dme-mir-2496- Best orthologs

dme-mir-2496	chrX:1904333-1904450 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 1904344-1904366
   star strand at position 1904418-1904439
   mutations
   read mismatches

Notes: Most reads are simple repeats. The hairpin structure only looks confident in dm3 - droEre2 except for droSim1 which has bifurcating stem

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:1904318-1904465 +		1	AAGAGC-GC------AAAAT-------------G-------------------AGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGCGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGCG-------GGG--------CACTCACACA----------------CGCATATTCAGCCGCACATCTGGGAAAA------------------------TGGG
droSim1	chrX:1343126-1343273 +	LASTZ	5	AAGAGC-GC------GAAAT-------------G-------------------AGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCG--AATTGCG-------GGG--------CACACACACA----------------CGCATATTCAGCCGCACATCTGGGAAAA------------------------TGGG
droSec1	super_10:1689518-1689665 +	LASTZ	4	AAGAGC-GC------AAAAT-------------G-------------------ATTGCG--CCTGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCG--AATTGCG-------GGG--------CACTCACACA----------------CGCATATTCAGCCGCACATCTGGGAAAA------------------------TGGG
droYak2	chrX:6422544-6422691 -	LASTZ	4	AAGAGC-GC------AAAAT-------------G-------------------TGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATCGGG-------GGG--------CACTCACACA----------------CGCACATACAGCCGCACATCTGGGAAAA------------------------TGGG
droEre2	scaffold_4644:1874871-1875018 +	LASTZ	4	AAGAGC-GC------AAAAT-------------G-------------------TGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACTTACACA----------------CGCACATACAGCCGCACATCTGGGAAAA------------------------TGGG
droEug1	scf7180000409182:447470-447608 +	LASTZ	5	AACAGC-GA------AAAAT-------------G-T---TT-------GCGT------------ATG--TG----T--G--T-------GAG----GGGCC--A---TAAAAGCCTTGTTTGCGCGTGGAATTTAACTGTTTTTTCGCCGTCTGCT--GGTTCGG-------GGGGTGGGGAGCACGTACA------------------------CTCAACCGCACATCTGGGAAAA------------------------TGGG
droBia1	scf7180000301760:4508970-4509126 +	LASTZ	5	GACAGC-GC------AAATT-------------G-------------------TGTGCG--CTCGTGTGTGCGTGTG----TGT-----GTGTGCGGGGCC--G---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCC--AATTGGG-------GGG--------CACTCACACAG------------AGGCACACGCACAGTCACACACCTGGGAAAA------------------------TGGG
droTak1	scf7180000415211:36485-36643 -	LASTZ	5	GACGGC-GC------AAA-----------------T---GTGCCATGTGTGTGTGTGCG--CTGGTG--TGCGTGT--G--C-------G------GGGCC--G---CAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACTCACACAG------------ACGCGCACACACAGCCGCACACCTGGGAAAA------------------------TGGG
droEle1	scf7180000491001:1416804-1416930 +	LASTZ	5	GAGAGC-GC------AAAAA-------------A-T---GT-------GGCT------------GTG--TG-------------------TG----TGGCC--A---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCA--AATTGGG-------GGG--------CACTAACACA------------------------CAGCCGTACACCTGGGAAAA------------------------TGGG
droRho1	scf7180000777610:12722-12848 -	LASTZ	5	AAGAGC-GC------AAAAA-------------A-T---GT-------GGCT------------GTG--TG-------------------TG----TGGCC--A---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACTCACACA------------------------CAGCCACACACCTGGGAAAA------------------------TGGG
droFic1	scf7180000454072:3017522-3017650 +	LASTZ	5	GAGAGC-GC------AAAAT-------------G------G-------GACT--GT--------GTG--TGCGTGT---------------G----TGGCC--A---AAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTTTCGCCGTCTGCG--AATTGGG-------GGG--------AACACACA--------------------------CAGCTGCACACCTGGGAAAA------------------------TGGG
droKik1	scf7180000302610:169951-170123 +	LASTZ	5	AAAGGCGGAGAGCGCCGCAG-------------A-T---GT-------GCCA------------GTG--TGTGAGT--GTGTCTGTGTTGAG----TGGCC--A---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACACACACAACCACACCAACCTA--CACGCACACACCGGCGCACCTGGGAAAA------------------------TGGG
droAna3	scaffold_12929:1897894-1898023 +	LASTZ	5	AAGGGG-GA------GAGAG-------------C---------AGTTTGCAT------------GTG--TGCGATT--T-----------TG----TGGTC--A---TAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCG--AATTGGG-------GGG--------GGGGG-----------------------------GGGCCATACAAGCTGGAAAA------------------------TAGG
droBip1	scf7180000396543:357925-358040 +	LASTZ	5	GGGGGA-AT----------A-------------G-T---TT-------GCAT------------GTG--TGCGATT--T-----------TG----TGGTC--A---TAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCG--AATTGGG-------GGG--------C-------------------------------------CATACAAGCTGGAAAA------------------------TAGG
dp4	chrXL_group1a:2576130-2576311 +	LASTZ	0	AAGAGG-GA------GAGATAGAGAGAGAGAATAATGGAG---TGCTGGTGTATATGTACCTACATATGTACGTGTGGT--T-------GAG----TACCC--A---TAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTG--TGTTGGG-------CGG--------CACACACACC----------------AGCGCCATTGGCTTTTCACAGGGCGA----------------------GAAGTAAG
droPer1	super_28:1013167-1013344 +	LASTZ	0	AAGAGG-GA------GAGATAGAGAGAGAGAATAATGGAG---TGCTGGTGTATATGTA--CCTATG--TACGTGTGGT--T-------GAG----TACCC--A---TAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTG--TGTTGGG-------CGG--------CACACACACC----------------AGCGCCATTGGCTTTTCACAGGGCGA----------------------GAAGTAAG
droWil1	scaffold_181096:6994288-6994457 -	LASTZ	0	GAGGCC-AA------AAGAG---A---------C-------------------AGTGCG--ATAGAG--AGAGGTA-------------GAG----AGAACGTACA-GAGAGAGCTTGTTCTGGTTTGTAACTAA-TTTTCCCC--CTCAAATGTAAGCATTTCGAATGCATGTG--------TGTGTACGTG------------------------TAATCACACACGCACACAAATACCACGTCATTACGATTTCCACATGGC
droVir3	scaffold_12928:6459245-6459266 +	LASTZ	0	GC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTATTTCTGTGCAAG------------------------TGTG
droMoj3	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15203:11679615-11679698 +	LASTZ	0	-------------------------------------------------------------------------------------------------------------------TTGTTTTCGCTTTTCATTT---TGTTTTACGATTAACTGTA--AACTGCA-------GCC--------GGC-----CA----------------ACCATTTTCGA---GCCCACTGGCAA----------------------AGAATGGG

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	AAGAG-CGC------AAAATG-------------AGTGCGCCGGTGTGCGTGT--G-------TGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGCGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGCGGGG--------CACTCACAC----------------ACGCATATTCAGCCGCACATCTGGGAAAATGGG
droSim1	AAGAG-CGC------GAAATG-------------AGTGCGCCGGTGTGCGTGT--G-------TGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCGGGG--------CACACACAC----------------ACGCATATTCAGCCGCACATCTGGGAAAATGGG
droSec1	AAGAG-CGC------AAAATG-------------ATTGCGCCTGTGTGCGTGT--G-------TGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCGGGG--------CACTCACAC----------------ACGCATATTCAGCCGCACATCTGGGAAAATGGG
droYak2	AAGAG-CGC------AAAATG-------------TGTGCGCCGGTGTGCGTGT--G-------TGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATCGGGGGG--------CACTCACAC----------------ACGCACATACAGCCGCACATCTGGGAAAATGGG
droEre2	AAGAG-CGC------AAAATG-------------TGTGCGCCGGTGTGCGTGT--G-------TGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGGGGGG--------CACTTACAC----------------ACGCACATACAGCCGCACATCTGGGAAAATGGG
droEug1	AACAG-CGA------AAAATG-------------TTTGCG--T----ATGTGT--G-------TGAGGGGCCA---TAAAAGCCTTGTTTGCGCGTGGAATTTAACTGTTTTTTCGCCGTCTGCTGGTTCGGGGGGTGGGGAGCA------------------------CGTACACTCAACCGCACATCTGGGAAAATGGG
droBia1	GACAG-CGC------AAATTG-------------TGTGCGCTCGTGTGTGCGTGTGTGTGTG-TGCGGGGCCG---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCCAATTGGGGGG--------CACTCACACAG------------AGGCACACGCACAGTCACACACCTGGGAAAATGGG
droTak1	GACGG-CGC------AAAT-GTGCCATGTGTGTGTGTGCGCTGGTGTGCGTGT--G-------CGG--GGCCG---CAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGGGGGG--------CACTCACACAG------------ACGCGCACACACAGCCGCACACCTGGGAAAATGGG
droEle1	GAGAG-CGC------AAAAAA---------------TGTGGCTGTGTG------TG-------T----GGCCA---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCAAATTGGGGGG--------CACTAACAC----------------A--------CAGCCGTACACCTGGGAAAATGGG
droRho1	AAGAG-CGC------AAAAAA---------------TGTGGCTGTGTG------TG-------T----GGCCA---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGGGGGG--------CACTCACAC----------------A--------CAGCCACACACCTGGGAAAATGGG
droFic1	GAGAG-CGC------AAAATG-----------------GGACTGTGTGTGCGTGTG-------T----GGCCA---AAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTTTCGCCGTCTGCGAATTGGGGGG--------AACACACA--------------------------CAGCTGCACACCTGGGAAAATGGG
droKik1	AAAGGCGGAGAGCGCCGCAGA---------------TGTGCCAGTGTGTGAGTGTGTCTGTGTTGAGTGGCCA---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGGGGGG--------CACACACACAACCACACCAACCTACACGCACA--CACCGGCGCACCTGGGAAAATGGG
droAna3	AAGGG-GGA------GAGAGC-------------AGTTTGCATGTGTGCGATTTTG-------T----GGTCA---TAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCGAATTGGGGGG--------GGGG-----------------------------GGGGCCATACAAGCTGGAAAATAGG
droBip1	GGGGG-AA----------TA---------------GTTTGCATGTGTGCGATTTTG-------T----GGTCA---TAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCGAATTGGGGGG--------C-------------------------------------CATACAAGCTGGAAAATAGG

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
UNAFold Image																		None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

AAGAGC-GC------GAAAT-------------G-------------------AGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCG--AATTGCG-------GGG--------CACACACACA----------------CGCATATTCAGCCGCACATCTGGGAAAA------------------------TGGG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................................................................................................................................ACACACACA----------------CGCATACTG...............................................	18	1	1.00	0.00	1.00	0.00	0.00
...................T-------------G-------------------TGTGCG--TCGGTG--TGCGT...............................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droSec1

AAGAGC-GC------AAAAT-------------G-------------------ATTGCG--CCTGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCG--AATTGCG-------GGG--------CACTCACACA----------------CGCATATTCAGCCGCACATCTGGGAAAA------------------------TGGG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................TGCG--CCTGTG--TGCGTGT--G--A-------GC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
......................................................GTGCG--CCTGTG--TGTGTGT--G--........................................................................................................................................................................................	19	3	0.33	0.00	0.33	0.00
..................................................................G--TGCGTGT--G--T-------GAG----AGGCC--ATCGTA............................................................................................................................................................	24	1	1.00	1.00	0.00	0.00
...............................................................TGTG--TGCGTGC--G--T-------GCG----AG.......................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50
...................................................................................................................TTGTTTGCGTGTGTAATG....................................................................................................................................	18	1	1.00	1.00	0.00	0.00
......................................................TTGCG--GGTGTG--TGCGTGT--G--T-------................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00
...........................................................................................................................GTGTGGAATTTGATTGTT............................................................................................................................	18	1	1.00	0.00	1.00	0.00
.......................................................TGCG--CCAGTG--TGTGTGT--G--........................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
..................AT-------------G-------------------ACTGCG--TCTGTG--TGCG................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00
..................................................................................................................................................GCCGTCTxCG--AGTTGCG-------GG...........................................................................................	18	1	1.00	0.00	0.00	1.00
.....................................................................TGCGTGT--G--T-------GAG----AGGCC--A.................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
..........................................................G--CCTGTG--TGCGTGT--G--T-------GTG----TGG......................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00
.........................................................CG--CCTGTG--TGTGTGC--G--T-------G...............................................................................................................................................................................	18	3	0.33	0.00	0.00	0.33
.......................................................TGTG--CATGTG--TGCGTGT--G--T-------................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00
...............................................................TGTG--TGTGTGT--G--T-------GTG----AGG......................................................................................................................................................................	19	4	0.25	0.00	0.25	0.00
.....................................................................TGCGTGT--G--T-------GAG----AGGCC--ATCGT.............................................................................................................................................................	22	1	1.00	0.00	1.00	0.00

droYak2

AAGAGC-GC------AAAAT-------------G-------------------TGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATCGGG-------GGG--------CACTCACACA----------------CGCACATACAGCCGCACATCTGGGAAAA------------------------TGGG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................CG--CCGGTG--TGAGTAT--G--T-------G...............................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
..................................................................G--TGCGTGT--G--T-------GAG----AGGCA--A.................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................CGAGTG--TGCGTGT--G--T-------G...............................................................................................................................................................................	16	4	0.25	0.00	0.00	0.00	0.25	0.00
.......................................................TGCG--CCGGTG--TGCGTGT--G--T-------G...............................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................GTG--TGCGTGT--G--C-------GAG----CGGC.....................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................GCTG--TGCGTGT--G--T-------GAC----AG.......................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................GTG--TGCGTGT--G--T-------GCG----CG.......................................................................................................................................................................	17	3	0.33	0.00	0.00	0.00	0.33	0.00
.................AAT-------------T-------------------TGTGCG--CCTGTG--TGC.................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................CGTG--TGCGTGT--G--T-------CAG----AGGC.....................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................GTG--TGCGTGT--G--T-------GGG----GG.......................................................................................................................................................................	17	3	0.33	0.00	0.00	0.00	0.33	0.00
.....................................................................................................................................................GACTGCG--AATCTGG-------GGG--------..................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................GTGCG--xCGGCG--TGCGTGT--G--T-------G...............................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AAGAGC-GC------AAAAT-------------G-------------------TGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACTTACACA----------------CGCACATACAGCCGCACATCTGGGAAAA------------------------TGGG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................T-------------G-------------------TGTGCG--CCAGTG--TGTGT...............................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
................................................................GTG--TGCGTGT--G--T-------GAG----AGGCC--A.................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
................................................................TTG--TGCGTGT--G--T-------CAG----AGGC.....................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
...................T-------------G-------------------TGTGCG--CCGGTG--TGCGTGT--G--........................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droEug1

AACAGC-GA------AAAAT-------------G-T---TT-------GCGT------------ATG--TG----T--G--T-------GAG----GGGCC--A---TAAAAGCCTTGTTTGCGCGTGGAATTTAACTGTTTTTTCGCCGTCTGCT--GGTTCGG-------GGGGTGGGGAGCACGTACA------------------------CTCAACCGCACATCTGGGAAAA------------------------TGGG

Size

Hit Count

Total Norm

droBia1

GACAGC-GC------AAATT-------------G-------------------TGTGCG--CTCGTGTGTGCGTGTG----TGT-----GTGTGCGGGGCC--G---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCC--AATTGGG-------GGG--------CACTCACACAG------------AGGCACACGCACAGTCACACACCTGGGAAAA------------------------TGGG

Size

Hit Count

Total Norm

droTak1

GACGGC-GC------AAA-----------------T---GTGCCATGTGTGTGTGTGCG--CTGGTG--TGCGTGT--G--C-------G------GGGCC--G---CAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACTCACACAG------------ACGCGCACACACAGCCGCACACCTGGGAAAA------------------------TGGG

Size

Hit Count

Total Norm

droEle1

GAGAGC-GC------AAAAA-------------A-T---GT-------GGCT------------GTG--TG-------------------TG----TGGCC--A---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCA--AATTGGG-------GGG--------CACTAACACA------------------------CAGCCGTACACCTGGGAAAA------------------------TGGG

Size

Hit Count

Total Norm

droRho1

AAGAGC-GC------AAAAA-------------A-T---GT-------GGCT------------GTG--TG-------------------TG----TGGCC--A---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACTCACACA------------------------CAGCCACACACCTGGGAAAA------------------------TGGG

Size

Hit Count

Total Norm

droFic1

GAGAGC-GC------AAAAT-------------G------G-------GACT--GT--------GTG--TGCGTGT---------------G----TGGCC--A---AAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTTTCGCCGTCTGCG--AATTGGG-------GGG--------AACACACA--------------------------CAGCTGCACACCTGGGAAAA------------------------TGGG

Size

Hit Count

Total Norm

droKik1

AAAGGCGGAGAGCGCCGCAG-------------A-T---GT-------GCCA------------GTG--TGTGAGT--GTGTCTGTGTTGAG----TGGCC--A---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACACACACAACCACACCAACCTA--CACGCACACACCGGCGCACCTGGGAAAA------------------------TGGG

Size

Hit Count

Total Norm

droAna3

AAGGGG-GA------GAGAG-------------C---------AGTTTGCAT------------GTG--TGCGATT--T-----------TG----TGGTC--A---TAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCG--AATTGGG-------GGG--------GGGGG-----------------------------GGGCCATACAAGCTGGAAAA------------------------TAGG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................................................................................................TGGTC--A---TAATAGCTTTGTTCG...............................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................AGAGGG-------GGG--------GGGGG-----------------------------GGGC............................................	18	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................AATCGGG-------TGG--------GGGGG-----------------------------GGG.............................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................TTGG-------GGG--------GGGAG-----------------------------GGGCCA..........................................	18	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................ATTGGG-------AGG--------GGGGG-----------------------------GGGC............................................	18	1	1.00	0.00	0.00	1.00	0.00
.AGGGG-GA------AAGAG-------------x---------AGTTTG........................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................TTGGG-------GGG--------GAGGG-----------------------------GGGC............................................	17	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................................TTTTTCTGTTTTCTAGCCGT..................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................GTGGG-------GGA--------GGGGG-----------------------------GGG.............................................	16	1	1.00	0.00	0.00	1.00	0.00

droBip1

GGGGGA-AT----------A-------------G-T---TT-------GCAT------------GTG--TGCGATT--T-----------TG----TGGTC--A---TAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCG--AATTGGG-------GGG--------C-------------------------------------CATACAAGCTGGAAAA------------------------TAGG

Size

Hit Count

Total Norm

dp4

AAGAGG-GA------GAGATAGAGAGAGAGAATAATGGAG---TGCTGGTGTATATGTACCTACATATGTACGTGTGGT--T-------GAG----TACCC--A---TAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTG--TGTTGGG-------CGG--------CACACACACC----------------AGCGCCATTGGCTTTTCACAGGGCGA----------------------GAAGTAAG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................AATGGAG---TGCCGGTGAAT...................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
........A------GAGAAAGAGAGAGAGAAAA.......................................................................................................................................................................................................................................	20	19	0.05	0.05	0.00	0.00	0.00
...............GAGATAGAGAGAGAGGAA........................................................................................................................................................................................................................................	18	30	0.03	0.00	0.03	0.00	0.00

droPer1

AAGAGG-GA------GAGATAGAGAGAGAGAATAATGGAG---TGCTGGTGTATATGTA--CCTATG--TACGTGTGGT--T-------GAG----TACCC--A---TAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTG--TGTTGGG-------CGG--------CACACACACC----------------AGCGCCATTGGCTTTTCACAGGGCGA----------------------GAAGTAAG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......GA------GAGATAGATCGAGAGA..........................................................................................................................................................................................................................................	18	8	0.63	0.00	0.00	0.00	0.00	0.63
..........................................................................................................................................GTTTCTTCGGTGTTCTTC--...........................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
........A------CAGATAGAGAGAGAGAAT........................................................................................................................................................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25	0.00
.......GA------GAGATAGAGAGAGAGA..........................................................................................................................................................................................................................................	18	137	0.01	0.01	0.00	0.00	0.00	0.00
...............................................GGTGTATATGTA--CATGTG--T...................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..GAGG-GA------GGGATAGAGAGAGA............................................................................................................................................................................................................................................	20	9	0.11	0.11	0.00	0.00	0.00	0.00
............................................................................................................................................................................CGG--------CACCCACAxC----------------AGCGCC..................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................AACGTGTGGT--T-------GAG----TGCC.....................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GAGATAGATCGAGAGAAT........................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
...................................................................................................................................................GTGCTCTTG--TGTCGGG-------CG...........................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.AGATG-GA------GAGATAGAGAAA..............................................................................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00

droWil1

GAGGCC-AA------AAGAG---A---------C-------------------AGTGCG--ATAGAG--AGAGGTA-------------GAG----AGAACGTACA-GAGAGAGCTTGTTCTGGTTTGTAACTAA-TTTTCCCC--CTCAAATGTAAGCATTTCGAATGCATGTG--------TGTGTACGTG------------------------TAATCACACACGCACACAAATACCACGTCATTACGATTTCCACATGGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........A------AAGAG---A---------G-------------------AGAGCG--ATAGA.......................................................................................................................................................................................................	19	50	0.08	0.08	0.00	0.00	0.00
......................................................................................................................................................................ATGCGTGTG--------TGTGTACGTG------------------------TC..............................................	21	1	1.00	1.00	0.00	0.00	0.00
..........................................................G--ATAGAG--AGAGGTA-------------GAG----AGA......................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................................................ATGAATGTG--------TGTGTATGT.........................................................................	18	13	0.08	0.00	0.00	0.08	0.00
...................G---A---------C-------------------AGAGCG--ATAGAG--AGA.................................................................................................................................................................................................	18	39	0.03	0.00	0.03	0.00	0.00
.............................................................................................................................................................................................................................CACACACGCACACAAACACT........................	20	7	0.14	0.00	0.14	0.00	0.00
.............................................................ATAGAG--AGAGGGA-------------GTG----AGA......................................................................................................................................................................	19	39	0.03	0.03	0.00	0.00	0.00
........A------AAGAG---A---------A-------------------AGTGCG--AAAGAG--AGA.................................................................................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.......................A---------C-------------------AGTGTG--AGAGAG--AGAG................................................................................................................................................................................................	18	50	0.02	0.00	0.00	0.02	0.00
.............................................................................................................................................................GCTTTTCGAATGTATGTG--------..................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..............................................................GAGAG--AGAGGTA-------------GGG----AGA......................................................................................................................................................................	18	34	0.03	0.03	0.00	0.00	0.00
..............................................................AAGAG--AGAGGTG-------------GAG----AGAA.....................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
.................GAG---A---------A-------------------AGTGCG--ACAGAG--AGAG................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............AAGAG---A---------A-------------------AGTGCG--AAAGA.......................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.............................................................ATAGAA--AGAGGTA-------------GAG----GGA......................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
........A------AAGAG---A---------A-------------------AGTGCG--AAAGA.......................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.................GAG---A---------A-------------------AGTGCG--ACAGAG--AGA.................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
...................G---A---------T-------------------AGAGCG--ATAGAG--AGA.................................................................................................................................................................................................	18	37	0.03	0.00	0.03	0.00	0.00
.......................................................................................................................................................................TGCAAGTG--------TGTGTGCGTG------------------------T...............................................	19	3	0.33	0.00	0.33	0.00	0.00
......................................................GTGCG--ACAGAG--AGAGGGA-------------GA..............................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00

droVir3

GC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTATTTCTGTGCAAG------------------------TGTG

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

-------------------------------------------------------------------------------------------------------------------TTGTTTTCGCTTTTCATTT---TGTTTTACGATTAACTGTA--AACTGCA-------GCC--------GGC-----CA----------------ACCATTTTCGA---GCCCACTGGCAA----------------------AGAATGGG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:25:07 EDT

dme-mir-2496

chrX:1904333-1904450 +

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