dme-mir-287- Best orthologs

dme-mir-287	chr2L:17574610-17574702 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 17574674-17574694
   mutations
   read mismatches

Notes: droBia1 folds better without the flanking regions

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:17574595-17574717 +		1	AA-GCC--------CAC---------TCAC-----------------AGAGGACGCCGGG--GATGTATGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droSim1	chr2L:17277816-17277938 +	LASTZ	5	AA-GCT--------CAC---------TCAC-----------------AGAGGACGCCGTG--GATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droSec1	super_7:1215433-1215555 +	LASTZ	5	AA-GCT--------CAC---------TCAC-----------------AGAGGACGCCGTG--GATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droYak2	chr2R:3525115-3525236 -	LASTZ	5	AC-A--------T----ATATACAC---AC-----------------AGAGCAAGCCGTG--GATGTATGGGTGT---GGGTCTGAAATTTTGCACACATTTACAGTAATTGTAAATGTGTTGAAAATCGTTTGCATG-ACTGTGAGCAA--AACAC---T-TCGGA
droEre2	scaffold_4845:6676077-6676186 -	LASTZ	5	GT-GTG-------------------------------------------GA--CGC--TG--GATGTATGGGTGTGTGGGCTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGCGAGCAA--AACAC---G-TCGGA
droEug1	scf7180000409016:198057-198168 +	LASTZ	5	AATA--------------------------------A----------AGTG--CTC--TA--GATGTATGGGTGTATAGGGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGT
droBia1	scf7180000302422:6132274-6132381 -	LASTZ	5	CG----------------------------------------------GGG--CGC--TG--GTTGTGTGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droTak1	scf7180000415617:9738-9849 -	LASTZ	5	CA-C----------------------T--------------------GGGG--CGC--TG--GTTGTATGGGTGTGTGGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droEle1	scf7180000491046:278921-279029 +	LASTZ	5	GC-A--------C----------------------------------GGGG--CAC--TG--GGTGTATGGGT--GTAAGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droRho1	scf7180000777709:31207-31296 +	LASTZ	5	G---------------------------------------------------------------------GTT--GTAAGGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGCTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droFic1	scf7180000453855:358907-359016 +	LASTZ	5	AC-A--------C----------------------------------TGGG--CGC--TG--GGTGTATGGGT--GTAAGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCCGA
droKik1	scf7180000302246:110146-110268 -	LASTZ	5	AG-GAC--------GAC---------GACA-ACG--A----------AGGC--CAG--TGCGTTTGTGTGGGT--GTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--GACAT---G-TCGGA
droAna3	scaffold_12916:3302442-3302546 -	LASTZ	5	AT-A--------------------------------------------GG----GC--TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGA
droBip1	scf7180000396737:1470812-1470916 +	LASTZ	5	AT-A--------------------------------------------GG----GC--TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGA
dp4	chr4_group3:10858860-10858990 -	LASTZ	5	AC-A--------C----ACACACATA----------AATATATTCACGGAGACAGTC--T--TATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droPer1	super_8:2069946-2070076 -	LASTZ	5	AC-A--------C----ACACACATA----------AATATATTCACGGAG--ACC--TGCTTATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droWil1	scaffold_180764:928810-928950 -	LASTZ	5	AC-T--------CCCAC---------ATACATTGGAAAGAGCTTCTCCGTAATATG--TA--TATGTATTGCT--GTAAAGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACAAACTGTGAGCAA--AATCCTGTAGCTGGG
droVir3	scaffold_12963:16502531-16502646 +	LASTZ	5	AG-ATT--------GAC---------TCCC-----------------ACGCTTTCGCACA--CACACAAACGTGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA-------------CCGA
droMoj3	scaffold_6500:21428983-21429089 +	LASTZ	5	AC-T--------CCCAC---------GCAC---------------------------------ACACACACGCGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--CCAAC---A---GCA
droGri2	scaffold_15252:13917089-13917209 +	LASTZ	5	CA-GTTTTCACTCCCAC---------ACA-----------------------------CT--CACACACACATGCATAATGCTTGAAATTTTGCACACATTTACAATATTTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAAGCAACAC---A-CATGT

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	AA-GCC--------CAC---------TCAC-----------------AGAGGACGCCGGG--GATGTATGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droSim1	AA-GCT--------CAC---------TCAC-----------------AGAGGACGCCGTG--GATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droSec1	AA-GCT--------CAC---------TCAC-----------------AGAGGACGCCGTG--GATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droYak2	AC-A--------T----ATATACAC---AC-----------------AGAGCAAGCCGTG--GATGTATGGGTGT---GGGTCTGAAATTTTGCACACATTTACAGTAATTGTAAATGTGTTGAAAATCGTTTGCATG-ACTGTGAGCAA--AACAC---T-TCGGA
droEre2	GT-GTG-------------------------------------------GA--CGC--TG--GATGTATGGGTGTGTGGGCTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGCGAGCAA--AACAC---G-TCGGA
droEug1	AATA--------------------------------A----------AGTG--CTC--TA--GATGTATGGGTGTATAGGGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGT
droBia1	CG----------------------------------------------GGG--CGC--TG--GTTGTGTGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droTak1	CA-C----------------------T--------------------GGGG--CGC--TG--GTTGTATGGGTGTGTGGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droEle1	GC-A--------C----------------------------------GGGG--CAC--TG--GGTGTATGGGT--GTAAGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droRho1	G---------------------------------------------------------------------GTT--GTAAGGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGCTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droFic1	AC-A--------C----------------------------------TGGG--CGC--TG--GGTGTATGGGT--GTAAGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCCGA
droKik1	AG-GAC--------GAC---------GACA-ACG--A----------AGGC--CAG--TGCGTTTGTGTGGGT--GTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--GACAT---G-TCGGA
droAna3	AT-A--------------------------------------------GG----GC--TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGA
droBip1	AT-A--------------------------------------------GG----GC--TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGA
dp4	AC-A--------C----ACACACATA----------AATATATTCACGGAGACAGTC--T--TATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droPer1	AC-A--------C----ACACACATA----------AATATATTCACGGAG--ACC--TGCTTATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droWil1	AC-T--------CCCAC---------ATACATTGGAAAGAGCTTCTCCGTAATATG--TA--TATGTATTGCT--GTAAAGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACAAACTGTGAGCAA--AATCCTGTAGCTGGG
droVir3	AG-ATT--------GAC---------TCCC-----------------ACGCTTTCGCACA--CACACAAACGTGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA-------------CCGA
droMoj3	AC-T--------CCCAC---------GCAC---------------------------------ACACACACGCGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--CCAAC---A---GCA
droGri2	CA-GTTTTCACTCCCAC---------ACA-----------------------------CT--CACACACACATGCATAATGCTTGAAATTTTGCACACATTTACAATATTTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAAGCAACAC---A-CATGT

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

AA-GCT--------CAC---------TCAC-----------------AGAGGACGCCGTG--GATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................................................................................................TTTGAAAATGGTTTGCAC..............................	18	1	1.00	0.00	0.00	1.00	0.00
................................................................TGTATGTGTGTGTAGGTTC....................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................TGAAAATGGTTTGCACG-C...........................	18	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................................CAAAAATTGTACATGTGT..............................................	18	2	0.50	0.50	0.00	0.00	0.00

droSec1

AA-GCT--------CAC---------TCAC-----------------AGAGGACGCCGTG--GATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................................CAAAAATTGTACATGTGT..............................................	18	2	1.00	0.00	1.00	0.00
.........................................................GTG--TATGTGTGGGTGTGT..........................................................................................	18	1	1.00	0.00	1.00	0.00
.........................................................................................................................TGAAAATGGTTTGCACG-C...........................	18	1	1.00	0.00	1.00	0.00

droYak2

AC-A--------T----ATATACAC---AC-----------------AGAGCAAGCCGTG--GATGTATGGGTGT---GGGTCTGAAATTTTGCACACATTTACAGTAATTGTAAATGTGTTGAAAATCGTTTGCATG-ACTGTGAGCAA--AACAC---T-TCGGA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................TG--GGTGGATGGGTGT---GGG......................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................GTG--GGTGTGTGGGTGT---GGGT.....................................................................................	20	3	0.33	0.00	0.00	0.33	0.00	0.00

droEre2

GT-GTG-------------------------------------------GA--CGC--TG--GATGTATGGGTGTGTGGGCTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGCGAGCAA--AACAC---G-TCGGA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.................................................................................................TATTTACAACAATTGTAA....................................................	18	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................AAAATTGTACATGTGTTGA...........................................	19	1	1.00	1.00	0.00	0.00	0.00
.................................................GA--CGC--xG--GATGGATGGGTG.............................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................................CAAAAATTGTACATGTGT..............................................	18	1	1.00	1.00	0.00	0.00	0.00

droEug1

AATA--------------------------------A----------AGTG--CTC--TA--GATGTATGGGTGTATAGGGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGT

Size

Hit Count

Total Norm

droBia1

CG----------------------------------------------GGG--CGC--TG--GTTGTGTGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA

Size

Hit Count

Total Norm

droTak1

CA-C----------------------T--------------------GGGG--CGC--TG--GTTGTATGGGTGTGTGGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA

Size

Hit Count

Total Norm

droEle1

GC-A--------C----------------------------------GGGG--CAC--TG--GGTGTATGGGT--GTAAGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA

Size

Hit Count

Total Norm

droRho1

G---------------------------------------------------------------------GTT--GTAAGGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGCTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA

Size

Hit Count

Total Norm

droFic1

AC-A--------C----------------------------------TGGG--CGC--TG--GGTGTATGGGT--GTAAGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCCGA

Size

Hit Count

Total Norm

droKik1

AG-GAC--------GAC---------GACA-ACG--A----------AGGC--CAG--TGCGTTTGTGTGGGT--GTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--GACAT---G-TCGGA

Size

Hit Count

Total Norm

droAna3

AT-A--------------------------------------------GG----GC--TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..............................................................................................................TGAAAATGCGTTGAAAAT.......................................	18	2	0.50	0.00	0.00	0.00	0.50
.......................................................................................................................GTTGAAAATAGTATGCACA-............................	19	2	0.50	0.50	0.00	0.00	0.00
...........................................................................................................AAGTGTAAATxTGTTGAAAA........................................	19	2	0.50	0.00	0.50	0.00	0.00

droBip1

AT-A--------------------------------------------GG----GC--TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGA

Size

Hit Count

Total Norm

dp4

AC-A--------C----ACACACATA----------AATATATTCACGGAGACAGTC--T--TATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

AC-A--------C----ACACACATA----------AATATATTCACGGAG--ACC--TGCTTATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................................C--TGCTTGTGTGTGTGT--GTG.........................................................................................	19	8	0.25	0.00	0.00	0.00	0.00	0.25
.......................................................C--TGTGTATGTGTGAGT--GT..........................................................................................	18	7	0.14	0.14	0.00	0.00	0.00	0.00
.............................................................................................................GTGTAAATxTGTTGAAAAT.......................................	18	3	0.33	0.00	0.00	0.00	0.00	0.33

droWil1

AC-T--------CCCAC---------ATACATTGGAAAGAGCTTCTCCGTAATATG--TA--TATGTATTGCT--GTAAAGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACAAACTGTGAGCAA--AATCCTGTAGCTGGG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
....................................................................................................TTACAATTxTTGGAAATGTG...............................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................GATTGTAAATGTGTGGAA..........................................	18	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................ATAATCGTTTGCACAAAA..........................	18	1	1.00	0.00	1.00	0.00	0.00
.................................................................................TCTGATATTTTGCACACC....................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................................AATAATCGTTTGCACAAA...........................	18	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................AAAATGTGTTGATAATCGT....................................	19	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................ATTGTAAATGTATTGAAT.........................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

AG-ATT--------GAC---------TCCC-----------------ACGCTTTCGCACA--CACACAAACGTGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA-------------CCGA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
........................................................CACA--CACACAACCGGGCA...........................................................................................	18	2	0.50	0.00	0.00	0.00	0.00	0.50

droMoj3

AC-T--------CCCAC---------GCAC---------------------------------ACACACACGCGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--CCAAC---A---GCA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
............................................................................................................................................................C---A---ACA	20	3	0.33	0.00	0.00	0.33	0.00
...............AT---------ACAC---------------------------------ACACACACGCGC............................................................................................	18	29	0.03	0.03	0.00	0.00	0.00
.....................................................................................................................GTGTTGAAAATxGGTTGCAC..............................	19	2	0.50	0.00	0.50	0.00	0.00

droGri2

CA-GTTTTCACTCCCAC---------ACA-----------------------------CT--CACACACACATGCATAATGCTTGAAATTTTGCACACATTTACAATATTTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAAGCAACAC---A-CATGT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:20:55 EDT

dme-mir-287

chr2L:17574610-17574702 +

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