dme-mir-289- Best orthologs

dme-mir-289	chr3L:13613922-13614020 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

mutations
read mismatches

Notes: "Very low read count even in dm3 so star/mature cannot be inferred. Conserved loci, good hairpins, but marking as '5', since this miRNA is still questionable. droAna3 has a large insertion that cause the structure to loose its long stem"

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3L:13613907-13614035 +		1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TT----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSim1	chr3L:12997848-12997976 +	LASTZ	5	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSec1	super_0:5775586-5775714 +	LASTZ	5	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droYak2	chr3L:13706954-13707082 +	LASTZ	5	TA------------------------CGGTTCTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCTCTCGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEre2	scaffold_4784:13614855-13614983 +	LASTZ	5	AA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACGGACTG-----------------------------GGGTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEug1	scf7180000409121:150423-150560 +	LASTZ	5	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------GCTTTCTCTCTCTCTCTCTCTTTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droBia1	scf7180000302428:6302592-6302720 -	LASTZ	5	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGTGAC-----------------------------------------------------CG----------------------------------------------CGACGACTCCCCTCCACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droTak1	scf7180000415161:62315-62434 +	LASTZ	5	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------CTTGCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEle1	scf7180000491255:2056112-2056232 +	LASTZ	5	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTGAGTGGAGCCTGCGAC-----------------------------------------------------TC------------------------------------------------------CTTGCCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droRho1	scf7180000779509:202440-202560 +	LASTZ	5	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTGAGTGGAGCCTGCGAC-----------------------------------------------------TC------------------------------------------------------CTTGCCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droFic1	scf7180000454048:90357-90510 -	LASTZ	5	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT------------------TCGCTA---A-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droKik1	scf7180000302808:404338-404457 -	LASTZ	5	TA------------------------GGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------TGGCTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droAna3	scaffold_13337:21827571-21827739 -	LASTZ	5	TT-CCGGCACTCCGGCATTCCAGCT-CGGGTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------TG--CTACTGCCACTGCCACTGCCACTGCCACTGCCGCTCGGGGAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droBip1	scf7180000396730:303852-303987 -	LASTZ	5	CA----GTACTCTGGCATTCCGGCT-CGGGTTCTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC---------------------------------------------------------TGCCACTG-----------------------------GGG-GAGTCACTTGAGCGTTTGCTGGCACGTAAAAGACATCATAATTAGCATT
dp4	chrXR_group8:6818889-6819024 -	LASTZ	5	TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGG---AC--------------------------------------------TC----------------------------------------------CAG-----CTCTCCGACTG-----------------------------GGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droPer1	super_36:488140-488275 +	LASTZ	5	TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGG---AC--------------------------------------------TC----------------------------------------------CAG-----CTCTCCGACTG-----------------------------GGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droWil1	scaffold_180698:607141-607313 -	LASTZ	5	TT------------------------TTTTTTTTAGGTTGAAGTTTACAGTAAAATAAATATTTAAGTGGAGTC---GACTGTGTCGACTACAGCCCGGACTACCCGGACTGCTAGAACGACTCGGTTCCGACTC-----------------------------------------------------TTTTTCTGTCGG-----------------------------GGTAAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droVir3	scaffold_13049:19817984-19818083 -	LASTZ	5	---------------------------GTTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-G----------------------------------------------------------------------------------------------------------------------------CCTG------------------------------GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droMoj3	scaffold_6680:7513468-7513568 -	LASTZ	5	G--------------------------GCTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGGGCCC-----------------------------------------------------------------------------------------------------------------------------------------------------------GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droGri2	scaffold_15110:17555344-17555443 +	LASTZ	5	---------------------------AGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-G----------------------------------------------------------------------------------------------------------------------------CCTG------------------------------GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TT----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSim1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSec1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droYak2	TA------------------------CGGTTCTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCTCTCGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEre2	AA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACGGACTG-----------------------------GGGTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEug1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------GCTTTCTCTCTCTCTCTCTCTTTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droBia1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGTGAC-----------------------------------------------------CG----------------------------------------------CGACGACTCCCCTCCACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droTak1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------CTTGCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEle1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTGAGTGGAGCCTGCGAC-----------------------------------------------------TC------------------------------------------------------CTTGCCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droRho1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTGAGTGGAGCCTGCGAC-----------------------------------------------------TC------------------------------------------------------CTTGCCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droFic1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT------------------TCGCTA---A-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droKik1	TA------------------------GGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------TGGCTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droAna3	TT-CCGGCACTCCGGCATTCCAGCT-CGGGTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------TG--CTACTGCCACTGCCACTGCCACTGCCACTGCCGCTCGGGGAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droBip1	CA----GTACTCTGGCATTCCGGCT-CGGGTTCTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC---------------------------------------------------------TGCCACTG-----------------------------GGG-GAGTCACTTGAGCGTTTGCTGGCACGTAAAAGACATCATAATTAGCATT
dp4	TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGG---AC--------------------------------------------TC----------------------------------------------CAG-----CTCTCCGACTG-----------------------------GGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droPer1	TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGG---AC--------------------------------------------TC----------------------------------------------CAG-----CTCTCCGACTG-----------------------------GGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droWil1	TT------------------------TTTTTTTTAGGTTGAAGTTTACAGTAAAATAAATATTTAAGTGGAGTC---GACTGTGTCGACTACAGCCCGGACTACCCGGACTGCTAGAACGACTCGGTTCCGACTC-----------------------------------------------------TTTTTCTGTCGG-----------------------------GGTAAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droVir3	---------------------------GTTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-G----------------------------------------------------------------------------------------------------------------------------CCTG------------------------------GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droMoj3	G--------------------------GCTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGGGCCC-----------------------------------------------------------------------------------------------------------------------------------------------------------GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droGri2	---------------------------AGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-G----------------------------------------------------------------------------------------------------------------------------CCTG------------------------------GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

Small RNA-seq read pileup

Species

Alignment

droSim1

TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................TCAGTGGAGCCTGCGGC-----------------------------------------------------T....................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................TAATTATTTAAGTGGGGCC................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...........................................................TATGTAAGTGGAGCCTGG.............................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................................................................................................................................................................................................................................................A	22	2	1.50	0.00	1.00	0.50
..............................................................................................................................................................................................................................................AGTTGAGCGTTTGGTGGCA.........................	19	1	2.00	1.00	1.00	0.00
.................................................................AGTGGAGCCTGCGAT-----------------------------------------------------CC----------------------------------------------C....................................................................................................	18	1	1.00	0.00	1.00	0.00
....................................................AAATAAATATCTAAGTGT....................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TA------------------------CGGTTCTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCTCTCGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................GAGTGGAGCCTGCGGC-----------------------------------------------------.....................................................................................................................................................	16	2	2.00	0.00	0.00	0.00	2.00	0.00
.....................................................AATAAATATGTAATTGGA...................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
................................................................GAGTGGAGCCTGCGGC-----------------------------------------------------T....................................................................................................................................................	17	2	0.50	0.00	0.00	0.00	0.50	0.00

droEre2

AA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACGGACTG-----------------------------GGGTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------GCTTTCTCTCTCTCTCTCTCTTTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

droBia1

TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGTGAC-----------------------------------------------------CG----------------------------------------------CGACGACTCCCCTCCACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

droTak1

TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------CTTGCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

droEle1

TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTGAGTGGAGCCTGCGAC-----------------------------------------------------TC------------------------------------------------------CTTGCCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

droRho1

Size

Hit Count

Total Norm

droFic1

TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT------------------TCGCTA---A-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

droKik1

TA------------------------GGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------TGGCTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

droAna3

TT-CCGGCACTCCGGCATTCCAGCT-CGGGTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------TG--CTACTGCCACTGCCACTGCCACTGCCACTGCCGCTCGGGGAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.........................................................................................................................................................................................................CACTGCCACTGCCACTGCCTCC...........................................................	22	2	0.50	0.00	0.50	0.00	0.00
.................................................................AGTGGAGCCTGCGGC-----------------------------------------------------TT-------------------------------------------------------............................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................................................CACTGCCACTGCCACTGCCTCC.....................................................	22	2	0.50	0.00	0.50	0.00	0.00
...............................................................................................................................................................................................................CCCTGCCACTGCCTCTGC.........................................................	18	5	0.20	0.00	0.00	0.00	0.20
...........................................................TATGTAAGTGGAGCCGGC.............................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................................................CTGTCTCTGCCACTGCCGCT.....................................................	20	2	0.50	0.00	0.50	0.00	0.00
................................................................................................................................................................................................................................CCGCTCGGGGAGGCAGT.........................................	17	1	1.00	0.00	0.00	1.00	0.00
................................................................GAGTGGAGCCTGCGGC-----------------------------------------------------T....................................................................................................................................................	17	2	0.50	0.00	0.00	0.50	0.00
................................................................................................................................................................................................................................CAGCTCGGGGAGGCACT.........................................	17	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................CCCTGCCACTGCCTCTGC...............................................................	18	5	0.20	0.00	0.00	0.00	0.20

droBip1

CA----GTACTCTGGCATTCCGGCT-CGGGTTCTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC---------------------------------------------------------TGCCACTG-----------------------------GGG-GAGTCACTTGAGCGTTTGCTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

dp4

TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGG---AC--------------------------------------------TC----------------------------------------------CAG-----CTCTCCGACTG-----------------------------GGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGG---AC--------------------------------------------TC----------------------------------------------CAG-----CTCTCCGACTG-----------------------------GGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
................................................................AAGTGGATCCGGCGACTGG.......................................................................................................................................................................................................	19	1	3.00	0.00	0.00	0.00	0.00	3.00
...........................................................................GCGACTGGA---AC--------------------------------------------TC----------------------------------------------CTG-----CTC..........................................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
......................................................................AGACTGAGACTGGG---AC--------------------------------------------TC----------------------------------------------C....................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................AGACTGCGACxGGG---AC--------------------------------------------TC----------------------------------------------CAG-----CTC..........................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

TT------------------------TTTTTTTTAGGTTGAAGTTTACAGTAAAATAAATATTTAAGTGGAGTC---GACTGTGTCGACTACAGCCCGGACTACCCGGACTGCTAGAACGACTCGGTTCCGACTC-----------------------------------------------------TTTTTCTGTCGG-----------------------------GGTAAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...................................................AATATxAATATTGAAGTGGA...................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
...................................................................................GTCGACTACACCCGGGAC.....................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................TTTTATATTGAAGTTTACA.........................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................TTTTTTAGGTTGxAGTTCAC..........................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.............................TTTATAGGTTGAAGTCTA...........................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...................................................AAGATAAATxTTTAAGTGG....................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

---------------------------GTTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-G----------------------------------------------------------------------------------------------------------------------------CCTG------------------------------GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.....................................................AATAATTATTGAAGAGG-G----------------------------------------------------------------------------------------------------------------------------......................................................................................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
.......................................................................................................................................................................................................................................................TTTGTTGGCACGGAACAG.................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

G--------------------------GCTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGGGCCC-----------------------------------------------------------------------------------------------------------------------------------------------------------GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

---------------------------AGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-G----------------------------------------------------------------------------------------------------------------------------CCTG------------------------------GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:21:04 EDT

dme-mir-289

chr3L:13613922-13614020 +

Known_mirbase

antisense_to_intron

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup