..............................TCAATTCCGTAGTGCATTGCAGTG.......................................................................	24	1	1.00	1	1

dp4

------------GCATTGGTGTCGTGGCTCTCAATTCCGTAGTGCATTGCAGTTTAATATAATTATCAACAACTGCAAGCGCTGTGGACTTGGCAGCTCCGATAGCCGCAAACA-CAGCTGCAGC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................TCAATTCCGTAGTGCATTGCAGT........................................................................	23	1	6811.00	6811	414	6397
..............................TCAATTCCGTAGTGCATTGCAG.........................................................................	22	1	1955.00	1955	15	1940
..............................TCAATTCCGTAGTGCATTGCA..........................................................................	21	1	310.00	310	3	307
.........................................................................TGCAAGCGCTGTGGACTTGGCA..............................	22	1	223.00	223	36	187
..............................TCAATTCCGTAGTGCATTGC...........................................................................	20	1	164.00	164	1	163
..............................TCAATTCCGTAGTGCATTGCAGTT.......................................................................	24	1	157.00	157	14	143
.........................................................................TGCAAGCGCTGTGGACTTGGC...............................	21	1	116.00	116	9	107
................................AATTCCGTAGTGCATTGCAGT........................................................................	21	1	73.00	73	8	65
.........................................................................TGCAAGCGCTGTGGACTTGG................................	20	1	37.00	37	0	37
..............................TCAATTCCGTAGTGCATTG............................................................................	19	1	27.00	27	0	27
................................AATTCCGTAGTGCATTGCAG.........................................................................	20	1	15.00	15	0	15
...............................CAATTCCGTAGTGCATTGCAGT........................................................................	22	1	13.00	13	1	12
........................................................................CTGCAAGCGCTGTGGACTTGGCA..............................	23	1	10.00	10	2	8
........................................................................CTGCAAGCGCTGTGGACTTGGC...............................	22	1	6.00	6	2	4
...............................CAATTCCGTAGTGCATTGCAG.........................................................................	21	1	4.00	4	0	4
.............................CTCAATTCCGTAGTGCATTGCAG.........................................................................	23	1	3.00	3	0	3
.............................CTCAATTCCGTAGTGCATTGCAGT........................................................................	24	1	3.00	3	1	2
.................................ATTCCGTAGTGCATTGCAGT........................................................................	20	1	3.00	3	0	3
................................AATTCCGTAGTGCATTGCA..........................................................................	19	1	3.00	3	0	3

Secondary Structure

dm3

-42.5	-41.5

droSim1

-42.5	-41.5

droSec1

-42.5	-41.5

droYak2

-37.9	-37.3

droEre2

-41.5

droAna3

-36.6	-36.6	-36.6	-36.6	-36.6	-36.6

dp4

-39.1	-38.8	-38.7	-38.4	-38.2	-38.1

droPer1

-39.1	-38.8	-38.7	-38.4	-38.2	-38.1

droWil1

-34.5	-34.2

droVir3

-40.5	-40.5	-40.4	-40.4	-39.6	-39.6

droMoj3

-35.5	-35.5	-34.6	-34.6	-34.6	-34.6

droGri2

-29.0	-29.0	-29.0	-29.0	-28.2	-28.2

Generated: 01/05/2013 at 05:30 PM