dme-mir-2493- Best orthologs

dme-mir-2493	chr3R:10956476-10956581 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 10956493-10956514
   star strand at position 10956539-10956559
   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	chr3R:10956461-10956596 -		1	TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACACACAG---------------------C---------------------------------------------------------------------CATGTGCATGGAGCA----------AAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTG-------ACCAGCAG------AAGAGGAAGATGG
droSim1	chr3R:10501806-10501941 +	LASTZ	4	TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACACACAG---------------------C---------------------------------------------------------------------CGTGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTG-------ACCAGCAG------AAGAGGAAGATAG
droSec1	super_0:10986595-10986730 +	LASTZ	4	TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACACACAG---------------------C---------------------------------------------------------------------CGTGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTG-------ACCAGCAG------AAGAGGAAGATAG
droYak2	chr3R:15471091-15471226 +	LASTZ	4	TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACACAGGG---------------------C---------------------------------------------------------------------CGTGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA
droEre2	scaffold_4770:10485021-10485154 -	LASTZ	4	TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACAG--AG---------------------C---------------------------------------------------------------------CGTGTGCATGGGGCA----------AAAAACTATGGCCATGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA
droEug1	scf7180000409794:36989-37146 +	LASTZ	4	TATA------------ATATGTGTG--------------TGT-GCTATTATTAAAACCCC-------------CAACGTT----CACACACACACAC-----------------------T----------------------------------CAT-----------ATACCCGTATGTATATGTATGTATGTGCATGGGGCA----------AAAAACTATGAACGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAAAAG------AAGAAGAACATAA
droBia1	scf7180000302402:3936102-3936224 -	LASTZ	5	TA---------------TGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAGCGCG------------TC-TC-------------------------------------------------------------------------------------------TGTGTGTGCATGGGGCA----------AAAAACTATGGCCGCATGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA
droTak1	scf7180000415310:989048-989182 +	LASTZ	5	TATA------------ATGTGTGTG--------------TGT-GCTATTATTAAAACCCCC------------CAACGTT----CACACACACAC--AG---------------------C---------------------------------------------------------------------CATGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA
droEle1	scf7180000486474:1021127-1021262 +	LASTZ	5	TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACTCT----CACACATACATCTAT---------------------G---------------------------------------------------------------------TATGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA
droRho1	scf7180000779540:26441-26580 -	LASTZ	5	TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACACACAC---------------------T-----------------------------------------------------------------CATTCGTGGGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAAATAA
droFic1	scf7180000454104:401646-401781 +	LASTZ	5	TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACATA----CACACACACACATTT---------------------T---------------------------------------------------------------------CATGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAAAAG------AAGAGGAAGATAA
droKik1	scf7180000302706:1113377-1113522 +	LASTZ	5	TATA------------ATGTGTGTG--------------TGT-GCTATTATTAAAACCCC--------------ACCGCA----CACACACACACCCAG----CACA-----------------------------------------------------------------CC---------AAGCATGCATGTGAATGGGGCA----------A-AAACTATGCGAGTGTGTATGTGTGCGAGGCGTTGGCGTTTTG-------ACCAGAAG------CCGAAGAAGAGAA
droAna3	scaffold_13340:6023187-6023339 -	LASTZ	5	TATA------------ATGTGTGTGTGTGTGTGTT----TGT-GCTATTATTAAAACCCC-------------CCTCGCA----AGCACCCCC-CACTG---------------------C---------------------------------------------------------------------CAC-TGCATAGAGCAAAAAAAAAAAAAAAACTATAGTGGTGTGTG-GCAGGCGAGGCGTTGGCGTTTTG-------ACCAAAAG------CTGAAGAAGAGGA
droBip1	scf7180000396708:2786123-2786257 +	LASTZ	5	TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CCTCGCC----AGAACACCTC-CCTG---------------------C---------------------------------------------------------------------CCG--GCATACAGCAA--------AAAAAACTATGGTAGTGTGTGTGTTTGCGAGGCGTTGGCGTTTTG-------ACCAAAAG------CTGAAGAAGAGGA
dp4	chr2:20937547-20937682 -	LASTZ	5	TATA------------ACGTGTGTGTGAGTG--------TGT-GCTATTATTAAACTCCC-------------TCCC--T----AACACGCACAC--AA---------------------C----------------------------------TAT-----------GT-------------------TA------TG-----------------TAAGTGTGTGTGTGTGTGTGTGTGTGAGGCGTTGGCGTTTTG-------ACCAGAAGCTGAAGAAGAGGAAGAATA
droPer1	super_3:3688114-3688249 -	LASTZ	5	TATA------------ACGTGTGTGTGAGTG--------TGT-GCTATTATTAAACTCCC-------------TCCC--T----AACACGCATAC--AA---------------------C----------------------------------TAT-----------GT-------------------TG--TGT---------------------AAGTGTGTGTGTGTGTGTGTGTGTGAGGCGTTGGCGTTTTG-------ACCAGAAGCTGAAGAAGAGGAAGAATA
droWil1	scaffold_181130:7306738-7306938 +	LASTZ	0	CAAATGGTATGCGTCTATGTGTATGTGTGTG--CCTGTGTGTGGCTATTATTAAAAATCCACACCTCCTACCCCAACCCCCCGTTACATATACACACAACCAATACATCCATACGCCCACACATACACATA-------------------------------------------------------CA--TGAAAAGAAAAGGAA------AAAAAAGAACTA------------------TGAGGCGTTGGCGTTCGTTCCGGGCACTACAAG------A---AGAAGAAGA
droVir3	scaffold_13047:7645546-7645687 -	LASTZ	0	CATA------------TTGTACGTG--------------TGT-GCTATTATTAAAATGCC-------------ACACGCA----CGCACACATAGAGAC---------------------G----GGGGGACACGGACACGGCAAAAAGAAAAACTAT-----------TC-------------------T-------------------------------CAGAGTGTGTGTGCGCCTACGAGGCGTTGGCGTTTTG-------GCTAGAAG------AAGC--------A
droMoj3	scaffold_6540:3604660-3604829 -	LASTZ	0	TATA------------TTGTATGTG--------------TGT-GCTATTATTAAAATACC-------------ACATGCA----CGCACACACAGAGAG---------------------G----CAGAGACACGGACACAGCAAAAAGAAAAACTATTTACAGTTGCTGCGACTGTGTG-----------------------------------------TATATACATATATGCGCCTACGAGGCGTTGGCGTTTCA-------GCAAGCGA------GAGAGTGAGAGAG
droGri2	scaffold_15245:14649244-14649349 +	LASTZ	0	AACA------------A------------------------------------------G-------------CAACACA----CACACACACACACAC---------------------A---------------------------------------------------------------------CA--CACGCA-GACA----------AAGAAACACACACTCACATACATC-TTGATGTGTTCATATTTATG------CCAAGTCA------AACTCAAAAGCTT

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	TATAATGTGTGTG------T----GCGCTATTATTAAAACCCCC-AACGCTCACACACACACACAGCCA------------------------TGTGCATGGAGCA----------AAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGCA------GAAGAGGAAGATGG
droSim1	TATAATGTGTGTG------T----GCGCTATTATTAAAACCCCC-AACGCTCACACACACACACAGCCG------------------------TGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGCA------GAAGAGGAAGATAG
droSec1	TATAATGTGTGTG------T----GCGCTATTATTAAAACCCCC-AACGCTCACACACACACACAGCCG------------------------TGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGCA------GAAGAGGAAGATAG
droYak2	TATAATGTGTGTG------T----GCGCTATTATTAAAACCCCC-AACGCTCACACACACACAGGGCCG------------------------TGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAA------GAAGAGGAAGATAA
droEre2	TATAATGTGTGTG------T----GCGCTATTATTAAAACCCCC-AACGCTCACACACACAG--AGCCG------------------------TGTGCATGGGGCA----------AAAAACTATGGCCATGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAA------GAAGAGGAAGATAA
droEug1	TATAATATGTGTG------T----GTGCTATTATTAAAACCCCC-AACGTTCACACACACACAC--TCATATACCCGTATGTATATGTATGTATGTGCATGGGGCA----------AAAAACTATGAACGTGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAAAA------GAAGAAGAACATAA
droBia1	TA---TGTGTGTG------T----GCGCTATTATTAAAACCCCC-AGCGC--------GT-CTC-------------------------TGTGTGTGCATGGGGCA----------AAAAACTATGGCCGCATGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAA------GAAGAGGAAGATAA
droTak1	TATAATGTGTGTG------T----GTGCTATTATTAAAACCCCCCAACGTTCACACACACAC--AGCCA------------------------TGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAA------GAAGAGGAAGATAA
droEle1	TATAATGTGTGTG------T----GCGCTATTATTAAAACCCCC-AACTCTCACACATACATCTATGTA------------------------TGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAA------GAAGAGGAAGATAA
droRho1	TATAATGTGTGTG------T----GCGCTATTATTAAAACCCCC-AACGCTCACACACACACACACTCA--------------------TTCGTGGGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAA------GAAGAGGAAAATAA
droFic1	TATAATGTGTGTG------T----GCGCTATTATTAAAACCCCC-AACATACACACACACACATTTTCA------------------------TGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAAAA------GAAGAGGAAGATAA
droKik1	TATAATGTGTGTG------T----GTGCTATTATTAAAACCC-C-ACCGCACACACACACACCCAGC---ACACC---------AAGCATGCATGTGAATGGGGCA----------A-AAACTATGCGAGTGTGTATGTGTGCGAGGCGTTGGCGTTTTGACCAGAA------GCCGAAGAAGAGAA
droAna3	TATAATGTGTGTGTGTGTGTGTTTGTGCTATTATTAAAACCCCC-CTCGCAAGCACCCCC-CACTGCCA------------------------C-TGCATAGAGCAAAAAAAAAAAAAAAACTATAGTGGTGTGTG-GCAGGCGAGGCGTTGGCGTTTTGACCAAAA------GCTGAAGAAGAGGA
droBip1	TATAATGTGTGTG------T----GCGCTATTATTAAAACCCCC-CTCGCCAGAACACCT-CCCTGCCC------------------------G--GCATACAGCAAA--------AAAAACTATGGTAGTGTGTGTGTTTGCGAGGCGTTGGCGTTTTGACCAAAA------GCTGAAGAAGAGGA
dp4	TATAACGTGTGTGTGAGTGT----GTGCTATTATTAAACTCCCT-CC--CTAACACGCACAC--AACTATGT-----------TA--------T--G---------------------TAAGTGTGTGTGTGTGTGTGTGTGTGAGGCGTTGGCGTTTTGACCAGAAGCTGAAGAAGAGGAAGAATA
droPer1	TATAACGTGTGTGTGAGTGT----GTGCTATTATTAAACTCCCT-CC--CTAACACGCATAC--AACTATGT-----------TG--------T--GT---------------------AAGTGTGTGTGTGTGTGTGTGTGTGAGGCGTTGGCGTTTTGACCAGAAGCTGAAGAAGAGGAAGAATA

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

TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACACACAG---------------------C---------------------------------------------------------------------CGTGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTG-------ACCAGCAG------AAGAGGAAGATAG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................................................................................................................................................................................................................ACCAGCAG------CGGAGGAAGA...	18	1	1.00	0.00	0.00	0.00	1.00
....................................................................................CACACACACACACxG---------------------C---------------------------------------------------------------------TGT....................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00

droSec1

TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACACACAG---------------------C---------------------------------------------------------------------CGTGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTG-------ACCAGCAG------AAGAGGAAGATAG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................TGTGTGTG--------------CGT-GxTATTAT..................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.................................................................................................................................................................................................................................GCCGTGTGTGTATGTGCG..................................................	18	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................CCGTGTGTATTTGTGCGAGGCG.............................................	22	1	1.00	1.00	0.00	0.00
...........................................................................ACACA----CACACACACACACA...................................................................................................................................................................................................	19	19	0.05	0.00	0.00	0.05

droYak2

TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACACAGGG---------------------C---------------------------------------------------------------------CGTGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................................................................................................................................................................................................................TGGCGTTCTG-------ACCAGAAG------AAGAGGAAG....	27	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACAG--AG---------------------C---------------------------------------------------------------------CGTGTGCATGGGGCA----------AAAAACTATGGCCATGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..................................................................................................................................................................................................................................................................C-------ACCAGGAG------AAGAGGAAG....	18	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................ATGTGTATGTGTGGGATG...............................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

TATA------------ATATGTGTG--------------TGT-GCTATTATTAAAACCCC-------------CAACGTT----CACACACACACAC-----------------------T----------------------------------CAT-----------ATACCCGTATGTATATGTATGTATGTGCATGGGGCA----------AAAAACTATGAACGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAAAAG------AAGAAGAACATAA

Size

Hit Count

Total Norm

droBia1

TA---------------TGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAGCGCG------------TC-TC-------------------------------------------------------------------------------------------TGTGTGTGCATGGGGCA----------AAAAACTATGGCCGCATGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA

Size

Hit Count

Total Norm

droTak1

TATA------------ATGTGTGTG--------------TGT-GCTATTATTAAAACCCCC------------CAACGTT----CACACACACAC--AG---------------------C---------------------------------------------------------------------CATGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA

Size

Hit Count

Total Norm

droEle1

TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACTCT----CACACATACATCTAT---------------------G---------------------------------------------------------------------TATGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAGATAA

Size

Hit Count

Total Norm

droRho1

TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACGCT----CACACACACACACAC---------------------T-----------------------------------------------------------------CATTCGTGGGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAGAAG------AAGAGGAAAATAA

Size

Hit Count

Total Norm

droFic1

TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CAACATA----CACACACACACATTT---------------------T---------------------------------------------------------------------CATGTGCATGGGGCA----------AAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTG-------ACCAAAAG------AAGAGGAAGATAA

Size

Hit Count

Total Norm

droKik1

TATA------------ATGTGTGTG--------------TGT-GCTATTATTAAAACCCC--------------ACCGCA----CACACACACACCCAG----CACA-----------------------------------------------------------------CC---------AAGCATGCATGTGAATGGGGCA----------A-AAACTATGCGAGTGTGTATGTGTGCGAGGCGTTGGCGTTTTG-------ACCAGAAG------CCGAAGAAGAGAA

Size

Hit Count

Total Norm

droAna3

TATA------------ATGTGTGTGTGTGTGTGTT----TGT-GCTATTATTAAAACCCC-------------CCTCGCA----AGCACCCCC-CACTG---------------------C---------------------------------------------------------------------CAC-TGCATAGAGCAAAAAAAAAAAAAAAACTATAGTGGTGTGTG-GCAGGCGAGGCGTTGGCGTTTTG-------ACCAAAAG------CTGAAGAAGAGGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...A------------GTGTGTGTGTGTGTGTG....................................................................................................................................................................................................................................................................	18	27	0.41	0.04	0.37	0.00	0.00
...................AGTGTGTGTGTGTGTG----TG............................................................................................................................................................................................................................................................	18	27	0.41	0.04	0.37	0.00	0.00
.................AGTGTGTGTGTGTGTGTG----..............................................................................................................................................................................................................................................................	18	27	0.41	0.04	0.37	0.00	0.00
.....................AGTGTGTGTGTGTG----TGT-G.........................................................................................................................................................................................................................................................	18	27	0.41	0.04	0.37	0.00	0.00
....................GTGTGTGTGTGTGTG----TGT-..........................................................................................................................................................................................................................................................	18	20	0.50	0.00	0.50	0.00	0.00
..................GTGTGTGTGTGTGTGTG----T.............................................................................................................................................................................................................................................................	18	20	0.50	0.00	0.50	0.00	0.00
................GTGTGTGTGTGTGTGTGT...................................................................................................................................................................................................................................................................	18	20	0.50	0.00	0.50	0.00	0.00
.................TGTGTGTGTGTGTGTGTG----TGT-G.........................................................................................................................................................................................................................................................	22	8	1.00	0.00	1.00	0.00	0.00
.................AGTGTGTGTGTGTGTGTG----T.............................................................................................................................................................................................................................................................	19	22	0.36	0.00	0.36	0.00	0.00
...A------------GTGTGTGTGTGTGTGTGT...................................................................................................................................................................................................................................................................	19	22	0.36	0.00	0.36	0.00	0.00
...................AGTGTGTGTGTGTGTG----TGT-..........................................................................................................................................................................................................................................................	19	22	0.36	0.00	0.36	0.00	0.00
.....................TGTGTGTGTGTGTG----TGT-G.........................................................................................................................................................................................................................................................	18	23	0.30	0.00	0.30	0.00	0.00
.................TGTGTGTGTGTGTGTGTG----..............................................................................................................................................................................................................................................................	18	23	0.30	0.00	0.30	0.00	0.00
...................TGTGTGTGTGTGTGTG----TG............................................................................................................................................................................................................................................................	18	23	0.30	0.00	0.30	0.00	0.00
...................TGTGTGTGTGTGTGTG----TGT-..........................................................................................................................................................................................................................................................	19	19	0.32	0.00	0.32	0.00	0.00
..................GTGTGTGTGTGTGTGTG----TGT-G.........................................................................................................................................................................................................................................................	21	8	0.75	0.00	0.75	0.00	0.00
.................TGTGTGTGTGTGTGTGTG----T.............................................................................................................................................................................................................................................................	19	19	0.32	0.00	0.32	0.00	0.00
...................TGTGTGTGTGTGTGTG----TGT-G.........................................................................................................................................................................................................................................................	20	15	0.33	0.00	0.33	0.00	0.00
.................TGTGTGTGTGTGTGTGTG----TG............................................................................................................................................................................................................................................................	20	15	0.33	0.00	0.33	0.00	0.00
..................GTGTGTGTGTGTGTGTT----G.............................................................................................................................................................................................................................................................	18	12	0.42	0.00	0.42	0.00	0.00
...A------------GTGTGTGTGTGTGTGTT....................................................................................................................................................................................................................................................................	18	13	0.23	0.00	0.23	0.00	0.00
...G------------GTGTGTGTGTGTGTGTGT...................................................................................................................................................................................................................................................................	19	21	0.14	0.05	0.10	0.00	0.00
..................GTGTGTGTGTGTGTGTG----TGT-..........................................................................................................................................................................................................................................................	20	10	0.30	0.00	0.30	0.00	0.00
...................GGTGTGTGTGTGTGTG----TGT-..........................................................................................................................................................................................................................................................	19	21	0.14	0.05	0.10	0.00	0.00
.....................TGTGTGTGTGTGTG----TGT-GC........................................................................................................................................................................................................................................................	19	8	0.38	0.00	0.38	0.00	0.00
.................GGTGTGTGTGTGTGTGTG----T.............................................................................................................................................................................................................................................................	19	21	0.14	0.05	0.10	0.00	0.00
.................TGTGTGTGTGTGTGTGTG----TGT-..........................................................................................................................................................................................................................................................	21	10	0.30	0.00	0.20	0.10	0.00
.................TGTGTGTGTGTGTGGGTG----..............................................................................................................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00
.................TGTGTGTGTGTGTGTGTT----GGT-G.........................................................................................................................................................................................................................................................	22	7	0.43	0.00	0.43	0.00	0.00
.................AGTGTGTGTGTGTGTGTT----..............................................................................................................................................................................................................................................................	18	13	0.23	0.00	0.23	0.00	0.00
..................GTGTGTGTGTGTTTGTG----TGT-GC........................................................................................................................................................................................................................................................	22	6	0.50	0.00	0.50	0.00	0.00
.................TGTGTGTGTGTGTGTGTT----..............................................................................................................................................................................................................................................................	18	10	0.30	0.00	0.30	0.00	0.00
.....................TGTGTGTGTGTGTG----GGT-G.........................................................................................................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00
......................GTGTGTGTGTGTG----TGT-GC........................................................................................................................................................................................................................................................	18	8	0.38	0.00	0.38	0.00	0.00
................ATGTGTGTGTGTCTGTGTG----TG............................................................................................................................................................................................................................................................	21	10	0.30	0.00	0.30	0.00	0.00
...................TGTGTGTGTGTGTGGG----TG............................................................................................................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00

droBip1

TATA------------ATGTGTGTG--------------TGC-GCTATTATTAAAACCCC-------------CCTCGCC----AGAACACCTC-CCTG---------------------C---------------------------------------------------------------------CCG--GCATACAGCAA--------AAAAAACTATGGTAGTGTGTGTGTTTGCGAGGCGTTGGCGTTTTG-------ACCAAAAG------CTGAAGAAGAGGA

Size

Hit Count

Total Norm

dp4

TATA------------ACGTGTGTGTGAGTG--------TGT-GCTATTATTAAACTCCC-------------TCCC--T----AACACGCACAC--AA---------------------C----------------------------------TAT-----------GT-------------------TA------TG-----------------TAAGTGTGTGTGTGTGTGTGTGTGTGAGGCGTTGGCGTTTTG-------ACCAGAAGCTGAAGAAGAGGAAGAATA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTGTG..................................................	24	35	0.71	0.11	0.00	0.60	0.00
.............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTGTG................................................	24	35	0.71	0.11	0.00	0.60	0.00
............................................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGTGTGTG................................................	25	28	0.29	0.04	0.00	0.25	0.00
.......................................................................................................................................................................................................G-----------------TACGTGTGTGTGTGTGTGC.........................................................	20	6	1.33	0.00	1.33	0.00	0.00
......................................................................................................................................................................................................TG-----------------TAAGTGTAAGTGTGTGTG..........................................................	20	1	7.00	5.00	0.00	2.00	0.00
............................................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGTGTG..................................................	23	41	0.15	0.00	0.00	0.15	0.00
..............................................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGTGTG................................................	23	41	0.15	0.00	0.00	0.15	0.00
................................................................................................................................................................................................................................GTACGTGTGTGTGTGTGTG..................................................	19	46	0.11	0.04	0.04	0.02	0.00
.......................................................................................................................................................................................................G-----------------TACGTGTGTGTGTGTGTG..........................................................	19	46	0.11	0.04	0.04	0.02	0.00
............................................................................................................................................................................................................................GTACGTGTGTGTGTGTGTG......................................................	19	46	0.11	0.04	0.04	0.02	0.00
.........................................................................................................................................................................TT-------------------TA------TG-----------------TGAGTGTGTGTGTG..............................................................	20	5	1.00	1.00	0.00	0.00	0.00
.......................................................................................................................................................................................................G-----------------TACGTGTGTGTGTGTGT...........................................................	18	53	0.09	0.00	0.09	0.00	0.00
..............................................................................................................................................................................................................................GTACGTGTGTGTGTGTGTG....................................................	19	46	0.11	0.04	0.04	0.02	0.00
..............................G--------TGT-GCTTTTATTAGACT............................................................................................................................................................................................................................................	18	1	4.00	0.00	4.00	0.00	0.00
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTG................................................	22	49	0.08	0.00	0.00	0.08	0.00
.............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTG..................................................	22	49	0.08	0.00	0.00	0.08	0.00
...........................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTG....................................................	22	49	0.08	0.00	0.00	0.08	0.00
......................................................................................................................................................................................................TG-----------------TAAGTGTAAGTGTGTGT...........................................................	19	1	3.00	2.00	0.00	1.00	0.00
......................................................................................................................................................................................................TG-----------------TAAGTGTGAGTGTGTGT...........................................................	19	3	1.00	0.33	0.00	0.67	0.00
............................................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGTGTGTGG...............................................	26	9	0.33	0.22	0.00	0.11	0.00
.............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT.....................................................	19	35	0.09	0.03	0.00	0.06	0.00
.......................................................................................................................................................................................................G-----------------TACGTGTGTGTGTGTGTGCG........................................................	21	4	0.75	0.00	0.50	0.25	0.00
.............................................................................................................................................................................................................................TTTGTGTGTGTGTGTGTG......................................................	18	49	0.06	0.02	0.02	0.02	0.00
..........................................................................................................................................................................................................................AAGTGTCTGTCTGTGTGTGT.......................................................	20	2	1.50	1.50	0.00	0.00	0.00
......................................................................................................................................................................................................TG-----------------TAAGTGTAAGTGTGTGTGT.........................................................	21	1	3.00	2.00	1.00	0.00	0.00
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT...................................................	19	35	0.09	0.03	0.00	0.06	0.00
.................................................................................................................................................................................................................................TTTGTGTGTGTGTGTGTG..................................................	18	49	0.06	0.02	0.02	0.02	0.00
...............................................................................................................................................................................................................................TTTGTGTGTGTGTGTGTG....................................................	18	49	0.06	0.02	0.02	0.02	0.00

droPer1

TATA------------ACGTGTGTGTGAGTG--------TGT-GCTATTATTAAACTCCC-------------TCCC--T----AACACGCATAC--AA---------------------C----------------------------------TAT-----------GT-------------------TG--TGT---------------------AAGTGTGTGTGTGTGTGTGTGTGTGAGGCGTTGGCGTTTTG-------ACCAGAAGCTGAAGAAGAGGAAGAATA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.............................................................................................................................................................................................................................TGTTTGTTTGTGTGTGTGTGT...................................................	21	29	0.55	0.55	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGTGC...................................................	20	50	0.24	0.06	0.18	0.00	0.00	0.00
............................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGTGC.....................................................	20	50	0.24	0.06	0.18	0.00	0.00	0.00
................................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGTGC.................................................	20	50	0.24	0.06	0.18	0.00	0.00	0.00
..............................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGTG....................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
................................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGTG..................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
............................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGTG......................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
..............................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGT.....................................................	18	47	0.17	0.02	0.15	0.00	0.00	0.00
................................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGT...................................................	18	47	0.17	0.02	0.15	0.00	0.00	0.00
............................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGT.......................................................	18	47	0.17	0.02	0.15	0.00	0.00	0.00
.................................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTG..................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
.............................................................................................................................................................................................................................TGTTTGTTTGTGTGTGTGTG....................................................	20	40	0.18	0.10	0.03	0.00	0.05	0.00
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTG....................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
.............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTG......................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
...............................................................................................................................................................................................................................TGTTTGTTTGTGTGTGTGTG..................................................	20	40	0.18	0.10	0.03	0.00	0.05	0.00
.............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT.....................................................	19	32	0.16	0.16	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTGTG................................................	24	29	0.17	0.10	0.00	0.03	0.03	0.00
................................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGTGCG................................................	21	41	0.12	0.10	0.02	0.00	0.00	0.00
..............................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGTGCG..................................................	21	41	0.12	0.10	0.02	0.00	0.00	0.00
...........................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTGTG..................................................	24	29	0.17	0.10	0.00	0.03	0.03	0.00
............................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGTGCG....................................................	21	41	0.12	0.10	0.02	0.00	0.00	0.00
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT...................................................	19	32	0.16	0.16	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................GTGTGTGTGTGTGxGTGTGTGTC..................................................	22	49	0.08	0.08	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTG..................................................	22	50	0.08	0.08	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................GTGTGTGCGTGTGTGTGTGTG..................................................	21	61	0.07	0.07	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTG................................................	22	50	0.08	0.08	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTG....................................................	22	50	0.08	0.08	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................GTGTTTGTGTGTGTGTTTGTG....................................................	21	32	0.09	0.09	0.00	0.00	0.00	0.00
..................GTGTGTGTGTGTG--------TGC-GCT.......................................................................................................................................................................................................................................................	19	15	0.20	0.13	0.00	0.07	0.00	0.00
............................................................................................................................................................................................................................GTGTGTGTGTTTGTGTGTA......................................................	19	49	0.06	0.06	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................GGTGTGTGTGTGTGTGTGT.......................................................	19	40	0.08	0.08	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................CGTGCGTGTGTGTGTGTGTG......................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................GTGTGTGTGTTTGTGTGTA..................................................	19	49	0.06	0.06	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................GGTGTGTGTGTGTGTGTGT...................................................	19	40	0.08	0.08	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................GTTTGTTTGTGTGTGTGTGT.....................................................	20	35	0.09	0.09	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................CGTGCGTGTGTGTGTGTGTG..................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................GTGTGTGTGTGCGxGTGAG................................................	18	8	0.38	0.38	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................GTTTGTTTGTGTGTGTGTGT...................................................	20	35	0.09	0.09	0.00	0.00	0.00	0.00
....................................................................................................................................................................................................T---------------------AAGTGTCTGTCTGTGTGTG........................................................	20	3	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................GTGTTTGTGTGTGTGTTTGTG..................................................	21	32	0.09	0.09	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................GTGTGTGTGTTTGTGTGTA....................................................	19	49	0.06	0.06	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................GTGTGTGTGCGTGTGTGAGTG..................................................	21	30	0.10	0.10	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................GGTGTGTGTGTGTGTGTGT.....................................................	19	40	0.08	0.08	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................GTGTGTGTGCGTGTGTGAGTG....................................................	21	30	0.10	0.10	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................CGTGCGTGTGTGTGTGTGTG....................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00

droWil1

CAAATGGTATGCGTCTATGTGTATGTGTGTG--CCTGTGTGTGGCTATTATTAAAAATCCACACCTCCTACCCCAACCCCCCGTTACATATACACACAACCAATACATCCATACGCCCACACATACACATA-------------------------------------------------------CA--TGAAAAGAAAAGGAA------AAAAAAGAACTA------------------TGAGGCGTTGGCGTTCGTTCCGGGCACTACAAG------A---AGAAGAAGA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........TGCGTATATGTGTGTGTGTG........................................................................................................................................................................................................................................................................	20	12	0.42	0.00	0.42	0.00	0.00
..........................................................................................................................................................................................................................................................................AATAGAAG------A---AGAAGAAGA	18	3	1.33	0.00	1.33	0.00	0.00
......................GTGCGTGTG--CCTGTGTGT...........................................................................................................................................................................................................................................................	18	5	0.60	0.00	0.60	0.00	0.00
.........TGCGTATATGTGTGTGTGTGT.......................................................................................................................................................................................................................................................................	21	12	0.25	0.00	0.25	0.00	0.00
...................................................................................................................................................................................................GAAAAAGGAA------AAAAAAGA..........................................................................	18	6	0.50	0.00	0.50	0.00	0.00
..................GTGTGTGTGTTTG--CCTGTGT.............................................................................................................................................................................................................................................................	20	6	0.50	0.00	0.50	0.00	0.00

droVir3

CATA------------TTGTACGTG--------------TGT-GCTATTATTAAAATGCC-------------ACACGCA----CGCACACATAGAGAC---------------------G----GGGGGACACGGACACGGCAAAAAGAAAAACTAT-----------TC-------------------T-------------------------------CAGAGTGTGTGTGCGCCTACGAGGCGTTGGCGTTTTG-------GCTAGAAG------AAGC--------A	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
............................................................................................................................................GGCAAAAAGAACAACCAT-----------............................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

TATA------------TTGTATGTG--------------TGT-GCTATTATTAAAATACC-------------ACATGCA----CGCACACACAGAGAG---------------------G----CAGAGACACGGACACAGCAAAAAGAAAAACTATTTACAGTTGCTGCGACTGTGTG-----------------------------------------TATATACATATATGCGCCTACGAGGCGTTGGCGTTTCA-------GCAAGCGA------GAGAGTGAGAGAG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..........................................................................................CACACAGAG---------------------G----GAGAGACA................................................................................................................................................................	18	16	0.06	0.00	0.00	0.00	0.06

droGri2

AACA------------A------------------------------------------G-------------CAACACA----CACACACACACACAC---------------------A---------------------------------------------------------------------CA--CACGCA-GACA----------AAGAAACACACACTCACATACATC-TTGATGTGTTCATATTTATG------CCAAGTCA------AACTCAAAAGCTT	Size	Hit Count	Total Norm	V109 Male body
........................................................................................TACACACACAC---------------------A---------------------------------------------------------------------CA--CACGCG-............................................................................................	20	42	0.02	0.02
......................................................................................TACACACACACAC---------------------A---------------------------------------------------------------------CA--CGCG...............................................................................................	20	42	0.02	0.02

Generated: 04/20/2012 at 05:19:22 EDT

dme-mir-2493

chr3R:10956476-10956581 -

Known_mirbase

intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup