dme-mir-4970- Best orthologs

dme-mir-4970	chr2L:10741884-10741987 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 10741905-10741926
   star strand at position 10741949-10741970
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:10741869-10742002 +		1	CATGTTTAGATCGGA-----CCCAAAGGTGGGCGACAAG---GGCTGGGAGCAGCAGTTGCTGGCGGTATTC---TGAAGCTGCTCTTCCGTGGGTTGCTCTT---------------------------GCTCCTG----------------------------ACCCTCCTCT---TCCTCCGCTTC------ATCCTCC--------------TCCGCAT
droSim1	chr2L:10541288-10541421 +	LASTZ	4	CATGTTTAGATCTGA-----CCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTC---TGAAGTTTCTTTTTCGTGGGCAGCTCTC---------------------------GCTCCTG----------------------------ACCCTCCTCT---TCCTCCGCTTC------GTCTTCC--------------CCCGCAT
droSec1	super_3:6159513-6159646 +	LASTZ	1	CATGTTTAGATCGGA-----CCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTC---TGAAGTTGCTTTTTCGTGGGCAGCTCTC---------------------------GCTCCTG----------------------------ACCCTCCTCT---TCCTCCGCTTC------GTCTTCC--------------CCCGCAT
droYak2	chr2L:7146365-7146495 +	LASTZ	1	CATGTTCAAATCGGA-----GCCAAAGGTGGGCGAGAGG---GGCTGTGAGCAGCCGTTGCTGGCGGTGTTC---TGTCTCTGCTCCTCCGCCGGCTGCTGTT---------------------------GCTCCTG----------------------------ACCCTCCTCG---TCCTC---CGC------GTCTTCC--------------TCGCCGT
droEre2	scaffold_4929:14689286-14689416 -	LASTZ	4	CATGTTCAAATCGGA-----CCCAAAGGTAGGTGAGAGG---GGCTGGGAGCAGCCGTTGCTGGCGGTATTC---TGCCTCTGCTCCTCCACCGGCTGCTGTT---------------------------GTTCCTG----------------------------AACCACCTCG---TCCT---CTGG------TTCGTCA--------------TCGCCTT
droEug1	scf7180000409554:3760859-3760992 +	LASTZ	5	CATGTTTAAATCGGA-----ACCAAATGTTGGTGAAAGA---GGCTGGGAGCAGCCGTTGCTTGCGTTATTC---TGCTGCTGCTCCTCCACTGGCTGCTGTT---------------------------TCTCCTG----------------------------ACCTTCCTCC---TCATCATCTTG------GTCTTCA--------------TCAACAT
droBia1	scf7180000302422:2382746-2382879 -	LASTZ	5	CATGTTTAGGTCGGA-----TCCATAGGTGGGAGAAAGG---GGCTGGGAACAGTTGTTGCTGGCGAAGTTT---TGCGGCTGCTCTTCCACCGGCTGCTGTT---------------------------GCTCTTG----------------------------ACCTTCTTCC---TCATCCTCCAG------GCCCTCG--------------GGGCCTT
droTak1	scf7180000415385:189147-189283 +	LASTZ	5	CATGTTCAAATCGGA-----GCCAAAGGTGGGCGAAAGC---GGCTGGGAACAGCCGTTGCTGGCGGAATCC---TTGCCCTGCTCCTCCGCCGGCTGCTGTTCCG------------------------CCTCCTG----------------------------ACCCTCCTCC---TCCTCCTCGAG------GTCCTCG--------------CCGCCGT
droEle1	scf7180000490971:131834-131988 -	LASTZ	5	CATGTTTAGATCTGA-----GCCAAAGGTGGGTGAAAGT---GGCTGGGAGCAGCCGTTGTTGGCGGAATTC---GGCTGCTCCTCCTCCGCCGGCGGCTGTG---------------------------GCTCCTGCCCTTCCTCCT-C---------CTCCAAA------------TCCTCCTCTTCCGGCTCCT-----CTTCAT-C--CTCCTCCTCGC
droRho1	scf7180000780267:27189-27328 +	LASTZ	5	CATGTTAAGGTCCGA-----GCCAAAAGTGGGTGAAAGT---GGCTGCGAGCAGCCGTTGTTGGCCGAATTCGGCTGCTGCTCCTCCTCCGCCGGCTGCTGTG---------------------------GCTCCTG----------------------------GCCTTCTTCCTCATCATTAGGCTC------CCCCTCC--------------TCTTCGT
droFic1	scf7180000454111:160465-160601 +	LASTZ	5	CATGTTGAGATCCGA-----ACCGAAGGTGGGCGAAAGC---GGCTGGGAGCATCCGTTGCTGGGGGAGTTC---TGCTGCTCCTTCTCCGTCGGCTGCTGTG---------------------------GCTCCTG----------------------------GCCTTCCTCCTCCTCGTCCTCCGC------CTCCTCC--------------TCTTCAT
droKik1	scf7180000302472:2579939-2580081 -	LASTZ	0	CATGTTTAGATCGGA-----ACCAAAGGTGGGCGACAGG---TTCTGCCCGCAGTCGGAGGCC---------------TCTTTCTCCTCCTCTGGCTTCTCAG---------------------AGTCTTCCTCCTG------ATTAT-------------------CCTCCACC---TCATCACCCTCTGCCTCAG-----GATCTT-C--CACTTCATCCT
droAna3	scaffold_13117:2651271-2651404 -	LASTZ	0	CAGCATTAGGGCGATCCTCCGCCAGTGGTTGATCGAA-G---GCATGGGATCCACCC----CAGCGTCTATC---TGAAAACGATGTTTATCCACCTGCTCCT---------------------------GCTCCTG----------------------------CTCCTCATCC---TCCTTCCCTTC------GTCTTCG--------------TCATCAT
droBip1	scf7180000396572:2390673-2390782 -	LASTZ	0	CATGTTCAGGTCGGA-----GCCAAAAGTGGGTGAAAGC---TGTTGCGAGCAATTATCTCCCTCTAC---------------------------TACATCCT---------------------------TCTCCTC----------------------------AGTATCCTCA---TCGTCCTCCAC------ATCTTCA--------------TTCTCTT
dp4	chr3:14693225-14693346 -	LASTZ	0	CATGTTCAGATCCGA-----TCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATG---TGCTGCTCCTCCCGC---------TCT----------------------------------------------CCCGTTGGCAGTTCCTCA---------------TCCTCCTC------GTCCGGG--------------TCTAGTT
droPer1	super_4:2921871-2921992 +	LASTZ	0	CATGTTCAGATCCGA-----TCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATG---TGCTGCTCCTCCCGC---------TCT----------------------------------------------CCCGTTGGCAGTTCCTCA---------------TCCTCCTC------GTCCGGG--------------TCTAGTT
droWil1	scaffold_180708:9012130-9012236 -	LASTZ	0	CATGTTTAAATCTGA-----ACCAAATGTGGCCGACAAT---GGTTGAGAGCAGCCATTTGTTAG------------------------------TTGTTCAT---------------------------CCTCTTC----------------------------ACAGGCTCCA---GCAGCTTGCTC------ACCCCCC--------------TCAGCGT
droVir3	scaffold_12963:15905405-15905563 -	LASTZ	0	CATGTTTAAATCGGA-----GCCATAGGTAGCCGACAATGCCGGCTGCGAGCAGCCATTGCTTAGGGTTATC---TGCGGCTTCTGTGGT------GCCTGTTCCGTTGCGTTAATCGGCTGGGAGT---AGAGCTC----------------------------ACCGGCGGCC---------TCCAG------ATCGCTG----TCGCCTCCTGTCGCGAT
droMoj3	scaffold_6500:3051871-3052002 +	LASTZ	0	CGTGCGTAGCT---G-----CTCGTGGCTGGGTGGCGTG---GCATTGTAGAGT-CTCAGC--------TGCTGCTGCTGCTGCTGCTCAGACTCCTGCTCTT---------------------------GCTCATG----------------------------CCCCTCCAGC---TCCTCCTCTTCAGCCTCGCTGTC-------------GCTCAGCGG
droGri2	scaffold_15252:8305990-8306138 -	LASTZ	0	CATGTTCAAATCGGA-----GCCATAGGTGGCCGACATG---GGTTGTGACCACTCATTGGCCGATGCTTGC---GGT---TCCTTCT---CGGGTTCCGGTTCCGCTTCGGTCGCTGGCTGGG------AATAGGG----------------------------TTCCTCAGCT---GCATTCGCTTC------CTGATCG--------------CTGTCCT

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	CATGTTTAGATCGGACCCAAAGGTGGGCGACAAGGGCTGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGCTGC---TCTTCCGTGGGTTGCTCTT---GCTCCTGACCCTCCTCTTCC---TCCGC------------TTC---------ATCCTCCTCCGCAT
droSim1	CATGTTTAGATCTGACCCAAAGGTGGGCGACAAGGGATGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGTTTC---TTTTTCGTGGGCAGCTCTC---GCTCCTGACCCTCCTCTTCC---TCCGC------------TTC---------GTCTTCCCCCGCAT
droSec1	CATGTTTAGATCGGACCCAAAGGTGGGCGACAAGGGATGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGTTGC---TTTTTCGTGGGCAGCTCTC---GCTCCTGACCCTCCTCTTCC---TCCGC------------TTC---------GTCTTCCCCCGCAT
droYak2	CATGTTCAAATCGGAGCCAAAGGTGGGCGAGAGGGGCTGTGAGCAGCCGTTGCTGGCGGTGTTCTGTCTCTGC---TCCTCCGCCGGCTGCTGTT---GCTCCTGACCCTCCTCGTCC---TCCGC------------------------GTCTTCCTCGCCGT
droEre2	CATGTTCAAATCGGACCCAAAGGTAGGTGAGAGGGGCTGGGAGCAGCCGTTGCTGGCGGTATTCTGCCTCTGC---TCCTCCACCGGCTGCTGTT---GTTCCTGAACCACCTCGTCC---TCTGG------------------------TTCGTCATCGCCTT
droEug1	CATGTTTAAATCGGAACCAAATGTTGGTGAAAGAGGCTGGGAGCAGCCGTTGCTTGCGTTATTCTGCTGCTGC---TCCTCCACTGGCTGCTGTT---TCTCCTGACCTTCCTCCTCA---TCATC------------TTG---------GTCTTCATCAACAT
droBia1	CATGTTTAGGTCGGATCCATAGGTGGGAGAAAGGGGCTGGGAACAGTTGTTGCTGGCGAAGTTTTGCGGCTGC---TCTTCCACCGGCTGCTGTT---GCTCTTGACCTTCTTCCTCA---TCCTC------------CAG---------GCCCTCGGGGCCTT
droTak1	CATGTTCAAATCGGAGCCAAAGGTGGGCGAAAGCGGCTGGGAACAGCCGTTGCTGGCGGAATCCTTGCCCTGC---TCCTCCGCCGGCTGCTGTTCCGCCTCCTGACCCTCCTCCTCC---TCCTC------------GAG---------GTCCTCGCCGCCGT
droEle1	CATGTTTAGATCTGAGCCAAAGGTGGGTGAAAGTGGCTGGGAGCAGCCGTTGTTGGCGGAATTCGGCTGCTCC---TCCTCCGCCGGCGGCTGTG---GCTCCTGCCCTTCCTCCTCC---TCCAAATCCTCCTCTTCCGGCTCCTCTTCATCCTCCTCCTCGC
droRho1	CATGTTAAGGTCCGAGCCAAAAGTGGGTGAAAGTGGCTGCGAGCAGCCGTTGTTGGCCGAATTCGGCTGCTGCTCCTCCTCCGCCGGCTGCTGTG---GCTCCTGGCCTTCTTCCTCATCATTAGG------------CTC---------CCCCTCCTCTTCGT
droFic1	CATGTTGAGATCCGAACCGAAGGTGGGCGAAAGCGGCTGGGAGCATCCGTTGCTGGGGGAGTTCTGCTGCTCC---TTCTCCGTCGGCTGCTGTG---GCTCCTGGCCTTCCTCCTCCTCGTCCTC------------CGC---------CTCCTCCTCTTCAT

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

CATGTTTAGATCTGA-----CCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTC---TGAAGTTTCTTTTTCGTGGGCAGCTCTC---------------------------GCTCCTG----------------------------ACCCTCCTCT---TCCTCCGCTTC------GTCTTCC--------------CCCGCAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................................................CAGCTCTA---------------------------GATCCTG----------------------------ACC.......................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

CATGTTTAGATCGGA-----CCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTC---TGAAGTTGCTTTTTCGTGGGCAGCTCTC---------------------------GCTCCTG----------------------------ACCCTCCTCT---TCCTCCGCTTC------GTCTTCC--------------CCCGCAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................................GATGGGAGCAGCAGTTGCTGG...............................................................................................................................................................	21	1	1.00	0.00	1.00	0.00
....................................................AGCAxTTGCTGGCGGTATG........................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

CATGTTCAAATCGGA-----GCCAAAGGTGGGCGAGAGG---GGCTGTGAGCAGCCGTTGCTGGCGGTGTTC---TGTCTCTGCTCCTCCGCCGGCTGCTGTT---------------------------GCTCCTG----------------------------ACCCTCCTCG---TCCTC---CGC------GTCTTCC--------------TCGCCGT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.............................................TGTGAGCAGCCGTTGCTGGCG.............................................................................................................................................................	21	1	18.00	3.00	8.00	0.00	7.00	0.00
.............................................TGTGAGCAGCCGTTGCTGGCGG............................................................................................................................................................	22	1	11.00	7.00	1.00	0.00	3.00	0.00
.............................................TGTGAGCAGCCGTTGCTGGCGGT...........................................................................................................................................................	23	1	3.00	1.00	1.00	0.00	1.00	0.00
.............................................TGTGAGCAGCCGTTGCTGGCGGC...........................................................................................................................................................	23	1	2.00	0.00	1.00	0.00	1.00	0.00
..............................................GTGAxCAACCGTTGCTGGC..............................................................................................................................................................	18	1	2.00	0.00	1.00	0.00	0.00	1.00
.............................................TGTGAGCAGCCGTTGCTGGCGGTT..........................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................CTCCTTCTCCGCCGGCTG.............................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................CTGTGAGCAGCCGTTGCTGGCG.............................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................TGGGAGCAGCCGTTGCTGGTGGT...........................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................TGTGAGCAGCCGTTGCTGGCGGG...........................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................TGTGAGCAGCCGTTGATGGCGGG...........................................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................................CCGGCTGCTGTT---------------------------TCTCCTG----------------------------ACCC......................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................AGGTGGGCTGGAGG---GGCT.................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................TGTGAxCAACCGTTGCTGGC..............................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................AAGGGTGGGCGAGAGG---GGC..................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

CATGTTCAAATCGGA-----CCCAAAGGTAGGTGAGAGG---GGCTGGGAGCAGCCGTTGCTGGCGGTATTC---TGCCTCTGCTCCTCCACCGGCTGCTGTT---------------------------GTTCCTG----------------------------AACCACCTCG---TCCT---CTGG------TTCGTCA--------------TCGCCTT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................................................ATGTTGGCGGTATTC---TGC.................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

CATGTTTAAATCGGA-----ACCAAATGTTGGTGAAAGA---GGCTGGGAGCAGCCGTTGCTTGCGTTATTC---TGCTGCTGCTCCTCCACTGGCTGCTGTT---------------------------TCTCCTG----------------------------ACCTTCCTCC---TCATCATCTTG------GTCTTCA--------------TCAACAT

Size

Hit Count

Total Norm

droBia1

CATGTTTAGGTCGGA-----TCCATAGGTGGGAGAAAGG---GGCTGGGAACAGTTGTTGCTGGCGAAGTTT---TGCGGCTGCTCTTCCACCGGCTGCTGTT---------------------------GCTCTTG----------------------------ACCTTCTTCC---TCATCCTCCAG------GCCCTCG--------------GGGCCTT

Size

Hit Count

Total Norm

droTak1

CATGTTCAAATCGGA-----GCCAAAGGTGGGCGAAAGC---GGCTGGGAACAGCCGTTGCTGGCGGAATCC---TTGCCCTGCTCCTCCGCCGGCTGCTGTTCCG------------------------CCTCCTG----------------------------ACCCTCCTCC---TCCTCCTCGAG------GTCCTCG--------------CCGCCGT

Size

Hit Count

Total Norm

droEle1

CATGTTTAGATCTGA-----GCCAAAGGTGGGTGAAAGT---GGCTGGGAGCAGCCGTTGTTGGCGGAATTC---GGCTGCTCCTCCTCCGCCGGCGGCTGTG---------------------------GCTCCTGCCCTTCCTCCT-C---------CTCCAAA------------TCCTCCTCTTCCGGCTCCT-----CTTCAT-C--CTCCTCCTCGC

Size

Hit Count

Total Norm

droRho1

CATGTTAAGGTCCGA-----GCCAAAAGTGGGTGAAAGT---GGCTGCGAGCAGCCGTTGTTGGCCGAATTCGGCTGCTGCTCCTCCTCCGCCGGCTGCTGTG---------------------------GCTCCTG----------------------------GCCTTCTTCCTCATCATTAGGCTC------CCCCTCC--------------TCTTCGT

Size

Hit Count

Total Norm

droFic1

CATGTTGAGATCCGA-----ACCGAAGGTGGGCGAAAGC---GGCTGGGAGCATCCGTTGCTGGGGGAGTTC---TGCTGCTCCTTCTCCGTCGGCTGCTGTG---------------------------GCTCCTG----------------------------GCCTTCCTCCTCCTCGTCCTCCGC------CTCCTCC--------------TCTTCAT

Size

Hit Count

Total Norm

droKik1

CATGTTTAGATCGGA-----ACCAAAGGTGGGCGACAGG---TTCTGCCCGCAGTCGGAGGCC---------------TCTTTCTCCTCCTCTGGCTTCTCAG---------------------AGTCTTCCTCCTG------ATTAT-------------------CCTCCACC---TCATCACCCTCTGCCTCAG-----GATCTT-C--CACTTCATCCT

Size

Hit Count

Total Norm

droAna3

CAGCATTAGGGCGATCCTCCGCCAGTGGTTGATCGAA-G---GCATGGGATCCACCC----CAGCGTCTATC---TGAAAACGATGTTTATCCACCTGCTCCT---------------------------GCTCCTG----------------------------CTCCTCATCC---TCCTTCCCTTC------GTCTTCG--------------TCATCAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................GAA-G---GCATGGGATCAACGC----..................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................................................GCTCCTC----------------------------CTCCTCCTCC---TCC..........................................	20	21	0.05	0.00	0.00	0.00	0.05

droBip1

CATGTTCAGGTCGGA-----GCCAAAAGTGGGTGAAAGC---TGTTGCGAGCAATTATCTCCCTCTAC---------------------------TACATCCT---------------------------TCTCCTC----------------------------AGTATCCTCA---TCGTCCTCCAC------ATCTTCA--------------TTCTCTT

Size

Hit Count

Total Norm

dp4

CATGTTCAGATCCGA-----TCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATG---TGCTGCTCCTCCCGC---------TCT----------------------------------------------CCCGTTGGCAGTTCCTCA---------------TCCTCCTC------GTCCGGG--------------TCTAGTT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...............................................................................................................................................................CTCGTCA---------------TCCTCCTC------GTCCG.......................	20	2	0.50	0.50	0.00	0.00	0.00

droPer1

CATGTTCAGATCCGA-----TCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATG---TGCTGCTCCTCCCGC---------TCT----------------------------------------------CCCGTTGGCAGTTCCTCA---------------TCCTCCTC------GTCCGGG--------------TCTAGTT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................................................................................................................................GTTCCTGA---------------TCCTCTTC------GTC.........................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

CATGTTTAAATCTGA-----ACCAAATGTGGCCGACAAT---GGTTGAGAGCAGCCATTTGTTAG------------------------------TTGTTCAT---------------------------CCTCTTC----------------------------ACAGGCTCCA---GCAGCTTGCTC------ACCCCCC--------------TCAGCGT

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CATGTTTAAATCGGA-----GCCATAGGTAGCCGACAATGCCGGCTGCGAGCAGCCATTGCTTAGGGTTATC---TGCGGCTTCTGTGGT------GCCTGTTCCGTTGCGTTAATCGGCTGGGAGT---AGAGCTC----------------------------ACCGGCGGCC---------TCCAG------ATCGCTG----TCGCCTCCTGTCGCGAT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.............................................................................................................CGTTAAACGGCxGGGAGT---A............................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................................................................CGGCTGAGAGG---AGAGCTC----------------------------..........................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
............................................................................................................GCGTTAAACGGCxGGGAGT---.............................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
............................TAGGCGACAATGCCGGCTTC...............................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................CTC----------------------------GCCGGxGGCC---------TCCA...................................	16	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

CGTGCGTAGCT---G-----CTCGTGGCTGGGTGGCGTG---GCATTGTAGAGT-CTCAGC--------TGCTGCTGCTGCTGCTGCTCAGACTCCTGCTCTT---------------------------GCTCATG----------------------------CCCCTCCAGC---TCCTCCTCTTCAGCCTCGCTGTC-------------GCTCAGCGG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....................................................................TGCTGCTACTGCTGCTGCTCGGA...................................................................................................................................	23	10	0.10	0.00	0.00	0.10	0.00
.......................................................CTCAGT--------TGCTGCTGCCGCT.............................................................................................................................................	19	20	0.05	0.00	0.05	0.00	0.00

droGri2

CATGTTCAAATCGGA-----GCCATAGGTGGCCGACATG---GGTTGTGACCACTCATTGGCCGATGCTTGC---GGT---TCCTTCT---CGGGTTCCGGTTCCGCTTCGGTCGCTGGCTGGG------AATAGGG----------------------------TTCCTCAGCT---GCATTCGCTTC------CTGATCG--------------CTGTCCT	Size	Hit Count	Total Norm	V109 Male body
...................................................................................................................CTGGxxGTA------AATAGGG----------------------------TTCCT.....................................................	19	1	21.00	21.00
...................................................................................................................CTGGxxGTG------AATAGGG----------------------------TTCCT.....................................................	19	1	2.00	2.00
...................................................................................................................CTGGxxGTC------AATAGGG----------------------------TTCCT.....................................................	19	1	1.00	1.00
...................................................................................................................CTGGxxGTA------AATAGGG----------------------------TTCC......................................................	18	1	1.00	1.00

Generated: 04/20/2012 at 05:33:32 EDT

dme-mir-4970

chr2L:10741884-10741987 +

Known_mirbase

intergenic

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