dme-mir-4987- Best orthologs

dme-mir-4987	chr2L:10840344-10840476 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 10840373-10840393
   star strand at position 10840425-10840447
   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:10840329-10840491 -		1	ATCAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAAAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-GT------
droSim1	chr2L:10648081-10648243 -	LASTZ	1	ATCAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-GT------
droSec1	super_3:6258415-6258577 -	LASTZ	1	ATCAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-GT------
droYak2	chr2L:7248063-7248225 -	LASTZ	1	AACAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAGAAGAAAATG-AT------
droEre2	scaffold_4929:14589948-14590110 +	LASTZ	1	ACCAGTCGTC---TGTTGGTGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-AT------
droEug1	scf7180000409554:3858304-3858465 -	LASTZ	4	--CAGTCGTC---CGTTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCAAGATTCTCACAGCAGAGCTCCAGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-AT------
droBia1	scf7180000302422:2276607-2276769 +	LASTZ	4	ACCAGTCGTC---CGTTGGCGGAGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTTTCGCAGCAGGGCTCCAGCTCGGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAAAAAATG-AT------
droTak1	scf7180000415385:307948-308110 -	LASTZ	4	ACCAGTCGTC---CGTTGGCGGAGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTTTCCCAGCAGGGCTCCAGCTCGGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAAAAAATG-AT------
droEle1	scf7180000490971:14087-14249 +	LASTZ	4	ACCAGTCGTC---CATTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCCGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAGATG-AT------
droRho1	scf7180000780178:25334-25496 -	LASTZ	4	ACCAGTCGTC---CATTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGAGCTCCAGCTCCGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAGGAAGATG-AT------
droFic1	scf7180000454111:287914-288076 -	LASTZ	4	ACCAGTCGTC---CGTTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCCCAGCAGGGCTCAAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATG-AT------
droKik1	scf7180000302472:2466198-2466360 +	LASTZ	4	ACCAATCGTC---CGTGGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCACAGCAGGGCTCAGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAAAAGAAGATG-AT------
droAna3	scaffold_12916:14695622-14695781 -	LASTZ	3	ACCAATCGTC---CGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAAAAGAAGAT----------
droBip1	scf7180000396572:2290367-2290527 +	LASTZ	4	ACCAGTCGTC---CGTGGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAAAAGAAGATG---------
dp4	chr4_group4:3045338-3045500 -	LASTZ	3	AACAATCGTC---TGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTG-AT------
droPer1	super_10:2060188-2060350 -	LASTZ	3	AACAATCGTC---TGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTG-AT------
droWil1	scaffold_180703:3531157-3531322 +	LASTZ	3	AACATTCGAGTAGTGTTGGCGGTGCCGTTGACGATGACTCAGCGCGTTTGCAACAGCGTGCGGCACGATTCTCTCAGCAGGGCTCTGGTTCGGCTAAGAAATCGGTCGTTGCGATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATG-TT------
droVir3	scaffold_12963:15772752-15772915 +	LASTZ	3	ATTCGTCGTC---GGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGTCTAAGAAATCTGTCGTCGCAATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------
droMoj3	scaffold_6500:18770378-18770547 +	LASTZ	3	ATTCGTCGTC---GGTTGGCGGTGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGACGAGCGGTGGCTCGGCTAAGAAATCTGTCGTCGCAATTGTAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAGGCCTCG
droGri2	scaffold_15126:2074135-2074298 -	LASTZ	4	ATTCGTCGTC---GGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------

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	ATCAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAAAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-GT------
droSim1	ATCAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-GT------
droSec1	ATCAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-GT------
droYak2	AACAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAGAAGAAAATG-AT------
droEre2	ACCAGTCGTC---TGTTGGTGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-AT------
droEug1	--CAGTCGTC---CGTTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCAAGATTCTCACAGCAGAGCTCCAGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-AT------
droBia1	ACCAGTCGTC---CGTTGGCGGAGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTTTCGCAGCAGGGCTCCAGCTCGGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAAAAAATG-AT------
droTak1	ACCAGTCGTC---CGTTGGCGGAGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTTTCCCAGCAGGGCTCCAGCTCGGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAAAAAATG-AT------
droEle1	ACCAGTCGTC---CATTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCCGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAGATG-AT------
droRho1	ACCAGTCGTC---CATTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGAGCTCCAGCTCCGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAGGAAGATG-AT------
droFic1	ACCAGTCGTC---CGTTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCCCAGCAGGGCTCAAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATG-AT------
droKik1	ACCAATCGTC---CGTGGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCACAGCAGGGCTCAGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAAAAGAAGATG-AT------
droAna3	ACCAATCGTC---CGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAAAAGAAGAT----------
droBip1	ACCAGTCGTC---CGTGGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAAAAGAAGATG---------
dp4	AACAATCGTC---TGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTG-AT------
droPer1	AACAATCGTC---TGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTG-AT------
droWil1	AACATTCGAGTAGTGTTGGCGGTGCCGTTGACGATGACTCAGCGCGTTTGCAACAGCGTGCGGCACGATTCTCTCAGCAGGGCTCTGGTTCGGCTAAGAAATCGGTCGTTGCGATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATG-TT------
droVir3	ATTCGTCGTC---GGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGTCTAAGAAATCTGTCGTCGCAATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------
droMoj3	ATTCGTCGTC---GGTTGGCGGTGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGACGAGCGGTGGCTCGGCTAAGAAATCTGTCGTCGCAATTGTAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAGGCCTCG
droGri2	ATTCGTCGTC---GGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------

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

ATCAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-GT------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................................CTCGGCCAAGAAATCGGTCGTCGCC............................................................	25	1	4.00	0.00	0.00	0.00	4.00
...............................................TTGCAACAGCGTGCGGCACGA.........................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
....................................................................................................ATCGGTCGTCGCCATTGCAAGC...................................................	22	1	2.00	0.00	0.00	0.00	2.00
...................CGGTGCCGTTGATGATGAC.......................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................GCTCGGCCAAGAAATCGGTCGTCGCC............................................................	26	1	1.00	0.00	1.00	0.00	0.00
................................GATGACACAGCGCGCTTGC..........................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...............................................TTGCAACAGCGTGCGGCACGG.........................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................TCGGTCGTCGCCATTGCAAGC...................................................	21	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................TCGGTCGTCGCCATTGCAAGCT..................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......GAC---TGTCGGCGGTGCCGT.................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................CGGCCAAGAACAAGAAGAAAATG-G.......	24	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................CCAAGAAACCCGTCGTCG..............................................................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................CAACAGCGTGCGGCACGA.........................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
......................TGCTGTTGATxATGACACA....................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

ATCAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-GT------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................................................GGCCAAGAACGTGAAGAA.............	18	1	2.00	1.00	1.00	0.00
.........C---TGTTGGCGGTGGCGTGG...............................................................................................................................................	18	1	1.00	0.00	1.00	0.00
..................................................................................CTCCAGCTCGGCCAAGAA.........................................................................	18	1	1.00	0.00	0.00	1.00
......AGTC---TGTTGGCGGTGGCGT.................................................................................................................................................	19	1	1.00	1.00	0.00	0.00
.....................................................................................................TCGGTCGTCGCCATTGCAAGCT..................................................	22	1	1.00	0.00	0.00	1.00
..............GTTGCCGGTGCAGTTGAT.............................................................................................................................................	18	4	0.25	0.00	0.25	0.00
......................................................................................................................................CTCACCACGGACAAGACCAA...................	20	1	1.00	1.00	0.00	0.00
...............................................TTGCAACGGCGTGCGGCACGATT.......................................................................................................	23	1	1.00	0.00	0.00	1.00
...................................................................ATTCTCACAGCAGGGCTCC.......................................................................................	19	1	1.00	0.00	1.00	0.00
..............................................................................................................................................GCCTAAGAACAAGAAGAA.............	18	2	0.50	0.00	0.50	0.00
...............................TGATAACACAACGCGCTT............................................................................................................................	18	1	1.00	0.00	1.00	0.00
...................................................................ATTCTCACAGCAGGGCTCCAGC....................................................................................	22	1	1.00	0.00	1.00	0.00
...............................................................................................................................................GCCAAGAACAAGAAGAAAATG-GT------	23	1	1.00	0.00	1.00	0.00
.....................................................................................................TCGGTCGTCGCCATTGCAAGC...................................................	21	1	1.00	0.00	0.00	1.00
...................................................AACAGCGTGCGGCACGATT.......................................................................................................	19	1	1.00	0.00	1.00	0.00
.........................................................................................................................................ACCAxGGCCAAGTACAAGA.................	18	1	1.00	0.00	1.00	0.00
..............................................................................................................................................GGCCAAGAACAAGAAGAAAATG-GT------	24	1	1.00	0.00	1.00	0.00
...................................................AACAGCGTGCGGCACGATTCTCACAGC...............................................................................................	27	1	1.00	0.00	1.00	0.00
................................................................................................................................................CTAAGAAGAAGAAGAAAA...........	18	2	0.50	0.00	0.00	0.50
...............................................TTGCGACGGCGTGCGGCACGATT.......................................................................................................	23	1	1.00	1.00	0.00	0.00

droYak2

AACAGTCGTC---TGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAGAAGAAAATG-AT------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...............................................................................................................................................GCCAAAAACAAGAAGAAAAT..........	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................................TCGGTCGTCGCCATTGCAAGCT..................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................TCGGTCGTCGCCATTGCAAGC...................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................................................GCCAAGAAATCGGTCGTCGCCATTG........................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
................TGGCGGTGCCGTTGATGATG.........................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
.....................................................................................................TCGGTCGTCGCCATTGCAA.....................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...................................................AACAGCGTGCGGCACGATT.......................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
..................................................................................CTCCAGCTCGGCCAAGAAATCGGTC..................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................................TCGGTCGTCGCCCTTGCAAGCTT.................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................................TCGGTCGTCGCCGTTGCAAGCT..................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................TGATGACACAGTGCGCTTGC..........................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.ACAGTCGTC---TGTTGGCGGTGCCGTTGAT.............................................................................................................................................	28	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

ACCAGTCGTC---TGTTGGTGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-AT------	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................................................................................................................................GGCCAAGAACGTGAAGAA.............	18	1	2.00	1.00	0.00	0.00	1.00
.....................................................................................................TCGGTCGTCGCCATTGCAAGC...................................................	21	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................TCGGTAGTCGCCATTGCAAGCT..................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................GTTTGGTATCACCACGTCC...........................	19	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................AAGAAGAAGAAGAAAAAG-A.......	19	1	1.00	1.00	0.00	0.00	0.00
..............GTTGTTGCTGCCGTTGAT.............................................................................................................................................	18	28	0.04	0.00	0.00	0.00	0.04
.....................................................................................................TCGGTCGTCGCCATTGCA......................................................	18	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................CCAAGAACAAGAAGAAAAT..........	19	1	1.00	1.00	0.00	0.00	0.00

droEug1

--CAGTCGTC---CGTTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCAAGATTCTCACAGCAGAGCTCCAGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATG-AT------

Size

Hit Count

Total Norm

droBia1

ACCAGTCGTC---CGTTGGCGGAGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTTTCGCAGCAGGGCTCCAGCTCGGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAAAAAATG-AT------

Size

Hit Count

Total Norm

droTak1

ACCAGTCGTC---CGTTGGCGGAGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTTTCCCAGCAGGGCTCCAGCTCGGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAAAAAATG-AT------

Size

Hit Count

Total Norm

droEle1

ACCAGTCGTC---CATTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCCGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAGATG-AT------

Size

Hit Count

Total Norm

droRho1

ACCAGTCGTC---CATTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGAGCTCCAGCTCCGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAGGAAGATG-AT------

Size

Hit Count

Total Norm

droFic1

ACCAGTCGTC---CGTTGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCCCAGCAGGGCTCAAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATG-AT------

Size

Hit Count

Total Norm

droKik1

ACCAATCGTC---CGTGGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCACAGCAGGGCTCAGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAAAAGAAGATG-AT------

Size

Hit Count

Total Norm

droAna3

ACCAATCGTC---CGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAAAAGAAGAT----------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..........................................................................................CAGCCAAGAGATCTGTCGTC...............................................................	20	1	3.00	0.00	3.00	0.00	0.00
...................................................AACAGCGATCGGCACGTTT.......................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
......................................................................CTAGCAGCAGAGCTCCGGCTCAGCC..............................................................................	25	1	1.00	0.00	1.00	0.00	0.00
....ATCTTC---CGTGGGCGCTGC....................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droBip1

ACCAGTCGTC---CGTGGGCGGAGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAAAAGAAGATG---------

Size

Hit Count

Total Norm

dp4

AACAATCGTC---TGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTG-AT------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
................................................TGCAACAGCGGGCGGCACGTTTCTC....................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00

droPer1

AACAATCGTC---TGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTG-AT------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.............................................GCTGGCCACAGCGGGCGGC.............................................................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
..........................................CGCGCTTGCAACAGCGGGC................................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
................................GATGACACAGCGCGCTTGC..........................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
.........C---TGTGGGTGGGGACGTGG...............................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................TAAGAAATTTGTCGTCGCCATTGCAAGT...................................................	28	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

AACATTCGAGTAGTGTTGGCGGTGCCGTTGACGATGACTCAGCGCGTTTGCAACAGCGTGCGGCACGATTCTCTCAGCAGGGCTCTGGTTCGGCTAAGAAATCGGTCGTTGCGATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATG-TT------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..............................................................................AGGGCTCTGGTTCGGCTAAGAAAT.......................................................................	24	1	2.00	2.00	0.00	0.00	0.00
...........................................................GCGGCACGATTCTCTCAGC...............................................................................................	19	1	2.00	0.00	0.00	0.00	2.00
...................................................AACAGCGTGCGGCACGATTCTCTCAG................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TAAGAAATCGGTCGTTGCGATT.........................................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................GGCTCTGGTTCGGCTAAGAAATCGGTC..................................................................	27	1	1.00	1.00	0.00	0.00	0.00
............................TGACGATGACTCAGCGCGT..............................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................................GTGCGGCACGATTCTCTCAGG...............................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................GTGCGGCACGATTCTCTCAGC...............................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................GGCACGATTCTCTCAGAA..............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...........................................................................AGCAGGGCTCTGGTTCGGCT..............................................................................	20	1	1.00	0.00	0.00	0.00	1.00
................................GATGACTCAGCGCGTTTGC..........................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................AAGGCCAAGAATAAGAAGT..............	19	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................AAGAAATCGGTCGTTGCGATTGCAA.....................................................	25	1	1.00	0.00	0.00	0.00	1.00
.............................................GTTTGCAACAGCGTGCGG..............................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..............GTTAGCGGTxCCGTTGACG............................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..CATTCGAGTAGTGTTGGCGGTGCCGT.................................................................................................................................................	26	1	1.00	1.00	0.00	0.00	0.00
..............................................................................AGGGCTCTGGTTCGGCTAAGAAATC......................................................................	25	1	1.00	0.00	1.00	0.00	0.00
........................CCGTTGTTGATGACTCAG...................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......CGAGTAGTGTTGGCGGTC.....................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..............................................................................AGGGCTCTGGTTCGGCTAAG...........................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droVir3

ATTCGTCGTC---GGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGTCTAAGAAATCTGTCGTCGCAATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..........................................................................................CGTCTAAGAAATCTGTCGTC...............................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

ATTCGTCGTC---GGTTGGCGGTGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGACGAGCGGTGGCTCGGCTAAGAAATCTGTCGTCGCAATTGTAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAGGCCTCG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
......................................................................CTCACAGACGAGCGGTGGCT...................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................CTTGCAACAGCGTGCGGCAC...........................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.......................................................................TCACAGACGAGCGGTGGCT...................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................GAACAAGAAGAGATTGAAG......	19	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................................ACAAGAAGAGATTGAAGGAC...	20	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................TCTGTCGTCGCAATTGTAAGC...................................................	21	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................................ACAAGAAGAGATTGAAGGA....	19	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................TCTGTCGTCGCAATTGTAAGCTCA................................................	24	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................GAACAAGAAGAGATTGAAGG.....	20	1	1.00	1.00	0.00	0.00	0.00
..........................GTTGATGATGGCGCAGCGCGC..............................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................TGTTGATGATGACACAGCGCGCTT............................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................GCACAAGAAGAGATTGCAG......	19	1	1.00	1.00	0.00	0.00	0.00
...................................................................................................AATCTGTCGTCGCAATTGTAGGCT..................................................	24	1	1.00	0.00	1.00	0.00	0.00

droGri2

ATTCGTCGTC---GGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:19:17 EDT

dme-mir-4987

chr2L:10840344-10840476 -

Known_mirbase

CDS

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