dme-mir-4947- 12- and 20-way alignments

dme-mir-4947	chr3R:24834474-24834574 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 24834532-24834554
   star strand at position 24834496-24834516
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:24834459-24834589 -	TAAAGTAATAATATGAAAGCGACCCA----CCCA------------------------------------------------------------------------------------------------------------------------TTCCCCTTCCGCCCATATTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGT-------------GGG---------CGGA---------GCACGGAATTCGGGGGCGTGGCGCA--------------------------CTGGG-T-------AGCGGGTA
droSim1	chr3R:24520998-24521128 -	TAAAGTAATAATATGAAAGCGACCCA----CCCA------------------------------------------------------------------------------------------------------------------------TTCGCCGCCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGG-------------GGG---------CGGA---------GCACGGAATTCGGGGGCGTGGCGCT--------------------------CTGGG-T-------AGCGGGTA
droSec1	super_4:3696490-3696620 -	TAAAGTAATAATATGAAAGCGACCCA----CCCA------------------------------------------------------------------------------------------------------------------------TTCGCCGCCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGG-------------GGG---------CGGA---------GCACGGAATTCGGGGGCGTGGCGCA--------------------------CTGGG-T-------AGCGGGTA
droYak2	chr3R:21664594-21664723 +	TAAAGTAATAATATGAAAGCGACCGG----CCCA------------------------------------------------------------------------------------------------------------------------CCCCT-CGCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGT-------------GGG---------CGGA---------GCACGGAATTCGGGGGCGTGGCACA--------------------------GTGGG-T-------AGTGGGTA
droEre2	scaffold_4820:3199292-3199428 +	TAAAGTAATAATATGAAAGCGACCGGCCCACCCC------------------------------------------------------------------------------------------------------------------------T-----TTCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGG-------------GGG---------CGTA---------GCACGGAATTCGGGGGCGTGGCACAGTGGCTA-------------------GTGGA-T-------AGTGGGTA
droAna3	scaffold_13340:19733656-19733776 +	TAAAGTAATAATATAAAAGCGACCAG----CCC-----------------------------------CTAC-------------------------------------TTCTACTCCACCCA-------------------ACCAGCCTCCC---------------GATCCTGGGCAGCGTTGGTTGTTTCAGAGG---CGGCTTGA---------------------------------------------------GGAACTCGGGGGCGTGCCGCT--------------------------CC------------------TA
dp4	chr2:13200189-13200291 +	TAAAGTAATAATATGAAAGCGACCAG----AGCT--------------------CCTCCCTCAAGCCCTTAT-------------------------------------TCATCCTCTATGCC-------------------ACCAGTGTTTCAG-------------GACC----GTAGCGTT------------------------------------GGTGGCCA---------------------------------------------------------------------------------------------AGGGGGGA
droPer1	super_0:7253259-7253361 -	TAAAGTAATAATATGAAAGCGACCAG----AGCT--------------------CCTCCCTCAAGCCCTTAT-------------------------------------TCATCCTCTATGCC-------------------ACCAGTGTTTCAG-------------GACC----GTAGCGTT------------------------------------GGTGGCCA---------------------------------------------------------------------------------------------AGGGGGGA
droWil1	scaffold_181089:11057506-11057708 -	TAAAGTAATAATATGAAAGCCACCAC----CTT-----------------------------------CCACTCCTCACTTGCTAACCGATTCCCCCACATCCTCTCCGCATAGTT------CTTCTCCTTTCATAGTACCAACCATCATC-C---------------GACATTGCCCA------ACTCTTTCAGAAA---ATGCTTCATGTATTTGGCTGCTGGCTAAGGCG------------GTCTGCTGGATGCTG---CTCTGGAGGCGTGGCCTT--------------------------TTGTA---------------TA
droVir3	scaffold_13047:18267580-18267775 -	TAAAGTAATAATATGAAAGCGCC-AA----AGCAGCACAAGACCAAGCCAAGCCCCCGTCCCAAGCACCCAA----------------------------CCCCAACCCCCAATTC------CCACTCCCAACACAGCAGCTACC----------------------------------------AATGTTTCAATAC---ATGTC-TA-GCTTGAGG-------------CAGCACAGTGGGGTGG------GCTGCCT---TTAAGGAGGCGTGGCAGT--------------------------T-GTAGTTCTCACAAGTAATCC
droMoj3	scaffold_6540:13460511-13460700 +	TAAAGTAATAATATGAAAGCGCC-AT----GTCC--------------------CAAACCCCATTCCCATTC-------------------------------------CCATACCCAAAACCCACTTACAGCGCAGCAGCTACTAGTGTTTCACTtgtTtTtTGTtTGTtTtTGTtTtTtGtTtTtTGTgTtGCTG-----------------GAGG-------------CG------------GC--------TGCATTGAAGCAGGAGGCGTGGCATT--------------------------T-GTAGTTCTCACAAGTATTGC
droGri2	scaffold_15074:6425135-6425301 +	TAAAGTAATAATATGAAAGCGCC-AA----AGCA--------------------CC----ACAAGCCCAAAC-------------------------------------CCAATTCC------------------AGCTTCTACC----------------------------------------AATGTTTCAATATACCATGTC-TA-GCTTCAGG-------------CGACACAGTAGGGGG-----------------AGGGGCGGGCGTAGTGGG-----CTGTGGCATGGGCGTGGCATTT-GTAGTTCTCACAAGTAATGC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:24834459-24834589 -	NA	TAAAGTAAT------AATATGAAAGCGACCCACC------C-ATT------CCCCTTC--CG-C---------------------C------CATATTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GTGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCGCACTGGGT-------AGCGGGTA
droSim1	chr3R:24520998-24521128 -	6	TAAAGTAAT------AATATGAAAGCGACCCACC------C-ATT------CGCCGCC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GGGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCGCTCTGGGT-------AGCGGGTA
droSec1	super_4:3696490-3696620 -	72	TAAAGTAAT------AATATGAAAGCGACCCACC------C-ATT------CGCCGCC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GGGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCGCACTGGGT-------AGCGGGTA
droYak2	chr3R:21664594-21664723 +	7	TAAAGTAAT------AATATGAAAGCGACCGGCC------C-A-C------CCCTCGC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GTGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCACAGTGGGT-------AGTGGGTA
droEre2	scaffold_4820:3199292-3199428 +	6	TAAAGTAAT------AATATGAAAGCGACCGGCC------C-A-C------CCCTTTC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GGGGGCG-------T-----------AG------------CACGGAATTCGGGGGCGTGGCACAGTGGCTAGTGGATAGTGGGTA
droEug1	scf7180000409787:744124-744277 +	9	TAAAGTAAT------AATATGAAAGCGACCGGCC------C-AGC------CCCTCTCTACGCC---------------------C------CCTTTTTATCC-------TTCGTCTACTGTTTCATCGCAGCACTC-------A-GGGGTGATAGGATAGGGGTTAGGGGTGAGGCT-GGGGCG-------G-----------T------------CCAAGGAATTCGGGGGCGTGGC-----------------GTTGGTA
droBia1	scf7180000302075:1908428-1908558 +	51	TAAAGTAAT------AATATGAAAGCAACCAGCC------C-T-C------CGCCAC---CGCC---------------------C------CCTCTTTATCC-------TTCGTCTAGTGTTTCATCGCAGGACTT-------T-G-------------------------------GG---TT-------TGTGCGCGGCGGGA-----------CCGAGGAATTCGGGGGCGTGGC--------T-------GGTTGGTA
droTak1	scf7180000415700:411921-412062 -	5	TAAAGTAAT------AATATGAAAGCGACCCTG----------------------GAC--CG-C---------------------CCCC---TTTCCTTATCC-------TTCGTCTACTGTTTCATCGCAGGACTT-------T-TGGGACGTAGGATAAGGG--AG-GCGAAGGCG-GGGGCA-------G-----------G------------ACAAGGAATTCGGGGGCGTGGC-----------------GTTGGTA
droEle1	scf7180000491261:1411208-1411334 -	21	TAAAGTAAT------AATATGAAAGCGACCAGCC------CCATA------C--------CG-C---------------------CTCCAACCGATTTTATCC-------TTCGTCTACTGTTTC-----AGGACTT-------TT---------------------GGGAT----CAGGGGGCG-------G-----------G------------CCAAGGAATTCGGGGGCGTGGCAGC--------------GTTGGTA
droRho1	scf7180000780007:218817-218951 +	10	TAAAGTAAT------AATATGAAAGCGACCACCC------CCAT-------CTC-G-C--CG-C-------------CGACCCGCCTCCATCCGATTTTATCC-------TTCGTCTACTGTTTC-----AGGACTT-------TT---------------------GGGAT----CAGGGGGCG-------G-----------G------------CCAAGGAACTCGGGGGCGTGGC-----------------GTTGGTA
droFic1	scf7180000454073:3512300-3512430 +	3	TAAAGTAAT------AATATGAAAGCGACCGGCC------C-T-C------CGAC-TC--CG-C---------------------C------TCCTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGACCC-------TGG----------AAAA------GGGGC----CGGGGGAGG-------G-----------G------------TCAAGGAATTCGGGGGCGTGGC-----------------GTGGGTA
droKik1	scf7180000302276:805592-805716 -	37	TAAAGTAAT------AATATGAAAGCGGCCAGCA------C-CTC------CTCCTC-----------------------------------GTCCTTGTTCC-------TGGGTCCTCTGTTTCAGGGCAGGACTCCGT--C-T----------------------------------CTGGCT-------G-----------AG------------GGGAAGATTCGGGGGCGTGGCGG---TGCT-------AGCTTCTA
droAna3	scaffold_13340:19733656-19733776 +	111	TAAAGTAAT------AATATAAAAGCGACCAGCC------C-CTA------CTTCTA---CTCC----------ACCCAACCAGCCTC---CCGATCCTGGGC-------AGCGTTGGTTGTTTCAGA-----------------------------------------------------GGCG-------G-----------C------------TTGAGGAACTCGGGGGCGTGCC-----------------GCTCCTA
droBip1	scf7180000396413:2657212-2657312 -	163	TAAAGTAAT------AATATAACAGCGGCCAGCC------C-CAG------CTCCACC-------------------CATCCAGCCTC---CCGATCCTGGCC-------AGCGCTTGCTGTTACAG-------------------------------------------------------------------------------------------------AGGCGGAGGCGTGGC-----------------GCTTCTA
dp4	chr3:722533-722667 -	31	TAAAGAGAT------AATGACAAAGCAACCCATT------A-AAAGCCATCCCTTGACAACACT---------------------C------CTCTCTCATCC-------CCT--TCATATTCCCATCTCCGAA----------A-A-------------------------------ATGAGCG-------A-----------AG------------AACGGAGAGCAACGTTTTAATAAATTTGTA-------AACAGATT
droPer1	super_26:1114277-1114391 -	86	GACGGTGGC------CTTCCA-------CTTCCT------C-TTC------CGCCGCC--AC-C-------------ACACCCCCTTC---CCAC-----TGCCAAGCA-CGC-----TCTTTTTATCGCAAT------------------------------------------------TGTTGTCGGCGG-------------------------------------ATTTTCGGCTTACATGCG-------AGGAGCTA
droWil1	scaffold_181096:10088805-10088934 +	100	CAAAATGTCCTTGATGACTGG-CATTCACACACA------C-A-C------ACACACA--CA-CACACATTTAAACACATCCATATGT---AC-------ATCCATGTATACATTTATCTAATA----------------------------------------------------CA-GATGCA-------G-----------AG------------CT---------------CGGAACTTCAAGT-------ATAAGGCA
droVir3	scaffold_13049:15807-15938 +	335	TATG-TGGC------AGTAGAAATTTCTCCCATAAATATAT-GTA------CCCTTTC--CG-T---------------------C------TTTATGTTTGT-------TTGGTTGAATGGATCGAACTACAAATC-------T-A-------------------------------GAGATTA-------G-----------AA------------ATTGGAAATCCGTATTCTAGTAA----TGT-------ATCCAGAA
droMoj3	scaffold_6500:17797597-17797712 +	353	CACACACAC------A--------------CACA------C-AGA------CTTTGGC--TA-C---------------------A------AAATGTTAACT-------TGAGTTTGAAATTTTCCAG-GGAATAT-------G-A-------------------------------GTGAGAG-------G-----------CG------------AGCGAAAGCAGTGAACAGAGTGAACAATGT-------ATAAAGTA
droGri2	scaffold_14853:8203259-8203387 +	111	CAAATTAAC------AACAAGAATTCTTTCCAGC------T-CCC------TCTCT----CTCT---------------------C------TCTCTCTCTCT-------CTAACTCCGTCTCTCATTTCCGAGAGA---GAGCT-A-------------------------------GTTACAT-------T-----------GCTGAGAGAGAAGTGAAGA-GA------GCCGAGC-----------------TTTGTTA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TAAAGTAATAATATGAAAGCGACCCA----CCCA------------------------------------------------------------------------------------------------------------------------TTCCCCTTCCGCCCATATTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGT-------------GGG---------CGGA---------GCACGGAATTCGGGGGCGTGGCGCA--------------------------CTGGG-T-------AGCGGGTA

Size

Hit Count

Total Norm

droSim1

TAAAGTAATAATATGAAAGCGACCCA----CCCA------------------------------------------------------------------------------------------------------------------------TTCGCCGCCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGG-------------GGG---------CGGA---------GCACGGAATTCGGGGGCGTGGCGCT--------------------------CTGGG-T-------AGCGGGTA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

TAAAGTAATAATATGAAAGCGACCCA----CCCA------------------------------------------------------------------------------------------------------------------------TTCGCCGCCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGG-------------GGG---------CGGA---------GCACGGAATTCGGGGGCGTGGCGCA--------------------------CTGGG-T-------AGCGGGTA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................................................................................................................................................................................................................................................CGTGGCGCA--------------------------ATTGG-T-------AGC.....	18	1	134.00	5.00	4.00	125.00
.................................................................................................................................................................................................................................................................................GTGGCGCA--------------------------GTTGG-T-------AGCG....	18	1	46.00	0.00	9.00	37.00
................................................................................................................................................................................................................................................................................CGTGGCGCA--------------------------ATTGG-T-------AGCG....	19	1	38.00	0.00	0.00	38.00
.................................................................................................................................................................................................................................................................................GTGGCGCA--------------------------ATTGG-T-------AGCG....	18	1	17.00	0.00	1.00	16.00
.................................................................................................................................................................................................................................................................................GTGGCGCA--------------------------ATGGA-T-------AGCG....	18	1	15.00	0.00	1.00	14.00
.................................................................................................................................................................................................................................................................................GTGGCGCA--------------------------ATGGG-T-------AACG....	18	1	9.00	0.00	0.00	9.00
.................................................................................................................................................................................................................................................................................GTGGCGCA--------------------------CTGGA-T-------AACG....	18	1	4.00	0.00	0.00	4.00
.................................................................................................................................................................................................................................................................................GTGGCGCA--------------------------ATCGG-T-------AGCG....	18	1	3.00	1.00	0.00	2.00
................................................................................................................................................................................................................................................................................CGTGGCGCA--------------------------GTTGG-T-------AGC.....	18	1	3.00	0.00	1.00	2.00
................................................................................................................................................................................................................................................................................CGTGGCGCA--------------------------TTGGT-T-------AGCG....	19	1	2.00	0.00	0.00	2.00
................................................................................................................................................................................................................................................................................CGTGGCGCA--------------------------TTGGT-T-------AGC.....	18	1	2.00	0.00	1.00	1.00
................................................................................................................................................................................................................................................................................CGTGGCGCA--------------------------GTCGG-T-------AGC.....	18	1	1.00	0.00	1.00	0.00
.....................................................................................................................................................................................................C---AGGATTTA------AGG-------------GGG---------CGGA---------GCA......................................................................	22	1	1.00	0.00	1.00	0.00
.................................................................................................................................................................................................................................................................................GTGGCGCA--------------------------GTGGG-T-------GGCG....	18	1	1.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................................................CGTGGCGCA--------------------------CxAGG-T-------AGCG....	18	1	1.00	0.00	0.00	1.00
...............................................................................................................................................................................................................................................................................GCGTGGCGTA--------------------------CTCGG-T-------AGCG....	20	1	1.00	1.00	0.00	0.00
.................................................................................................................................................................................................................................................................................GTGGCGCA--------------------------CTGGA-T-------ACCG....	18	1	1.00	0.00	0.00	1.00
...............................................................................................................................................................................................................................................................................CCGTGGCGCA--------------------------CTTGG-T-------AGC.....	19	1	1.00	1.00	0.00	0.00
.................................................................................................................................................................................................................................................................................GTGGCGCA--------------------------CTTGG-T-------AGCG....	18	1	1.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................................................CGTGGCGCA--------------------------CxCGG-T-------AGCG....	18	1	1.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................................................TGTGGCGCA--------------------------ATGGG-T-------AGCG....	19	1	1.00	0.00	0.00	1.00
.................................................................................................................................................................................................................................................................................GTGGCGTA--------------------------CTCGG-T-------AGCG....	18	1	1.00	0.00	0.00	1.00

droYak2

TAAAGTAATAATATGAAAGCGACCGG----CCCA------------------------------------------------------------------------------------------------------------------------CCCCT-CGCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGT-------------GGG---------CGGA---------GCACGGAATTCGGGGGCGTGGCACA--------------------------GTGGG-T-------AGTGGGTA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..................................................................................................................................................................................................................................................................................TGGCAGA--------------------------GTGGG-T-------AGTGGGG.	20	1	3.00	0.00	0.00	0.00	3.00	0.00
..............................................................................................................................................................................................................................................................................GGCGTAGCACA--------------------------GTxGG-T-------AGT.....	19	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................................................................................................AATTCxGGGGCGTGGCA..................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................TGGCAGT--------------------------GTGGG-T-------AGTGGGT.	20	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................TGGCACA--------------------------GCCGG-T-------AGTGGG..	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................CCCA------------------------------------------------------------------------------------------------------------------------CCCCG-GGCCGCCC.................................................................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................TGGCAGA--------------------------GTGGG-T-------AGTGGGT.	20	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................TGGCACT--------------------------GTGGG-T-------AGTGGGTT	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................................................................................................CAATTCxGGGGCGTGGCA..................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................TGGCAGT--------------------------GTGGG-T-------AGTGGG..	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................TGGCAGA--------------------------GTGGG-T-------AGTTGGT.	20	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................TGGCACC--------------------------GTGGG-T-------AGTTGGT.	20	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................TGGCAGA--------------------------GTGGG-T-------AGTGGGTT	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................TGGCAGA--------------------------GTGGG-T-------AGCGGG..	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

TAAAGTAATAATATGAAAGCGACCGGCCCACCCC------------------------------------------------------------------------------------------------------------------------T-----TTCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGC---AGGATTTA------AGG-------------GGG---------CGTA---------GCACGGAATTCGGGGGCGTGGCACAGTGGCTA-------------------GTGGA-T-------AGTGGGTA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

TAAAGTAATAATATAAAAGCGACCAG----CCC-----------------------------------CTAC-------------------------------------TTCTACTCCACCCA-------------------ACCAGCCTCCC---------------GATCCTGGGCAGCGTTGGTTGTTTCAGAGG---CGGCTTGA---------------------------------------------------GGAACTCGGGGGCGTGCCGCT--------------------------CC------------------TA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................................................................CTAC-------------------------------------TTCTTCTCCACCCA-------------------TC.........................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................CTGGGAAGCGTGGGTTG............................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................CATCCTCAC---------------GATCCTGGGC.......................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...............AAAGTGACCAG----CCC-----------------------------------CTCC-------------------------------------............................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................................................GAGG---CGGCGTGC---------------------------------------------------GGAAC................................................................	17	1	1.00	0.00	0.00	1.00	0.00

dp4

TAAAGTAATAATATGAAAGCGACCAG----AGCT--------------------CCTCCCTCAAGCCCTTAT-------------------------------------TCATCCTCTATGCC-------------------ACCAGTGTTTCAG-------------GACC----GTAGCGTT------------------------------------GGTGGCCA---------------------------------------------------------------------------------------------AGGGGGGA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TAAAGTAATAATATGAAAGCGACCAG----AGCT--------------------CCTCCCTCAAGCCCTTAT-------------------------------------TCATCCTCTATGCC-------------------ACCAGTGTTTCAG-------------GACC----GTAGCGTT------------------------------------GGTGGCCA---------------------------------------------------------------------------------------------AGGGGGGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...................CGAAAAG----AGCT--------------------CCTCCCTC...........................................................................................................................................................................................................................................................................	19	1	3.00	0.00	0.00	0.00	0.00	3.00

droWil1

TAAAGTAATAATATGAAAGCCACCAC----CTT-----------------------------------CCACTCCTCACTTGCTAACCGATTCCCCCACATCCTCTCCGCATAGTT------CTTCTCCTTTCATAGTACCAACCATCATC-C---------------GACATTGCCCA------ACTCTTTCAGAAA---ATGCTTCATGTATTTGGCTGCTGGCTAAGGCG------------GTCTGCTGGATGCTG---CTCTGGAGGCGTGGCCTT--------------------------TTGTA---------------TA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................................................................................................................................................................................................................................CTCTGGAGGCTTGGACTT--------------------------......................	18	1	4.00	0.00	4.00	0.00	0.00
.......................................................................................................................................................................................................................................CG------------GTCTTCTGGATGATG---CTC...............................................................	20	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................................................................................................................................TGAATCTGGCTGCTGGCT......................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................................................................GCTTCTTGTATTTGGCTGGT..........................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................................GGCx------------GTCTGCTGGATGATG---..................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

TAAAGTAATAATATGAAAGCGCC-AA----AGCAGCACAAGACCAAGCCAAGCCCCCGTCCCAAGCACCCAA----------------------------CCCCAACCCCCAATTC------CCACTCCCAACACAGCAGCTACC----------------------------------------AATGTTTCAATAC---ATGTC-TA-GCTTGAGG-------------CAGCACAGTGGGGTGG------GCTGCCT---TTAAGGAGGCGTGGCAGT--------------------------T-GTAGTTCTCACAAGTAATCC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....GTAAAAATATGAAAGCGG...................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................AGCTGCAGAAGACCAAGC.........................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
....GTAAAAATATGAAAGCGT...................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droMoj3

TAAAGTAATAATATGAAAGCGCC-AT----GTCC--------------------CAAACCCCATTCCCATTC-------------------------------------CCATACCCAAAACCCACTTACAGCGCAGCAGCTACTAGTGTTTCACTtgtTtTtTGTtTGTtTtTGTtTtTtGtTtTtTGTgTtGCTG-----------------GAGG-------------CG------------GC--------TGCATTGAAGCAGGAGGCGTGGCATT--------------------------T-GTAGTTCTCACAAGTATTGC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......................................................................................................................................................TCACTTGTTTATTGTTGGT...............................................................................................................................................................	19	1	8.00	1.00	3.00	1.00	3.00
..............................................................................................................................................................TTGTGTGTTTGTTTTTGTTTT......................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................CACTTGTTTATTGTTGGT...............................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................TTGTTTTTTGTTTGTTGTT...........................................................................................................................................................	19	3	0.33	0.33	0.00	0.00	0.00
...............................................................................................................................................................TGTTTGTTTGTTTTTATTT.......................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................TTGTTTTTGTTGTTTTTTTTT..............................................................................................................................................	21	12	0.08	0.08	0.00	0.00	0.00
..........................................................................................................................................................................GTTTGTTTTTTGTTTGTTGT...........................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................................................................................................................GCAGAAGGAGGCGTGGCA..................................................	18	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................TTTGTTTGTGTGTTTTGTTT................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................TTTGTGxTTGTTTTTGTTTGTT....................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................................................................................................................................................................................................AGAAGGAGGCGTGGCAG.................................................	17	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................TTTAGTTTTGTTTTTTGTTTT...............................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................TTGTTTGCTGTTGTTTTTTG...................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................TGTGGTTGTTTTTGTTTTT.....................................................................................................................................................	19	3	0.33	0.00	0.00	0.33	0.00
.......................................................................................................................................................................TTTTTTTGTTTTTTGTTTGTT.............................................................................................................................................	21	12	0.08	0.08	0.00	0.00	0.00
.......................................................................................................................................................TCACTTGTTTATTGTTTGT...............................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................TTGTTTTTTGTTTGTTGTT..........................................................................................................................................	19	3	0.33	0.33	0.00	0.00	0.00

droGri2

TAAAGTAATAATATGAAAGCGCC-AA----AGCA--------------------CC----ACAAGCCCAAAC-------------------------------------CCAATTCC------------------AGCTTCTACC----------------------------------------AATGTTTCAATATACCATGTC-TA-GCTTCAGG-------------CGACACAGTAGGGGG-----------------AGGGGCGGGCGTAGTGGG-----CTGTGGCATGGGCGTGGCATTT-GTAGTTCTCACAAGTAATGC

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