dme-mir-4981- 12- and 20-way alignments

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
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chr2R:3902738-3902863 +	GGTTATCCCT--------------------------------GCCACATGGCCACGTGCCCG-CAAG-----ACGCCTTC-----GGCCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTCGAG--CAGCGTCTTGGGG-TTGTTCG--------TGGATTAAGTTC-----------------------------GATTCCT----------AT
droSim1	chr2R_random:1106077-1106202 +	GGATATCCCT--------------------------------GCCACATGGCCACGTGCCTG-CAAG-----ACGCCTTC-----GGCCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTCGAG--CAGCGTCTTGGGG-TTGTTCC--------TGGATTAAGTTC-----------------------------GATTCCT----------AT
droSec1	super_1:1540674-1540799 +	GGATATCCCT--------------------------------GCCACATGGCCACGTGCCCG-CAAG-----ACGCCTTC-----GGCCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTCGAG--CAGCGTCTTGGGG-TTGTTCC--------TGGATTAAGTTC-----------------------------GATTCCT----------AT
droYak2	chr2L:16559915-16560042 +	GGATATCCCT--------------------------------GCCACATGGCCACGTGCCTG-CAAG-----ACGCCTTC-----GACCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----AACGAACGGAGCGTCTTGGGG-TTGTTTC--------GGGATTACGTTC-----------------------------GATTCCG----------AT
droEre2	scaffold_4929:18723379-18723500 -	GGATA-CCCA--------------------------------GCCACATGGCCACGTGCCTG-CAAG-----ACGCCTTC-----GGCCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTC-----GAGCGTCTTGGGG-TTGTTTC--------GGGATTGAGTTC-----------------------------GATTCCG----------AT
droAna3	scaffold_13266:16222514-16222676 +	GGAGATCCTT--------------------------------G-CGTGTGGCCACGTGCCGGGTGAG-----ACGCCTTC-----GGCCGGT------------ACAAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTTGAGCGTCTTGGGG-TTGTTCC--GGGCCATGGATTAAGTTG--AGA-AAATG---CAGACTATGTTTTCTGGTCCTG----------AT
dp4	chr3:5536552-5536719 +	GGTTG-CGCTGCTGCTTATGG----------------TGCTG---GTGTTGCCACGTGCCA--CAAG-----ACGCCTTC-----ATCTGGCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGC-CTT-------GCC--GAGCGTCTTGGGG-TTGTTTC--AGGGCATGGATTAAGTTTTCAGGCAACTGGAGCAGCAT--------------CC----------gt
droPer1	super_2:5730715-5730882 +	GGTTG-CGCTGCTGCTTATGG----------------TGCTG---GTGTTGCCACGTGCCA--CAAG-----ACGCCTTC-----ATCTGGCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGC-CTT-------GCC--GAGCGTCTTGGGG-TTGTTTC--AGGGCATGGATTAAGTTTTCAGGCAACTGGAGCAGCAT--------------CC----------gt
droWil1	scaffold_181141:2380510-2380679 -	GTCT--CGGTCTCAATTTTTT----------------TACTG---GTGTGGCCACGTGCCATACGAGTAGTAAGGTCTTGCAACAGGGCGGT-------GCGAACAAAAGTTTCAATTTGATATTCCCTTGC-CTTGACTTGGCCG--TAGCGTCTTAGGG-ATGTTTCC-GAAGCAAGGATTAAGTTTTCAAA----G------GCA--------------GCT----------GT
droVir3	Unknown	GCTTCTTTGT---GTCCATGG----------------CCCTTGCCGTGTGGCCACGTGCCAT--CAG-----ACGCCTTC-----GCGCAG-------TTTGACTCACAGTTTCAATTTGCAAGCATGTTGC-CT-----TTTGTA--GAACGTCTTGGGGGTTGTTCGCCAGCTGACGGATTAAGTTTTGAGG--------------------------------GCA-GCCAGAt
droMoj3	scaffold_6496:7113417-7113501 -	----------------------------------------------------------------------------------------------------------ACAGTTTCAATTTGCAAGCTTGTTGC-CT-----TTTACG--GAACGTCTTGGGG-TGTCTGA--------GGGATTAAGTTT-----------------------------AAGTCTGGGCATGCCAgct
droGri2	Unknown	GTTTCTTTGT---GTCCA-GACCCTTGCCGCCTTGCCGCCTTGCCGTGTGGCCACGTGCCAGCAGAG-----ACGCCTTC-----GCGCTC-------ACTGACTCACAGTTTCAATTTGCAAGCTTGTTGC-CT-----TTTGCA--GAACGTCTTGGGG-TTGTTTC--AGCTGGCGGATTAAGGTTTCAGACAG-----------------------------TCA-GCCAGCT

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:3902738-3902863 +	NA	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 +	276	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 +	5	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 +	23	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 -	642	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 +	1	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 +	22	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 -	549	GGTT-------------------------------------------------------------------------------------------T-----GGCCTGCCACATGGC-CAAATGGCCACGTGCCATGCAAGACGCCGGT-G----------------------------------------------------------------------------------------------------CCG--CTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGC-C----AG--GAGGCG--AGCGTCTTGGTCTTGTTGGGG-TTGTTTCGC-TTCCGAG-CCCTGGATTAAGTTC------------------------------GATT---------------CCGAATCCGAT
droEle1	scf7180000491258:123314-123472 -	119	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 +	43	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 -	40	GGGG------------------------------------------------------------------------------------AT------CCTTCGACAT--------GC-CACATGGCCACGTGCC-GGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CTG--GCA-------------AAAGTTTCAATTTGATATTCCTTAGGC------CA--T---CC--AGCGTCTTG---------GGG-TTGCTTT---------G-CCCTGGATTAAGTTC------------------------------GAGT---------------------CGGGC
droKik1	scf7180000302471:525269-525433 +	49	GATC---------------------------------------------------------------------------------------CTTTC-----GGCCG--------GC--CCATGGCCACGTGCC-AGCAAGACGCCTTCAG----------------------------------------------------------------------------------------------------CCGGTGTG-----------C-ACAGTTTCAATTTGATATTCCTTTGGA-C----CG--GCGAAC--AACGTCTTG---------GGG-TTGTTTCT------------CGGGATTAAGTTCACAGGCA-GCTGGAGCAGT--------------G-----CGGGCTTAGTCTGATTCTTAC
droAna3	scaffold_13266:16222514-16222662 +	45	GGAG------------------------------------------------------------------------------------AT------CC------TT--------G--CGTGTGGCCACGTGCCGGGTGAGACGCCTTCGG----------------------------------------------------------------------------------------------------CCG--GTA-----------C-AAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTTG--AGCGTCTTG---------GGG-TTGTTCCGG-------G-CCATGGATTAAGTTG--AGAAA------------------------ATG-----CA----------GAC-TATGT
droBip1	scf7180000396567:704320-704511 +	1	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 +	1	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 +	1	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 -	1	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 +	2	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 -	3	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACAGTTTCAATTTGCAAGCTTGTTG-C-C----TT--TTACGG--AACGTCTTG---------GGG-TGTCTGA--------------GGGATTAAGTTT------------------------------AAGTCTGGG-----CATGCCAG----CTGC
droGri2	scaffold_15245:14811478-14811742 +	1	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

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GGTTATCCCT--------------------------------GCCACATGGCCACGTGCCCG-CAAG-----ACGCCTTC-----GGCCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTCGAG--CAGCGTCTTGGGG-TTGTTCG--------TGGATTAAGTTC-----------------------------GATTCCT----------AT

Size

Hit Count

Total Norm

droSim1

GGATATCCCT--------------------------------GCCACATGGCCACGTGCCTG-CAAG-----ACGCCTTC-----GGCCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTCGAG--CAGCGTCTTGGGG-TTGTTCC--------TGGATTAAGTTC-----------------------------GATTCCT----------AT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................................................................................TTGGC-CG-----GTCGAG--CAGCGTCTTG...............................................................................	23	1	3.00	0.00	3.00	0.00	0.00
........CT--------------------------------GGCACATGCCCACGTGC..................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00

droSec1

GGATATCCCT--------------------------------GCCACATGGCCACGTGCCCG-CAAG-----ACGCCTTC-----GGCCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTCGAG--CAGCGTCTTGGGG-TTGTTCC--------TGGATTAAGTTC-----------------------------GATTCCT----------AT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............................................................................................................................TTGGC-CG-----GTCGAG--CAGCGTCT.................................................................................	21	1	2.00	0.00	0.00	2.00
...................................................CCACGTGACCG-CAAG-----AAGC.................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00

droYak2

GGATATCCCT--------------------------------GCCACATGGCCACGTGCCTG-CAAG-----ACGCCTTC-----GACCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----AACGAACGGAGCGTCTTGGGG-TTGTTTC--------GGGATTACGTTC-----------------------------GATTCCG----------AT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............................................................................................................................................................CGGGG-TTGATTC--------GGGATTA.....................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................CGGAGCGTGTTGGGA-T..........................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

GGATA-CCCA--------------------------------GCCACATGGCCACGTGCCTG-CAAG-----ACGCCTTC-----GGCCGGC------------GCAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTC-----GAGCGTCTTGGGG-TTGTTTC--------GGGATTGAGTTC-----------------------------GATTCCG----------AT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................................................................................GTTTCxTGGGG-TTGTTTC--------G...........................................................	18	1	1.00	0.00	0.00	1.00	0.00

droAna3

GGAGATCCTT--------------------------------G-CGTGTGGCCACGTGCCGGGTGAG-----ACGCCTTC-----GGCCGGT------------ACAAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTTGAGCGTCTTGGGG-TTGTTCC--GGGCCATGGATTAAGTTG--AGA-AAATG---CAGACTATGTTTTCTGGTCCTG----------AT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................................................TACTTGCCGGGTGAG-----ACGC.................................................................................................................................................................	19	1	5.00	0.00	0.00	0.00	5.00
....................................................TACTTGCCGGGTGAG-----ACG..................................................................................................................................................................	18	1	3.00	0.00	0.00	0.00	3.00
...................................................................................................................................................................................................AAATG---CAGACTxTGTTATC....................	18	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................ATTAAGTTG--AGA-AAGTG---CT................................	19	1	1.00	0.00	0.00	0.00	1.00

dp4

GGTTG-CGCTGCTGCTTATGG----------------TGCTG---GTGTTGCCACGTGCCA--CAAG-----ACGCCTTC-----ATCTGGCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGC-CTT-------GCC--GAGCGTCTTGGGG-TTGTTTC--AGGGCATGGATTAAGTTTTCAGGCAACTGGAGCAGCAT--------------CC----------gt	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
................TGTTG----------------TGCTG---GTGTTGCCA.......................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................GCGTGTTGCGG-TTGTTTC--..................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................ACTCCTTC-----ATCAGGCGGTTG............................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

GGTTG-CGCTGCTGCTTATGG----------------TGCTG---GTGTTGCCACGTGCCA--CAAG-----ACGCCTTC-----ATCTGGCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGC-CTT-------GCC--GAGCGTCTTGGGG-TTGTTTC--AGGGCATGGATTAAGTTTTCAGGCAACTGGAGCAGCAT--------------CC----------gt	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........CTGCTGCTGCTGG----------------TGCTG---................................................................................................................................................................................................	18	2	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................CGGTTGGCCTGGACAAAAT...............................................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
.........TGCTGCTGATGT----------------TGCTG---GTG.............................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.........TGCTGCTGATGT----------------TGCTG---GTGT............................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
......................................................................................................................................................GCGTGTTAGGG-TTGTTTC--..................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

GTCT--CGGTCTCAATTTTTT----------------TACTG---GTGTGGCCACGTGCCATACGAGTAGTAAGGTCTTGCAACAGGGCGGT-------GCGAACAAAAGTTTCAATTTGATATTCCCTTGC-CTTGACTTGGCCG--TAGCGTCTTAGGG-ATGTTTCC-GAAGCAAGGATTAAGTTTTCAAA----G------GCA--------------GCT----------GT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........................................................................................TAGT-------GCGAACAAAAGTTTC...........................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................GATATTCCGTTGC-CGTGAC..................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................TTAGGG-ATGTTTCC-GAAGCAAGGAT.......................................................	25	1	1.00	0.00	1.00	0.00	0.00

droVir3

GCTTCTTTGT---GTCCATGG----------------CCCTTGCCGTGTGGCCACGTGCCAT--CAG-----ACGCCTTC-----GCGCAG-------TTTGACTCACAGTTTCAATTTGCAAGCATGTTGC-CT-----TTTGTA--GAACGTCTTGGGGGTTGTTCGCCAGCTGACGGATTAAGTTTTGAGG--------------------------------GCA-GCCAGAt	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.....................................................................................................................................CT-----CTTGTA--GACCGTCTTG...............................................................................	18	1	3.00	3.00	0.00	0.00	0.00	0.00
................................................................................................................................TTGC-CT-----TTTGTA--GAATGA...................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................................................................................................TTGCATGCATGTTGC-CG-----TT...............................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................................................................................................................GTCTTGGGGGTGGTTGGC...................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

----------------------------------------------------------------------------------------------------------ACAGTTTCAATTTGCAAGCTTGTTGC-CT-----TTTACG--GAACGTCTTGGGG-TGTCTGA--------GGGATTAAGTTT-----------------------------AAGTCTGGGCATGCCAgct	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

GTTTCTTTGT---GTCCA-GACCCTTGCCGCCTTGCCGCCTTGCCGTGTGGCCACGTGCCAGCAGAG-----ACGCCTTC-----GCGCTC-------ACTGACTCACAGTTTCAATTTGCAAGCTTGTTGC-CT-----TTTGCA--GAACGTCTTGGGG-TTGTTTC--AGCTGGCGGATTAAGGTTTCAGACAG-----------------------------TCA-GCCAGCT

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

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