dme-mir-4981- Best orthologs

dme-mir-4981	chr2R:3902753-3902848 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 3902810-3902830
   star strand at position 3902770-3902791
   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	chr2R:3902738-3902863 +		1	GGTT------------------------------------------------------------------------------------AT------CC------CT--------GC-CACATGGCCACGTGCC-CGCAAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTTGG-C-C----GG--TCGAGC--AGCGTCTTG---------GGG-TTGTTCG--------------TGGATTAAGTTC------------------------------GATT---------------------CCTAT
droSim1	chr2R_random:1106077-1106202 +	LASTZ	4	GGAT------------------------------------------------------------------------------------AT------CC------CT--------GC-CACATGGCCACGTGCC-TGCAAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTTGG-C-C----GG--TCGAGC--AGCGTCTTG---------GGG-TTGTTCC--------------TGGATTAAGTTC------------------------------GATT---------------------CCTAT
droSec1	super_1:1540674-1540799 +	LASTZ	4	GGAT------------------------------------------------------------------------------------AT------CC------CT--------GC-CACATGGCCACGTGCC-CGCAAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTTGG-C-C----GG--TCGAGC--AGCGTCTTG---------GGG-TTGTTCC--------------TGGATTAAGTTC------------------------------GATT---------------------CCTAT
droYak2	chr2L:16559915-16560042 +	LASTZ	4	GGAT------------------------------------------------------------------------------------AT------CC------CT--------GC-CACATGGCCACGTGCC-TGCAAGACGCCTTCGA----------------------------------------------------------------------------------------------------CCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTTGG-C-C----GA--ACGAACGGAGCGTCTTG---------GGG-TTGTTTC--------------GGGATTACGTTC------------------------------GATT---------------------CCGAT
droEre2	scaffold_4929:18723379-18723500 -	LASTZ	4	GGAT------------------------------------------------------------------------------------A-------CC------CA--------GC-CACATGGCCACGTGCC-TGCAAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTTGG-C-C----GG--T---CG--AGCGTCTTG---------GGG-TTGTTTC--------------GGGATTGAGTTC------------------------------GATT---------------------CCGAT
droEug1	scf7180000409474:2738124-2738301 +	LASTZ	5	GCTCA----------------ACCCATT----CCC----AT------T-----CCCCAATTGCAGCG------------GG------GATCCTTTT-----GGCCT--------GC-CGCATGGCCACGTGCC-CGCAAGACGCCTCCAG----------------------------------------------------------------------------------------------------CCG--GCA-----------G-AAAGTTTCAATTTGATATTCCTTTGGC-C----AG--AAGGCA--AGCATCTTG---------GGG-TTGTTCCTGGGCCCGAG-CCCTGGATTAAGTTC------------------------------GATT---------------------CCGAC
droBia1	scf7180000302291:1753447-1753666 +	LASTZ	4	GCTCA---------------------CCCCT----------------TCT------CCGTTGCAGCGGGCGGGGGCATGGGGATCGGGGTCCCT-T-----GGCCT--------GC-CACATGGCCACGTGCC-TGCAAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GTA-----------C-AAAGTTTCAATTTGGTGCTCCTTGGGC-C----GG--CAGGCG--AGCGTCTTG---------GGG-TTGTTTCGG---CCGAG-TCCGGGATTAAGTTCTCGTCTGCGTCGGACCAGTATTCCGATTCCGATT---------------CCGATTCCGGT
droTak1	scf7180000415088:209457-209618 -	LASTZ	5	GGTT-------------------------------------------------------------------------------------------T-----GGCCTGCCACATGGC-CAAATGGCCACGTGCCATGCAAGACGCCGGT-G----------------------------------------------------------------------------------------------------CCG--CTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGC-C----AG--GAGGCG--AGCGTCTTGGTCTTGTTGGGG-TTGTTTCGC-TTCCGAG-CCCTGGATTAAGTTC------------------------------GATT---------------CCGAATCCGAT
droEle1	scf7180000491258:123314-123472 -	LASTZ	5	GGA--------------------------------------------------------------------------------------TCCTTTT-----CGCCT--------GC-CACACGGGCACGTGCC-TGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CCAAGGTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGC-C----AG--A---CG--AGCATCTTG---------GGG-TTGTTTCAGG--CCAAGTCCCTGGATTAAGTTC-CAGGCG-GC----------------------------C-----CAAGACCGATTGCGAT
droRho1	scf7180000774573:162056-162212 +	LASTZ	5	GGA--------------------------------------------------------------------------------------TCCTTTT-----CGCCT--------GC-CACACGGCCACGTGCC-CGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CCAAGGTA-----------C-GAACTTTCAATTTGATATTCCCTTGGC-C----CG--G---CG--AGCATCTTG---------GGG-TTGTTCG-GG--CCAGG-CCCTGGATTAAGTTC-GAGGCG-GG----------------------------C-----CAGGAGCGATTGCGAT
droFic1	scf7180000453215:304266-304397 -	LASTZ	5	GGGG------------------------------------------------------------------------------------AT------CCTTCGACAT--------GC-CACATGGCCACGTGCC-GGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CTG--GCA-------------AAAGTTTCAATTTGATATTCCTTAGGC------CA--T---CC--AGCGTCTTG---------GGG-TTGCTTT---------G-CCCTGGATTAAGTTC------------------------------GAGT---------------------CGGGC
droKik1	scf7180000302471:525269-525433 +	LASTZ	5	GATC---------------------------------------------------------------------------------------CTTTC-----GGCCG--------GC--CCATGGCCACGTGCC-AGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CCGGTGTG-----------C-ACAGTTTCAATTTGATATTCCTTTGGA-C----CG--GCGAAC--AACGTCTTG---------GGG-TTGTTTCT------------CGGGATTAAGTTCACAGGCA-GCTGGAGCAGT--------------G-----CGGGCTTAGTCTGATTCTTAC
droAna3	scaffold_13266:16222514-16222662 +	LASTZ	5	GGAG------------------------------------------------------------------------------------AT------CC------TT--------G--CGTGTGGCCACGTGCCGGGTGAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTTG--AGCGTCTTG---------GGG-TTGTTCCGG-------G-CCATGGATTAAGTTG--AGAAA------------------------ATG-----CA----------GAC-TATGT
droBip1	scf7180000396567:704320-704511 +	LASTZ	5	GTTC-TGCTCCTGTTCTCGCAACCCACT----CCAGAGCATACCCCTTCT-GACCACCGTCGC--------------TGGG------AAT------CC------TT--------G--CGTGCTGCCACGTGCC-TGTGAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTCG--AGCGTCTTG---------GGG-TTGCTTCGG-------G-CCATGGATTAAGTTG--------------------------------------------------------AGAA
dp4	chr3:5536552-5536721 +	LASTZ	4	GGTTGCGCTGCTGCT-------------------T----A----------TGG------------------------------------------------------------TGCTGGTGTTGCCACGTGCC--ACAAGACGCCTTCAT----------------------------------------------------------------------------------------------------CTG--GCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGCC-T----TG--C---CG--AGCGTCTTG---------GGG-TTGTTTCAG-------G-GCATGGATTAAGTTTTCAGGCA-ACTGGAGCAGC------------ATC---------------------CGTGC
droPer1	super_2:5730715-5730884 +	LASTZ	4	GGTTGCGCTGCTGCT-------------------T----A----------TGG------------------------------------------------------------TGCTGGTGTTGCCACGTGCC--ACAAGACGCCTTCAT----------------------------------------------------------------------------------------------------CTG--GCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGCC-T----TG--C---CG--AGCGTCTTG---------GGG-TTGTTTCAG-------G-GCATGGATTAAGTTTTCAGGCA-ACTGGAGCAGC------------ATC---------------------CGTGC
droWil1	scaffold_181141:2380508-2380690 -	LASTZ	0	ACCCA---------------------TTTCTG--------G------TCTCGGTCTCAA------------------------------TTTTTT------------------TACTGGTGTGGCCACGTGCCATACGAGTA-----------------------------------------------------------------------------------GTAAGGTCTTGCA-ACAGGGCGGTGC---------------GAACAAAAGTTTCAATTTGATATTCCCTTGCC-TTGACTTGGCC--GT--AGCGTCTTA---------GGG-ATGTTTCC------GAA-GCAAGGATTAAGTTTTCAAAG-----------G---------------------CA----------G-C-TGTGC
droVir3	scaffold_12875:14800808-14801017 +	LASTZ	0	GCTTC---------------------TTTGTGTCC----A----------TGG-C-----------------------------------------CC------TT--------GC-CGTGTGGCCACGTGCC-A-TCAGACGCCTTCGCGCAGTTTGACTC--------------------------------------------TGGAATGGCTGAGGGCTG-GTGGGG---CGGA-ACGGGGCAGCGG--GGATT-----------G-ACAGTTTCAATTTGCAAGCATGTTG-C-C----TT--TTGTAG--AACGTCTTG---------GGGGTTGTTCG-----CCAGC-TGACGGATTAAGTTTTGAGGGC------------------------A---------------GCCAGATGCTGCT
droMoj3	scaffold_6496:7113415-7113501 -	LASTZ	0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACAGTTTCAATTTGCAAGCTTGTTG-C-C----TT--TTACGG--AACGTCTTG---------GGG-TGTCTGA--------------GGGATTAAGTTT------------------------------AAGTCTGGG-----CATGCCAG----CTGC
droGri2	scaffold_15245:14811478-14811742 +	LASTZ	0	GTTTC---------------------TTTGTGTCC----A-----------GACCCTTGCCGC--------------CT--------------------------TGCCGCCTTGC-CGTGTGGCCACGTGCCAGCAGAGACGCCTTCGCGCTCACTGACTCGTCCCGGCCCGGCAATTGTCAGAGACGCAGATGACTGTTGCGAATAGGTTGGCAGGGGGGGGAGT-CGG---CGGACAGGGGGAAGGGGTG--GTT-----------G-ACAGTTTCAATTTGCAAGCTTGTTG-C-C----TT--TTGCAG--AACGTCTTG---------GGG-TTGTTTCAG-------C-TGGCGGATTAAGGTTTCAGACA-GT-----------------------------CA----------G---CCAGC

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	GGTT-------------------------------------------------------------------------------AT------CC------CT------------GCC--ACATGGCCACGTGCC-CGCAAGACGCCTTCGGCCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTT-GGC------C-G---GTCGAGC--AGCGTCTT---------GGGGTTGTTC--------------GTGGATTAAGTTC------------------------------GATT----------------CCTAT
droSim1	GGAT-------------------------------------------------------------------------------AT------CC------CT------------GCC--ACATGGCCACGTGCC-TGCAAGACGCCTTCGGCCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTT-GGC------C-G---GTCGAGC--AGCGTCTT---------GGGGTTGTTCC--------------TGGATTAAGTTC------------------------------GATT----------------CCTAT
droSec1	GGAT-------------------------------------------------------------------------------AT------CC------CT------------GCC--ACATGGCCACGTGCC-CGCAAGACGCCTTCGGCCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTT-GGC------C-G---GTCGAGC--AGCGTCTT---------GGGGTTGTTCC--------------TGGATTAAGTTC------------------------------GATT----------------CCTAT
droYak2	GGAT-------------------------------------------------------------------------------AT------CC------CT------------GCC--ACATGGCCACGTGCC-TGCAAGACGCCTTCGACCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTT-GGC------C-G---AACGAACGGAGCGTCTT---------GGGGTTGTTTC--------------GGGATTACGTTC------------------------------GATT----------------CCGAT
droEre2	GGAT-------------------------------------------------------------------------------A-------CC------CA------------GCC--ACATGGCCACGTGCC-TGCAAGACGCCTTCGGCCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTT-GGC------C-G---GTCG-----AGCGTCTT---------GGGGTTGTTTC--------------GGGATTGAGTTC------------------------------GATT----------------CCGAT
droEug1	GCTCA----------------ACCCATTCCC----AT-----TCCC-----CAATTGCAGCG------------GG------GATCCTTTT-----GGCCT------------GCC--GCATGGCCACGTGCC-CGCAAGACGCCTCCAGCCG--GCA-----------G-AAAGTTTCAATTTGATATTCCTTTGGC------C-AGAAGGCA-----AGCATCTT---------GGGGTTGTTCCTGGGCCCGAG-CCCTGGATTAAGTTC------------------------------GATT----------------CCGAC
droBia1	GCTCAC---------------------------------CCCTTCT-----CCGTTGCAGCGGGCGGGGGCATGGGGATCGGGGTCCC-TT-----GGCCT------------GCC--ACATGGCCACGTGCC-TGCAAGACGCCTTCGGCCG--GTA-----------C-AAAGTTTCAATTTGGTGCTCCTTGGGC------C-GGCAGGCG-----AGCGTCTT---------GGGGTTGTTTCGG---CCGAG-TCCGGGATTAAGTTCTCGTCTGCGTCGGACCAGTATTCCGATTCCGATT----------CCGATTCCGGT
droTak1	GGTT--------------------------------------------------------------------------------------T-----GGCCTGCCAC--ATG--GCC--AAATGGCCACGTGCCATGCAAGACGCCGGT-GCCG--CTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGC------C-AGGAGGCG-----AGCGTCTTGGTCTTGTTGGGGTTGTTTCGC-TTCCGAG-CCCTGGATTAAGTTC------------------------------GATT----------CCGAATCCGAT
droEle1	GG---------------------------------------------------------------------------------ATCCTTTT-----CGCCT------------GCC--ACACGGGCACGTGCC-TGCAAGACGCCTTCAGCCAAGGTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGC------C-A---GACG-----AGCATCTT---------GGGGTTGTTTCAGG--CCAAGTCCCTGGATTAAGTTC-CAG-----------------------------GCGGCCCAAGACCGATTGCGAT
droRho1	GG---------------------------------------------------------------------------------ATCCTTTT-----CGCCT------------GCC--ACACGGCCACGTGCC-CGCAAGACGCCTTCAGCCAAGGTA-----------C-GAACTTTCAATTTGATATTCCCTTGGC------C-C---GGCG-----AGCATCTT---------GGGGTTGTTCG-GG--CCAGG-CCCTGGATTAAGTTC-GAG-----------------------------GCGGGCCAGGAGCGATTGCGAT
droFic1	GGGG-------------------------------------------------------------------------------AT------CCTTCGACAT------------GCC--ACATGGCCACGTGCC-GGCAAGACGCCTTCAGCTG--GCA-------------AAAGTTTCAATTTGATATTCCTTAGG-------C-C---ATCC-----AGCGTCTT---------GGGGTTGCTTT---------G-CCCTGGATTAAGTTC------------------------------GAGT----------------CGGGC
droKik1	G----------------------------------------------------------------------------------ATCCTTTC-----GGCCG------------GC---CCATGGCCACGTGCC-AGCAAGACGCCTTCAGCCGGTGTG-----------C-ACAGTTTCAATTTGATATTCCTTTGGA------C-C---GGCGAAC--AACGTCTT---------GGGGTTGTTTCT------------CGGGATTAAGTTCACAGGCA-GCTGGAGCAGT--------------GCGGGCTTAGTCTGATTCTTAC
droAna3	GGAG-------------------------------------------------------------------------------AT------CC------TT------------G-C--GTGTGGCCACGTGCCGGGTGAGACGCCTTCGGCCG--GTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTTG-----AGCGTCTT---------GGGGTTGTTCCGGG--------CCATGGATTAAGTTGA---GAA-A----------------------ATGCAGAC-----------TATGT
droBip1	GTTC-TGCTCCTGTTCTCGCAACCCACTCCAGAGCATACCCCTTCTGACCACCGTCGC--------------TGGG------AAT------CC------TT------------G-C--GTGCTGCCACGTGCC-TGTGAGACGCCTTCGGCCG--GTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTCG-----AGCGTCTT---------GGGGTTGCTTCGGG--------CCATGGATTAAGTTG---------------------------------------------------AGAA
dp4	GGTTGCGCTGCTG--------------------------------------------------------------------------------------------CTTATGGTG-CTGGTGTTGCCACGTGCC--ACAAGACGCCTTCATCTG--GCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGCC------T-T---GCCG-----AGCGTCTT---------GGGGTTGTTTCAGG--------GCATGGATTAAGTTTTCAGGCA-ACTGGAGCAGC------------ATC----------------CGTGC
droPer1	GGTTGCGCTGCTG--------------------------------------------------------------------------------------------CTTATGGTG-CTGGTGTTGCCACGTGCC--ACAAGACGCCTTCATCTG--GCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGCC------T-T---GCCG-----AGCGTCTT---------GGGGTTGTTTCAGG--------GCATGGATTAAGTTTTCAGGCA-ACTGGAGCAGC------------ATC----------------CGTGC

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

GGAT------------------------------------------------------------------------------------AT------CC------CT--------GC-CACATGGCCACGTGCC-TGCAAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTTGG-C-C----GG--TCGAGC--AGCGTCTTG---------GGG-TTGTTCC--------------TGGATTAAGTTC------------------------------GATT---------------------CCTAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................................................................................................................................................................................TTGG-C-C----GG--TCGAGC--AGCGTCTTG---------.................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
........................................................................................................CT--------GG-CACATGCCCACGTGC...........................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00

droSec1

GGAT------------------------------------------------------------------------------------AT------CC------CT--------GC-CACATGGCCACGTGCC-CGCAAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTTGG-C-C----GG--TCGAGC--AGCGTCTTG---------GGG-TTGTTCC--------------TGGATTAAGTTC------------------------------GATT---------------------CCTAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
....................................................................................................................................................................................................................................................................................................TTGG-C-C----GG--TCGAGC--AGCGTCT............................................................................................................	21	1	2.00	0.00	0.00	2.00
............................................................................................................................CCACGTGAC-CGCAAGAAGC...............................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00

droYak2

GGAT------------------------------------------------------------------------------------AT------CC------CT--------GC-CACATGGCCACGTGCC-TGCAAGACGCCTTCGA----------------------------------------------------------------------------------------------------CCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTTGG-C-C----GA--ACGAACGGAGCGTCTTG---------GGG-TTGTTTC--------------GGGATTACGTTC------------------------------GATT---------------------CCGAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................................................................................................................................................................................................................................................................................................CG---------GGG-TTGATTC--------------GGGATTA.................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................................................................................................................CGGAGCGTGTTG---------GGA-T............................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

GGAT------------------------------------------------------------------------------------A-------CC------CA--------GC-CACATGGCCACGTGCC-TGCAAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GCG-----------C-AAAGTTTCAATTTGATATTCCTTGG-C-C----GG--T---CG--AGCGTCTTG---------GGG-TTGTTTC--------------GGGATTGAGTTC------------------------------GATT---------------------CCGAT

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

GCTCA----------------ACCCATT----CCC----AT------T-----CCCCAATTGCAGCG------------GG------GATCCTTTT-----GGCCT--------GC-CGCATGGCCACGTGCC-CGCAAGACGCCTCCAG----------------------------------------------------------------------------------------------------CCG--GCA-----------G-AAAGTTTCAATTTGATATTCCTTTGGC-C----AG--AAGGCA--AGCATCTTG---------GGG-TTGTTCCTGGGCCCGAG-CCCTGGATTAAGTTC------------------------------GATT---------------------CCGAC

Size

Hit Count

Total Norm

droBia1

GCTCA---------------------CCCCT----------------TCT------CCGTTGCAGCGGGCGGGGGCATGGGGATCGGGGTCCCT-T-----GGCCT--------GC-CACATGGCCACGTGCC-TGCAAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GTA-----------C-AAAGTTTCAATTTGGTGCTCCTTGGGC-C----GG--CAGGCG--AGCGTCTTG---------GGG-TTGTTTCGG---CCGAG-TCCGGGATTAAGTTCTCGTCTGCGTCGGACCAGTATTCCGATTCCGATT---------------CCGATTCCGGT

Size

Hit Count

Total Norm

droTak1

GGTT-------------------------------------------------------------------------------------------T-----GGCCTGCCACATGGC-CAAATGGCCACGTGCCATGCAAGACGCCGGT-G----------------------------------------------------------------------------------------------------CCG--CTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGC-C----AG--GAGGCG--AGCGTCTTGGTCTTGTTGGGG-TTGTTTCGC-TTCCGAG-CCCTGGATTAAGTTC------------------------------GATT---------------CCGAATCCGAT

Size

Hit Count

Total Norm

droEle1

GGA--------------------------------------------------------------------------------------TCCTTTT-----CGCCT--------GC-CACACGGGCACGTGCC-TGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CCAAGGTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGC-C----AG--A---CG--AGCATCTTG---------GGG-TTGTTTCAGG--CCAAGTCCCTGGATTAAGTTC-CAGGCG-GC----------------------------C-----CAAGACCGATTGCGAT

Size

Hit Count

Total Norm

droRho1

GGA--------------------------------------------------------------------------------------TCCTTTT-----CGCCT--------GC-CACACGGCCACGTGCC-CGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CCAAGGTA-----------C-GAACTTTCAATTTGATATTCCCTTGGC-C----CG--G---CG--AGCATCTTG---------GGG-TTGTTCG-GG--CCAGG-CCCTGGATTAAGTTC-GAGGCG-GG----------------------------C-----CAGGAGCGATTGCGAT

Size

Hit Count

Total Norm

droFic1

GGGG------------------------------------------------------------------------------------AT------CCTTCGACAT--------GC-CACATGGCCACGTGCC-GGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CTG--GCA-------------AAAGTTTCAATTTGATATTCCTTAGGC------CA--T---CC--AGCGTCTTG---------GGG-TTGCTTT---------G-CCCTGGATTAAGTTC------------------------------GAGT---------------------CGGGC

Size

Hit Count

Total Norm

droKik1

GATC---------------------------------------------------------------------------------------CTTTC-----GGCCG--------GC--CCATGGCCACGTGCC-AGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CCGGTGTG-----------C-ACAGTTTCAATTTGATATTCCTTTGGA-C----CG--GCGAAC--AACGTCTTG---------GGG-TTGTTTCT------------CGGGATTAAGTTCACAGGCA-GCTGGAGCAGT--------------G-----CGGGCTTAGTCTGATTCTTAC

Size

Hit Count

Total Norm

droAna3

GGAG------------------------------------------------------------------------------------AT------CC------TT--------G--CGTGTGGCCACGTGCCGGGTGAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTTG--AGCGTCTTG---------GGG-TTGTTCCGG-------G-CCATGGATTAAGTTG--AGAAA------------------------ATG-----CA----------GAC-TATGT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.............................................................................................................................TACTTGCCGGGTGAGACGC...............................................................................................................................................................................................................................................................................................	19	1	5.00	0.00	0.00	0.00	5.00
.............................................................................................................................TACTTGCCGGGTGAGACG................................................................................................................................................................................................................................................................................................	18	1	3.00	0.00	0.00	0.00	3.00
..........................................................................................................................................................................................................................................................................................................................................................................ATTAAGTTG--AGAAA------------------------GTG-----CT----------.........	19	1	1.00	0.00	0.00	0.00	1.00

droBip1

GTTC-TGCTCCTGTTCTCGCAACCCACT----CCAGAGCATACCCCTTCT-GACCACCGTCGC--------------TGGG------AAT------CC------TT--------G--CGTGCTGCCACGTGCC-TGTGAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTCG--AGCGTCTTG---------GGG-TTGCTTCGG-------G-CCATGGATTAAGTTG--------------------------------------------------------AGAA

Size

Hit Count

Total Norm

dp4

GGTTGCGCTGCTGCT-------------------T----A----------TGG------------------------------------------------------------TGCTGGTGTTGCCACGTGCC--ACAAGACGCCTTCAT----------------------------------------------------------------------------------------------------CTG--GCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGCC-T----TG--C---CG--AGCGTCTTG---------GGG-TTGTTTCAG-------G-GCATGGATTAAGTTTTCAGGCA-ACTGGAGCAGC------------ATC---------------------CGTGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..................................T----G----------TTG------------------------------------------------------------TGCTGGTGTTGCCA................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................GCGTGTTG---------CGG-TTGTTTC......................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................ACTCCTTCAT----------------------------------------------------------------------------------------------------CAG--GCGGTTG.........................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

GGTTGCGCTGCTGCT-------------------T----A----------TGG------------------------------------------------------------TGCTGGTGTTGCCACGTGCC--ACAAGACGCCTTCAT----------------------------------------------------------------------------------------------------CTG--GCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGCC-T----TG--C---CG--AGCGTCTTG---------GGG-TTGTTTCAG-------G-GCATGGATTAAGTTTTCAGGCA-ACTGGAGCAGC------------ATC---------------------CGTGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
................................................................................................................................................................................................................................................................CGGTTGGCCTGGACAAAAT............................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................................................................................................................................................................................................................................GCGTGTTA---------GGG-TTGTTTC......................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

ACCCA---------------------TTTCTG--------G------TCTCGGTCTCAA------------------------------TTTTTT------------------TACTGGTGTGGCCACGTGCCATACGAGTA-----------------------------------------------------------------------------------GTAAGGTCTTGCA-ACAGGGCGGTGC---------------GAACAAAAGTTTCAATTTGATATTCCCTTGCC-TTGACTTGGCC--GT--AGCGTCTTA---------GGG-ATGTTTCC------GAA-GCAAGGATTAAGTTTTCAAAG-----------G---------------------CA----------G-C-TGTGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........................TTCTG--------G------TCTTGGTCTCAA------------------------------C.....................................................................................................................................................................................................................................................................................................................................................	19	1	3.00	0.00	0.00	0.00	3.00
............................TCTG--------G------TCTTGGTCTCAA------------------------------C.....................................................................................................................................................................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
............................................................................................................................................................................................................................................................................................GATATTCCGTTGCC-GTGAC...............................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................................................................................................................................................................................TTA---------GGG-ATGTTTCC------GAA-GCAAGGAT...................................................................	25	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................................................TAGTGC---------------GAACAAAAGTTTC........................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00

droVir3

GCTTC---------------------TTTGTGTCC----A----------TGG-C-----------------------------------------CC------TT--------GC-CGTGTGGCCACGTGCC-A-TCAGACGCCTTCGCGCAGTTTGACTC--------------------------------------------TGGAATGGCTGAGGGCTG-GTGGGG---CGGA-ACGGGGCAGCGG--GGATT-----------G-ACAGTTTCAATTTGCAAGCATGTTG-C-C----TT--TTGTAG--AACGTCTTG---------GGGGTTGTTCG-----CCAGC-TGACGGATTAAGTTTTGAGGGC------------------------A---------------GCCAGATGCTGCT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...........................................................................................................................................................................................................................................................................................................C----TC--TTGTAG--ACCGTCTTG---------.................................................................................................	18	1	3.00	3.00	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................CGGGGCAGCGG--GGxTT-----------G-ATAG............................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................CGGGGCATCGG--GGATG-----------..................................................................................................................................................................	16	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................GTCTTG---------GGGGTGGTTGG-----C................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................................................................................TTGCATGCATGTTG-C-C----GT--T..........................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................CGGGGGAGCxG--GGATT-----------G-AC..............................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................TTG-C-C----TT--TTGTAG--AATGA..............................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................................................................GCTGAGGGCxG-GTGGGG---TGG..................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................................CGGGGCAGCGG--GGAxT-----------G-ATAG............................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................TGGGGCAGCGG--GGTTT-----------..................................................................................................................................................................	16	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACAGTTTCAATTTGCAAGCTTGTTG-C-C----TT--TTACGG--AACGTCTTG---------GGG-TGTCTGA--------------GGGATTAAGTTT------------------------------AAGTCTGGG-----CATGCCAG----CTGC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..................................................................................................................................................................................................................................................................................................................................................AGGCTGA--------------GGGATTAAGTT.............................................................	18	1	1.00	0.00	1.00	0.00	0.00

droGri2

GTTTC---------------------TTTGTGTCC----A-----------GACCCTTGCCGC--------------CT--------------------------TGCCGCCTTGC-CGTGTGGCCACGTGCCAGCAGAGACGCCTTCGCGCTCACTGACTCGTCCCGGCCCGGCAATTGTCAGAGACGCAGATGACTGTTGCGAATAGGTTGGCAGGGGGGGGAGT-CGG---CGGACAGGGGGAAGGGGTG--GTT-----------G-ACAGTTTCAATTTGCAAGCTTGTTG-C-C----TT--TTGCAG--AACGTCTTG---------GGG-TTGTTTCAG-------C-TGGCGGATTAAGGTTTCAGACA-GT-----------------------------CA----------G---CCAGC

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:33:58 EDT

dme-mir-4981

chr2R:3902753-3902848 +

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