dme-mir-966- Best orthologs

dme-mir-966	chr2L:6045627-6045713 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 6045678-6045698
   star strand at position 6045642-6045663
   mutations
   read mismatches

Notes: Mirna is only present in dm3 - droSec1 ancestor and lost in droSim1 due to small insertion in the miR. Small deletion also in droYak2 and droEre2. Surprising that the miR* is more conserved than the miR strand.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:6045612-6045728 -		1	A-TT----TC-GC---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGTTGTGGGCTGTG-------TGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGACCCACTGGTCGTCAACCGC
droSim1	chr2L:5834370-5834493 -	LASTZ	4	A-TT----TC-GT---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGCTGTGGGCTGTGGGCTGTAAGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droSec1	super_5:4116543-4116659 -	LASTZ	1	A-TT----TC-GT---TCGGCTGTAACCTGATCC-----------------GCTG--CTGCGGGTTGTGGGCTGTG-------AGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droYak2	chr2L:13146709-13146824 +	LASTZ	4	A-TT----CC-GC---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGATGTGGGATGTG--------GGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droEre2	scaffold_4929:11075516-11075624 +	LASTZ	5	A-TT-CCATC-AT---TCGGCTGTAACCTGATCC-----------------CCTG--CTGTGGG----------------------CTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-AGCA-----------------CAGCGTGGGCA-CGG-CCCACTGGTCGTCAACCGC
droEug1	scf7180000409676:526352-526439 +	LASTZ	5	T-------TT-GA---TCGGCTGTAACCTGATCT-----------------ACAT--CTG-----------------------------C------GG-----TAAAGGTG---CCAATTGATAACC--C-A----------------------GCGTGGGCA-CTG-CTAACTGGTCGTCAACGGC
droBia1	scf7180000302055:11613-11705 +	LASTZ	5	T-------TC-GA---TCGTCTGTAACCTGATCC-----------------AAGG--CTG-----------------------------C------GT-----TATAGGTGTCGCCGGTTGATAACCCCC-A----------------------GCGTGGGCA-CGG-CTCACTAGTCGTCAACAGC
droTak1	scf7180000415447:53169-53260 -	LASTZ	5	--------TC-GA---TCGGCTGTAACCTGATCC-----------------GCGG--CTG-----------------------------C------GG-----TATAGGTGTCGCCAGTTGATAACCCTC-A----------------------GCGTGGGCA-CGG-CCCACTAGTCGTCAACGGC
droEle1	scf7180000490399:107074-107177 -	LASTZ	5	--------TC-GA---TCTGCTGTAACCTAATCCGA--TCG----------GCTG--CTGTGGTATATGTA--------------------------------CATAGGTGCCGCCAGTTGATAACCC-C-A----------------------GTGTAGGCA-CGG-CCCACTGGCTGTCAACGGC
droRho1	scf7180000779105:24952-25021 -	LASTZ	5	--------TC-GA---TCTGCTGTAACCTGATCT-----------------GCTG--CTG-----------------------------T------GG-----TATAGGTGCCGCAAGTTGATAACCCCA--------------------------GTGGGCA-CGG--------------------
droFic1	scf7180000452562:15607-15693 +	LASTZ	5	A-------TC---------GATGTAACCTGATCG-----------------GCGG--CTG-----------------------------T------GG-----TCTAGGTGGATTCAGTTGATAACCCTC-A----------------------GCGTGGGCT-CAG-CCTACTGGTTGTCAACGGC
droKik1	scf7180000302468:107704-107788 -	LASTZ	5	G-ATTGGATCGGA---TTGGCTGTAACCTGAACC-----------------GCGG--CTGTG-------------------------------------------------------GTTGATAACCCCC-A----------------------ACGTGGGCT-GCGGCCCACTGGTTGTCAACGGC
droAna3	scaffold_12916:8156171-8156273 +	LASTZ	5	C-ATCCGATCTGA---TTGGCAGTAACCTGATCC-----------------GCGG--TTGTGG-----------------------TTGT------GG-----TGGAGGT---GCTACTTGATAACCCAC-T----------------------GCGTGGGCA-CTGGCCTTTCGGTTGTCAACGGC
droBip1	scf7180000396554:766763-766860 +	LASTZ	5	G-AT----CT-GA---TTGGCAGTAACCTGATCC-----------------GCGG--TTGTGG-----------------------TTGT------GC-----TGGAGGT---GCTACTTGATAACCCAC-T----------------------GCGTGGGCA-CTGGCCTTTCGGTTGTCAACGGC
dp4	chr4_group1:223208-223319 +	LASTZ	5	G-GA----TC-GG---GTGGCTGTAACCTGATCTGGGAGCGGTGCAGC---AGGG--CTG-----------------------------CGGTGGAGT-----TGGAGGTGTCGGCTGTTGATAACCCCC-A----------------------GCGTAGGCA-CTGG---TATGGTTGTGAACGGC
droPer1	super_1:219437-219548 +	LASTZ	5	G-GA----TC-GG---GTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTG--CTGTGGA--------------------------------GT-----TGGAGGTGTCGGCTGTTGATAACCCCC-A----------------------GCGTAGGCA-CTGG---TATGGTTGTCAACGGC
droWil1	scaffold_180708:7887454-7887585 +	LASTZ	5	GGATTGCAATTGGTTGTGGGCTGTAACCTGATCTGG----------------AAG--CTATAG-----------------------ATGT------GATGATGCGGAGGTGTCGTCAGATGATAACCCCCCAG----GGTAGACAGCTTAGACATCGTAGGCA-TTGGC---CTGGTTGTCAACGGC
droVir3	scaffold_12963:3941701-3941794 -	LASTZ	5	A-TT-------GGGCGTCTGCTGTAACTTGAAGC-----------------GCTGATCTG-------------------------------------------------------TGGTTGATAACCCCC-TGCCAAGGTG------------CTCGTAGGCAGCTACCGCTCCGGTTGTCAACGGC
droMoj3	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15252:1454932-1454939 +	LASTZ	0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTAG

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	A-TT-----TC-GC---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGTTGTGGGCTGTG-------TGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGACCCACTGGTCGTCAACCGC
droSim1	A-TT-----TC-GT---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGCTGTGGGCTGTGGGCTGTAAGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droSec1	A-TT-----TC-GT---TCGGCTGTAACCTGATCC-----------------GCTG--CTGCGGGTTGTGGGCTGTG-------AGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droYak2	A-TT-----CC-GC---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGATGTGGGATGTG--------GGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droEre2	A-TT-CCA-TC-AT---TCGGCTGTAACCTGATCC-----------------CCTG--CTGTGGG----------------------CTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-AGCA-----------------CAGCGTGGGCA-CGG-CCCACTGGTCGTCAACCGC
droEug1	T--------TT-GA---TCGGCTGTAACCTGATCT-----------------ACAT--CTG-----------------------------C------GG-----TAAAGGTG---CCAATTGATAACC--C-A----------------------GCGTGGGCA-CTG-CTAACTGGTCGTCAACGGC
droBia1	T--------TC-GA---TCGTCTGTAACCTGATCC-----------------AAGG--CTG-----------------------------C------GT-----TATAGGTGTCGCCGGTTGATAACCCCC-A----------------------GCGTGGGCA-CGG-CTCACTAGTCGTCAACAGC
droTak1	---------TC-GA---TCGGCTGTAACCTGATCC-----------------GCGG--CTG-----------------------------C------GG-----TATAGGTGTCGCCAGTTGATAACCCTC-A----------------------GCGTGGGCA-CGG-CCCACTAGTCGTCAACGGC
droEle1	---------TC-GA---TCTGCTGTAACCTAATCCGA--TCG----------GCTG--CTGTGGTATATGTA--------------------------------CATAGGTGCCGCCAGTTGATAACCC-C-A----------------------GTGTAGGCA-CGG-CCCACTGGCTGTCAACGGC
droRho1	---------TC-GA---TCTGCTGTAACCTGATCT-----------------GCTG--CTG-----------------------------T------GG-----TATAGGTGCCGCAAGTTGATAACCCCA--------------------------GTGGGCA-CGG--------------------
droFic1	A--------TC---------GATGTAACCTGATCG-----------------GCGG--CTG-----------------------------T------GG-----TCTAGGTGGATTCAGTTGATAACCCTC-A----------------------GCGTGGGCT-CAG-CCTACTGGTTGTCAACGGC
droKik1	G-ATTGGA-TCGGA---TTGGCTGTAACCTGAACC-----------------GCGG--CTGTG-------------------------------------------------------GTTGATAACCCCC-A----------------------ACGTGGGCT-GCGGCCCACTGGTTGTCAACGGC
droAna3	C-ATCCGA-TCTGA---TTGGCAGTAACCTGATCC-----------------GCGG--TTGTGG-----------------------TTGT------GG-----TGGAGGT---GCTACTTGATAACCCAC-T----------------------GCGTGGGCA-CTGGCCTTTCGGTTGTCAACGGC
droBip1	G-AT-----CT-GA---TTGGCAGTAACCTGATCC-----------------GCGG--TTGTGG-----------------------TTGT------GC-----TGGAGGT---GCTACTTGATAACCCAC-T----------------------GCGTGGGCA-CTGGCCTTTCGGTTGTCAACGGC
dp4	G-GA-----TC-GG---GTGGCTGTAACCTGATCTGGGAGCGGTGCAGC---AGGG--CTG-----------------------------CGGTGGAGT-----TGGAGGTGTCGGCTGTTGATAACCCCC-A----------------------GCGTAGGCA-CTGG---TATGGTTGTGAACGGC
droPer1	G-GA-----TC-GG---GTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTG--CTGTGGA--------------------------------GT-----TGGAGGTGTCGGCTGTTGATAACCCCC-A----------------------GCGTAGGCA-CTGG---TATGGTTGTCAACGGC
droWil1	GGATTGCAATT-GGTTGTGGGCTGTAACCTGATCTGG----------------AAG--CTATAG-----------------------ATGT------GATGATGCGGAGGTGTCGTCAGATGATAACCCCCCAG----GGTAGACAGCTTAGACATCGTAGGCA-TTGGC---CTGGTTGTCAACGGC
droVir3	A--------TT-GGGCGTCTGCTGTAACTTGAAGC-----------------GCTGATCTG-------------------------------------------------------TGGTTGATAACCCCC-TGCCAAGGTG------------CTCGTAGGCAGCTACCGCTCCGGTTGTCAACGGC

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																			None	None
UNAFold Image																			None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

A-TT----TC-GT---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGCTGTGGGCTGTGGGCTGTAAGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................................................GTGGGCTGGGGGCTGGGGGC............................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
......................................................G--CTGTTGGCTGTTGGCTG.................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...............................................................GCTGTTGGCTGTTGGCTG..........................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droSec1

A-TT----TC-GT---TCGGCTGTAACCTGATCC-----------------GCTG--CTGCGGGTTGTGGGCTGTG-------AGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................................TGCGGGTTGTGGGCTGTG-------AGG.....................................................................................................	21	1	5.00	1.00	2.00	2.00
..........................................................TGCGGGTTGTGGGCTGTG-------AGGCT...................................................................................................	23	1	5.00	2.00	1.00	2.00
..........................................................TGCGGGTTGTGGGCTGTG-------AGGC....................................................................................................	22	1	3.00	1.00	1.00	1.00
..........................................................TTCGGGTTGTGGGCTGTG-------AGG.....................................................................................................	21	1	1.00	0.00	0.00	1.00
...............................................................................................................CCGCCAGTTGATAACCCCC-A----------------------GC...............................	22	1	1.00	0.00	1.00	0.00
..........................................................TGCGGGTTGTGGGCTGTG-------........................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

A-TT----CC-GC---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGATGTGGGATGTG--------GGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................CTGxGCGATGTGGGATG.................................................................................................................	16	1	2.00	0.00	0.00	0.00	2.00	0.00
..........................................................TGTGGGATGGGGGATCT................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................GTGGGAGGTGGGAGGTG--------GG.....................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................TGGGAGGTGGGAGGTG--------GG.....................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................GTGGGATGTG--------GGxGGT------GG-----T...................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

A-TT-CCATC-AT---TCGGCTGTAACCTGATCC-----------------CCTG--CTGTGGG----------------------CTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-AGCA-----------------CAGCGTGGGCA-CGG-CCCACTGGTCGTCAACCGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................................................CCTG--CxGTGGG----------------------CTGT------AG-----TA..................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
A-TT-CCATC-AT---CAGGCTGT...................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

T-------TT-GA---TCGGCTGTAACCTGATCT-----------------ACAT--CTG-----------------------------C------GG-----TAAAGGTG---CCAATTGATAACC--C-A----------------------GCGTGGGCA-CTG-CTAACTGGTCGTCAACGGC

Size

Hit Count

Total Norm

droBia1

T-------TC-GA---TCGTCTGTAACCTGATCC-----------------AAGG--CTG-----------------------------C------GT-----TATAGGTGTCGCCGGTTGATAACCCCC-A----------------------GCGTGGGCA-CGG-CTCACTAGTCGTCAACAGC

Size

Hit Count

Total Norm

droTak1

--------TC-GA---TCGGCTGTAACCTGATCC-----------------GCGG--CTG-----------------------------C------GG-----TATAGGTGTCGCCAGTTGATAACCCTC-A----------------------GCGTGGGCA-CGG-CCCACTAGTCGTCAACGGC

Size

Hit Count

Total Norm

droEle1

--------TC-GA---TCTGCTGTAACCTAATCCGA--TCG----------GCTG--CTGTGGTATATGTA--------------------------------CATAGGTGCCGCCAGTTGATAACCC-C-A----------------------GTGTAGGCA-CGG-CCCACTGGCTGTCAACGGC

Size

Hit Count

Total Norm

droRho1

--------TC-GA---TCTGCTGTAACCTGATCT-----------------GCTG--CTG-----------------------------T------GG-----TATAGGTGCCGCAAGTTGATAACCCCA--------------------------GTGGGCA-CGG--------------------

Size

Hit Count

Total Norm

droFic1

A-------TC---------GATGTAACCTGATCG-----------------GCGG--CTG-----------------------------T------GG-----TCTAGGTGGATTCAGTTGATAACCCTC-A----------------------GCGTGGGCT-CAG-CCTACTGGTTGTCAACGGC

Size

Hit Count

Total Norm

droKik1

G-ATTGGATCGGA---TTGGCTGTAACCTGAACC-----------------GCGG--CTGTG-------------------------------------------------------GTTGATAACCCCC-A----------------------ACGTGGGCT-GCGGCCCACTGGTTGTCAACGGC

Size

Hit Count

Total Norm

droAna3

C-ATCCGATCTGA---TTGGCAGTAACCTGATCC-----------------GCGG--TTGTGG-----------------------TTGT------GG-----TGGAGGT---GCTACTTGATAACCCAC-T----------------------GCGTGGGCA-CTGGCCTTTCGGTTGTCAACGGC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................GTGG-----------------------TGGT------GG-----TGGAGGC---G.........................................................................	18	2	1.50	0.00	1.50	0.00	0.00
......................................................G--TGGTGG-----------------------TGGT------GG-----TGGAGGT---G.........................................................................	21	2	1.00	0.00	1.00	0.00	0.00
....................................................CGG--GTGTGG-----------------------TTGT------GG-----TGGTGG..............................................................................	21	1	1.00	0.00	1.00	0.00	0.00
..........................................................AGTGG-----------------------TGGT------GG-----TGGAG...............................................................................	16	2	0.50	0.00	0.00	0.50	0.00
...........................................................GTGG-----------------------TGGT------GG-----TGGTGGT---G.........................................................................	18	14	0.07	0.00	0.07	0.00	0.00
.....................................................GG--TGGTGG-----------------------TTGT------GG-----TGGT................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
......................................................G--TGGTGG-----------------------TGGT------GG-----TGGAG...............................................................................	18	5	0.20	0.00	0.20	0.00	0.00
.......................................................................................GGT------GG-----TGGAGCT---GCTACT....................................................................	18	4	0.25	0.00	0.25	0.00	0.00
.....................................................GG--TGGTGG-----------------------TGGT------GG-----TGGA................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
.....................................................GG--TGGTGG-----------------------TGGT------GG-----TGGAGG..............................................................................	20	3	0.33	0.00	0.33	0.00	0.00
......................................................G--TTGTGG-----------------------TGGT------GG-----TGGTGGT---..........................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.........................................................TGGTGG-----------------------TGGT------GG-----TGGAGGT---..........................................................................	19	2	0.50	0.00	0.50	0.00	0.00
...................................................GCGG--GTGTGG-----------------------TTGT------GG-----TGGTG...............................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................TTGGGG-----------------------TTGT------GG-----GGGAG...............................................................................	17	1	1.00	0.00	0.00	1.00	0.00
......................................................G--TTGTGG-----------------------TGGT------GG-----TGGAA...............................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droBip1

G-AT----CT-GA---TTGGCAGTAACCTGATCC-----------------GCGG--TTGTGG-----------------------TTGT------GC-----TGGAGGT---GCTACTTGATAACCCAC-T----------------------GCGTGGGCA-CTGGCCTTTCGGTTGTCAACGGC

Size

Hit Count

Total Norm

dp4

G-GA----TC-GG---GTGGCTGTAACCTGATCTGGGAGCGGTGCAGC---AGGG--CTG-----------------------------CGGTGGAGT-----TGGAGGTGTCGGCTGTTGATAACCCCC-A----------------------GCGTAGGCA-CTGG---TATGGTTGTGAACGGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.....................................................AT--CTG-----------------------------CGGTGGAGT-----TGGAG...............................................................................	19	1	8.00	8.00	0.00	0.00	0.00
..........................................................TG-----------------------------CGGTGGAGT-----TGGAGCG.............................................................................	18	1	1.00	1.00	0.00	0.00	0.00
..........................................................TG-----------------------------CGGTGGAGT-----TGGAGTTT............................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.................................TGGGAGTGGTGCGGC---AGGG--..................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................................CTG-----------------------------CGGTGGAGT-----TGGAGTTT............................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

G-GA----TC-GG---GTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTG--CTGTGGA--------------------------------GT-----TGGAGGTGTCGGCTGTTGATAACCCCC-A----------------------GCGTAGGCA-CTGG---TATGGTTGTCAACGGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................G--CTGTGGA--------------------------------GT-----TxGCGGTGTC..........................................................................	19	1	2.00	2.00	0.00	0.00	0.00	0.00
...................................AGTGCxGTGCAGCAGGGCTG--C.................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................GGCTG--CTGTGGA--------------------------------TC-----TGGA................................................................................	18	3	0.33	0.00	0.00	0.00	0.00	0.33
.................................................................................................................................................................CA-CTGG---TATGGTTGTCAACGG.	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.................................TGGGAGTGGTGCGGCAGGG.......................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

GGATTGCAATTGGTTGTGGGCTGTAACCTGATCTGG----------------AAG--CTATAG-----------------------ATGT------GATGATGCGGAGGTGTCGTCAGATGATAACCCCCCAG----GGTAGACAGCTTAGACATCGTAGGCA-TTGGC---CTGGTTGTCAACGGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................TATAG-----------------------ATGA------GATGATGTGG.................................................................................	19	1	7.00	0.00	7.00	0.00	0.00
...TTGCTATTGGTTGGGGGCTG....................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...........................................................ATAG-----------------------ATGA------GATGATGTGG.................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................TTC---CTGGTTGTCAACGGC	18	1	1.00	0.00	0.00	0.00	1.00
..........................................................TATAG-----------------------ATGA------GATGATGTG..................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......ATATGGTTGTGGGCTGTA..................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.......AATTGGTTGAGGGTTGTA..................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...TTGCTATTGGTTGGGGGCT.....................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droVir3

A-TT-------GGGCGTCTGCTGTAACTTGAAGC-----------------GCTGATCTG-------------------------------------------------------TGGTTGATAACCCCC-TGCCAAGGTG------------CTCGTAGGCAGCTACCGCTCCGGTTGTCAACGGC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTAG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:31:05 EDT

dme-mir-966

chr2L:6045627-6045713 -

Known_mirbase

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