sblock221622- 12- and 20-way alignments

sblock221622	chr3R:19094949-19095044 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_CDS

Legend:

   mature strand at position 19095007-19095027
   star strand at position 19094968-19094987
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:19094934-19095059 +	GGACAGTTGagcgcc---------------atcaccggcagccgcggcggcagcggcagcagca------------ctggcgagcagcagATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCCACCGA------AGCTGGCTGATGGGTTAGCCGCTGAGGT
droSim1	chr3R:18910498-18910623 +	GGACAGTTGagcgcc---------------atcaccggcagccgcggcggcagcggcagcagca------------ctggcgagcagcagATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCCACCGA------AGCTGGCGGATGGGTTAGCCGCTGAGGT
droSec1	super_0:19459752-19459877 +	GGACAGTTGAGAGCc---------------atcaccggcagccgcggcggcagcggcagcagca------------ctggcgagcagcagATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCCACCGA------AGCTGGCGGATGGGTTAGCCGTTGAGGT
droYak2	chr3R:19969866-19969991 +	GGACAATTGAACGCC---------------ATCACCGGCAGCCGCGGCGGCAGCGGCAGCGGCA------------CTGGCGAGCAGCAGATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCCACCGA------AGCTGGCGGATGGGTTAGCCGCCGATGG
droEre2	scaffold_4820:8959323-8959448 -	GGACAGTTGGACGCc---------------atcaccggcagccgcggcggcagcggcagcagca------------ctggcgagcagcagATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCAACCGA------AGCTGGCGGATGGGTTGGCCGCCGAGGT
droAna3	scaffold_13340:8296287-8296436 -	CGACAGTTGGACGCCAACACC---------ATCGCcagcagccgcggcggcagcggcagcagcagcggcTGCCGCACTGGCGAGCAGCAGATTGTTCA---------CGCCGCTGCTACTG------CCGTTGCCACCAACGCCGACGCTGGCCGATGCGTGGCTCGCGGGGCT
dp4	chr2:9553440-9553562 -	CGACAGTTGGACACCAACGCCAACGCCCACACCATCGCCAGAGGCGGCGGCAACGGCAGTAGTA------------GCGGCATTCAGACGATTCGTGC---------TGCCACTGCTGATG------CCGTTGTCTCCGC------TGCTC-----T-------------GGTT
droPer1	super_0:10926574-10926696 +	CGACAGTTGGACACCAACGCCAACGCCCACACCATCGCCAGAGGCGGCGGCAACGGCAGTAGTA------------GCGGCATTCAGACGATTCGTGC---------TGCCACTGCTGATG------CCGTTGTCTCCGT------TGCTC-----T-------------GGAT
droWil1	scaffold_181089:723997-724131 -	GGACAATTGGACGCC---------------GTCTCcagcagcggcggcggcagcggcagcagca------gccgcaCTGGCGAGCAGCAAGTTGTTGACTc------cgccgctgctgctg------ccgttgccgctga------cgcagacgctactgttggtcatattgtt
droVir3	scaffold_13047:13398210-13398326 +	CGACAATTGACCGCA---------------ATCGCCAGTGGCAGCGACAGCGG---CAGCTGCAGCAGTCGCCGAATTGCCAAGTAGCAAGTTATTAA---------Cgccgctgctgctgctgctgccgttacctccgg------cgcc------------------------
droMoj3	scaffold_6540:10633913-10634029 +	CGACAATTGACCGCA---------------ATCGCCAGTGGCAGCGACAGCGG---CAGCTGCAGCAGTCGCCGAATTGCCAAGTAGCAAGTTATTAA---------Cgccgctgctgctgctgctgccgttacctccgg------cgcc------------------------
droGri2	scaffold_14906:4290750-4290869 -	CGTCAATTGACCGCA---------------ATCGTCAGGGGCAGCGACAGCGG---CAGTTGCAACAGTCGCCGAATTGCCAAGTAGCAAgttattaacgccgctgctgctgctgctgctg------ccgttacctccgg------cgcc------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:19094934-19095059 +	NA	GGACAGTTG------AGCGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCTGATGGGTTAGCCGCT------GA-GGT
droSim1	chr3R:18910498-18910623 +	1	GGACAGTTG------AGCGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGCT------GA-GGT
droSec1	super_0:19459752-19459877 +	1	GGACAGTTG------AGAGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGTT------GA-GGT
droYak2	chr3R:19969866-19969991 +	1	GGACAATTG------AACGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCGGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTTAGCCGCC------GA-TGG
droEre2	scaffold_4820:8959323-8959448 -	13	GGACAGTTG------GACGCCATCACCGGCAGCCGCGG---------CGGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCT---GCTGCCGTTGCAACCG-A---------AGCTGGCGGATGGGTTGGCCGCC------GA-GGT
droEug1	scf7180000409473:254972-255094 -	8	GGACAGTTG------AACGCCATCACCGGC------------------GGCAGC---G------------GCAGCAGC------------ACTGGCGAGCAGTAGA----TTATTGACGTCGCTACT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGAGTTGACCGCCGGATGGGA-GTT
droBia1	scf7180000302075:4604033-4604149 +	3	GGACAGTTG------GACGCCATCACCGGCGGCAGCGG---------CAGCAGC---AGCGGCTG------CGG------------CCGCACTGGCGAGCAGCAGA----TTATTGACGTCGCTGCC---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGG----------------------
droTak1	scf7180000414295:164513-164629 +	1	GGACAGTTG------AACGCCATCGCCGGCGGCAGCGG---------C------------AGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTATTGACATCGCTGCC---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGGGTT-------------------
droEle1	scf7180000491280:209279-209416 +	17	GGACAGTTG------AGCGCCATCGCCGGCAGCCGCGG---------CGGCAGC---GGAAGCAGC------------AGCGGCTGCCGCATTGGCGAGCAGCAGA----TTGTTGACGTCGCCGCT---GCTGCCGTTGCCCCCG-A---------AGCTGGCGGATGGGTTGCCCGCC------GG-GCT
droRho1	scf7180000780140:23288-23411 -	11	AGCCGCAGT------AGCAGCAGCATCGGCAGCAGCAG---------CAGCAGC---A------------GCAGCAGCAGCGGCTGCAGCAGCGGGATCCAG------------CAGCGGCGCCGGC---TTGGATGTGGCCA--------------GTCTGGTGGGTCTGG--TGCGCG------GC-GGT
droFic1	scf7180000453906:760202-760324 -	19	GGACAGTTG------AACGCCATCGCCGGCAGCCGCGG---------CGGCAGC---GGCAGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTGTTCACTTCGCTGCT---GCTGCCGTTGCCACCG-A---------AGCTGGCGGATGG----------------------
droKik1	scf7180000302307:473329-473451 -	12	GGAAAGTTG------GATGCCATCACCGGCAGACGCGG---------CGACAGC---GGCAGCGG------CAG------------CAGCGCTGGCGAGCAGCAGA----TTGTTGACGCCGCTGCT---GCTGCCGTTGCCACCA-A---------AGCTGCCGGG-GGTTT--------------G-GCT
droAna3	scaffold_13340:8296287-8296436 -	8	CGACAGTTGGACGCCAACACCATCGCCAGCAGCCGCGG---------CGGCAGC---GGCAGCAGC------------AGCGGCTGCCGCACTGGCGAGCAGCAGA----TTGTTCACGCCGCTGCT---ACTGCCGTTGCCACCA-ACGCCGA---CGCTGGCCGATGCGTGGCTCGCG------GG-GCT
droBip1	scf7180000396691:1677356-1677480 +	10	TGGCCTCCA------CGCTG----CCCAACGGCGG------------CGCCAGC---ACCAGCCTG------------AGCGGCACCAGCGTTGGCTCGC---AGA----GCGTGGCTGCCGCTGCT---GCTGCCGCTGCCGCCG-C---------CTCTGCCGGATCGGGGG---GCG------GA-GGC
dp4	chrXR_group6:8583769-8583897 +	7	CAACAGCCA------ACGGCTATAACCAACAACCGCAG---------CAGCAGC---GGCAGCAG------------CAGCAGCGGC------AGC-AGCAGCA-A----TTGTTGCCATTGTCGTAGTTGTTGCCGCTGCTTGTATA---------CCCTGGCGCAGAGGGTAGT-----------A-TGA
droPer1	super_0:10926574-10926696 +	3	CGACAGTTG------GACACCAACGCCAACGCCCACAC---------CATCGCCAGAGGCGGCGGCAACGGCAGTAGT------------AGCGGCATTCAGACGA----TTCGTGCTGCCACTGCT---GATGCCGTTGTCTCCG-T---------TGCTC------------------------TG-GAT
droWil1	scaffold_181089:723997-724131 -	24	GGACAATTG------GACGCCGTCTCCAGCAGCGGCGG---------CGGCAGC---GGCAGCAGC------AG------------CCGCACTGGCGAGCAGCAAG----TTGTTGACTCCGCCGCTGCTGCTGCCGTTGCCGCTG-A---------CGCAGACGCTACTGTTGGTCATA------TT-GTT
droVir3	scaffold_12932:1166920-1167036 +	10	---------------------ATCGCCAGCGGCGGCGG---------CGGCGGC---GGCAGCGAC------AA------CTGC------TGCG----GCAGCATTTGCATTGTTGACCTCGCTGCT---GCTGCC--CGCCGCGA-------CAGCAGCCG-CCGTTGAGTTGGCGGCG------AC-GGC
droMoj3	scaffold_6328:387888-388007 +	7	C----------------------CGCCAGCAGCCGGAACAGGGACAGCAGCGCTT--------GA---------------CG---------GCGGCG-ACAGCGGA----CTGGCGCCGCTGCTGCT---GCTGCCGCTGCCACCG-CTGCTAA---AGTAGTTCATTGTGTTTGCCGCC------GACGTT
droGri2	scaffold_14906:4290741-4290869 -	55	CGTCAATTG------ACCGCAATCGTCAGGGGCAGCGA---------CAGCGGC------AGTTGC------------AACAGTCGCCGAATTGCCAAGTAGCAAG----TTATTAACGCCGCTGCTGCTGCTGCTGCTGCCGTTA-CCTCCGG---CGCCG---------------CTT------GC-AAT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GGACAGTTGagcgcc---------------atcaccggcagccgcggcggcagcggcagcagca------------ctggcgagcagcagATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCCACCGA------AGCTGGCTGATGGGTTAGCCGCTGAGGT

Size

Hit Count

Total Norm

droSim1

GGACAGTTGagcgcc---------------atcaccggcagccgcggcggcagcggcagcagca------------ctggcgagcagcagATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCCACCGA------AGCTGGCGGATGGGTTAGCCGCTGAGGT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................CCGAxxGA------AGCTGGCGGATGG...............	19	1	1.00	0.00	1.00	0.00	0.00
.....................................GCAGCAGCAGCGGCAGCGGCAGC..................................................................................................................	23	2	0.50	0.50	0.00	0.00	0.00
....................................................................................................................................GTCACCGA------AGCTxGCGGAT.................	18	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................TGA---------CGTCGTTGCTGCTG------A..............................................	18	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................CCGAxxGA------AGCTGGCGGATG................	18	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................GTCATCGA------AGCTGGCGGATG................	20	1	1.00	0.00	0.00	1.00	0.00

droSec1

GGACAGTTGAGAGCc---------------atcaccggcagccgcggcggcagcggcagcagca------------ctggcgagcagcagATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCCACCGA------AGCTGGCGGATGGGTTAGCCGTTGAGGT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................CGCTGCTGCTG------CCGCCGC........................................	18	3	0.33	0.00	0.33	0.00
...................................................AGCGGCAGCAGCA------------GTAGC.............................................................................................	18	2	0.50	0.00	0.50	0.00
............................................CAGCGGCAGCAGCAGCAGC...............................................................................................................	19	2	0.50	0.00	0.50	0.00
.....................................GCAGCAGCGGCGGCAGCGGCAGC..................................................................................................................	23	2	0.50	0.00	0.50	0.00
...........................................GCAGCGGCAGCAGCAGCAGC...............................................................................................................	20	2	0.50	0.00	0.00	0.50
......TTGGGAGCG---------------ATCACCGGC.......................................................................................................................................	18	1	1.00	0.00	1.00	0.00
..............................................GCAGCAGCAGCAGCAGCA------------..................................................................................................	18	4	0.25	0.00	0.25	0.00
.....................................GCAGCAGCAGCGGCAGCGGCA....................................................................................................................	21	3	0.33	0.00	0.33	0.00
................................................................................................................CTGCTGCTG------CCGCCGCCA......................................	18	1	1.00	0.00	1.00	0.00
..............................................................................................................CGATGCCGCTG------CCGTTGC........................................	18	1	1.00	0.00	1.00	0.00
...........................................GTGGCGGCAGCAGCAGCA.................................................................................................................	18	2	0.50	0.00	0.50	0.00
...................................CAGCAGCGGCGGCGGCAGC........................................................................................................................	19	2	0.50	0.00	0.50	0.00
.........................................CAGCGGCGGCGGCGGCAGCAG................................................................................................................	21	1	1.00	0.00	0.00	1.00
.......................................................................................................................................ATCGA------AGCTGGCGGATGGTT.............	20	1	1.00	1.00	0.00	0.00
........................................GCAGCAGCGGCAGCGGCAGC..................................................................................................................	20	3	0.33	0.00	0.33	0.00
................................................................................................GA---------CGTCGCTGTGGCTG------CC.............................................	18	1	1.00	1.00	0.00	0.00
.........................................CAGCGGCGGCAGCGACAGCAG................................................................................................................	21	1	1.00	0.00	0.00	1.00
.............................................GGGAGCAGCGGCAGCAGC...............................................................................................................	18	1	1.00	0.00	1.00	0.00
................................CAGCGGCAGCAGCGGCGGCAG.........................................................................................................................	21	2	0.50	0.00	0.50	0.00
..............................................................................................................CGCTGCTGCTG------CCGCCGCC.......................................	19	1	1.00	0.00	1.00	0.00
...............................................CGGCAGCGGCAGCAGGA------------C.................................................................................................	18	1	1.00	1.00	0.00	0.00
....................................GGCAGCGGCGGCAGCAGCG.......................................................................................................................	19	2	0.50	0.00	0.50	0.00
.........................................CTGCGGCGGCAACGGCAGCA.................................................................................................................	20	2	0.50	0.50	0.00	0.00
........................................................CAGCAGCA------------ACGGCGAGCAGC......................................................................................	20	1	1.00	1.00	0.00	0.00

droYak2

GGACAATTGAACGCC---------------ATCACCGGCAGCCGCGGCGGCAGCGGCAGCGGCA------------CTGGCGAGCAGCAGATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCCACCGA------AGCTGGCGGATGGGTTAGCCGCCGATGG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.................................................................................GAGCAGCAGATTATAGA---------GG.................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................................................GCTGCTGCTC------CCGTCGCC.......................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
...........................................GCAGTGGCAGCGGCAGCGGC...............................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................AGCAGCGGCGGCGGCGGCAGC..................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................GCAGCAGCAGCGGCAGCGGCA------------..................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00	0.00
.....................................GCAGCAGCAGCGGCAGCGGCA....................................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00	0.00
..................................................CCACGGCAGCGGCA------------CTGGC.............................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................GCGGCAGCGGCAGCCGCG------------..................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................GCAGCAGCGGCGGCAGCGGA.....................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
....................................GGCAGCGGCGGCAGCAGCGGCA....................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................GAGCAACAGATTATTGG---------CGT................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................CGAGCAGCAGATTATAGA---------G..................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................TGGCGGACGGGTTAGCTGCC.....	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

GGACAGTTGGACGCc---------------atcaccggcagccgcggcggcagcggcagcagca------------ctggcgagcagcagATTATTGA---------CGTCGCTGCTGCTG------CCGTTGCAACCGA------AGCTGGCGGATGGGTTGGCCGCCGAGGT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................TCGGCGGCGGCAGCGGCAGC..................................................................................................................	20	1	2.00	0.00	0.00	0.00	2.00
............................................CAGCAGCAGCGGCAGCAGC...............................................................................................................	19	4	0.50	0.00	0.00	0.25	0.25
........................................GCAGCGGTGGCAGCGGCAGC..................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................AGCAGCAGCGGCGGCAGCGGC.....................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................GTTGCTGCTGCTG------CTGTTG.........................................	19	1	1.00	0.00	0.00	0.00	1.00
..................................................CAGTGGCAGxAGCA------------CTGGC.............................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.............................................AGCGACAGCGGCAGCAGC...............................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................GCAGCGGCAGCAGCAGCAGCA------------..................................................................................................	21	3	0.33	0.00	0.00	0.00	0.33
.............................................GGCAACAGCGGCAGCAGCA------------..................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...................................................AGCAGCAGCAGCA------------GTGGC.............................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
.............................................AGCAGCAGCGGCAGCAGC...............................................................................................................	18	5	0.20	0.00	0.00	0.20	0.00
...........................................................................................................CGGCGCTGCTGCTT------CCGT...........................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................CGCTGCAGCTG------CCGTTGGA.......................................	19	1	1.00	0.00	0.00	0.00	1.00
.......................................AGCGGCGGCGGCAGCAGCAGC..................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00

droAna3

CGACAGTTGGACGCCAACACC---------ATCGCcagcagccgcggcggcagcggcagcagcagcggcTGCCGCACTGGCGAGCAGCAGATTGTTCA---------CGCCGCTGCTACTG------CCGTTGCCACCAACGCCGACGCTGGCCGATGCGTGGCTCGCGGGGCT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.................................................GCGGTGGCAGCAGCAGCGGC.........................................................................................................	20	1	8.00	0.00	8.00	0.00	0.00
.............................................GGCGGCxGCGGCAGCAGGAGC............................................................................................................	20	1	3.00	1.00	2.00	0.00	0.00
................................................GGCAGCGGCAGTAGCAGCGGC.........................................................................................................	21	2	1.50	0.00	1.50	0.00	0.00
.................................................GCAGCAGCAGCAGCAGCGGC.........................................................................................................	20	3	1.00	0.00	1.00	0.00	0.00
.................................................GCAGAGGCAGCAGCAGCGGC.........................................................................................................	20	2	1.00	0.00	1.00	0.00	0.00
..............................................GCGGCxGCGGCAGCAGGAGC............................................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
............................................CGGCGGCxGCGGCAGCAGGAGC............................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................TGCAGCAGCGGCAGCAGCAG.............................................................................................................	20	3	0.33	0.00	0.33	0.00	0.00
.......................................................GCAGCAGCAGCGGCGGCGGC...................................................................................................	20	3	0.33	0.00	0.33	0.00	0.00
..................................CCAGxAGCAGCGGCGGCAGC........................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.................................................GCAGCAGCAGCAGGAGCGGC.........................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00
..............................................GCAGCAGCGGCAGCAGCAGCG...........................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00
.............................................GTCAGCAGCGGCAGCAGCAG.............................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
....................................AGCAGAGGCGGCGGCAGCGGC.....................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................GCAGCAGCGGCAGCAGCAGCA...........................................................................................................	21	4	0.25	0.00	0.25	0.00	0.00
..................AAC---------TTCGCCAGCAGCCGC.................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.................................................GCAGCGGCAGCAGCAGCAGCA........................................................................................................	21	5	0.20	0.00	0.20	0.00	0.00
...........................................................................................................................................................................TCT	22	3	0.33	0.00	0.00	0.33	0.00
.......................................................GCAGCAGCAGCAGCGGCCGC...................................................................................................	20	5	0.20	0.00	0.20	0.00	0.00
...................................CAGCAGCAGCGGAGGCAGC........................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..............................................GCGGCAGCGGTAGCGGCAGC............................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................T	23	51	0.02	0.00	0.02	0.00	0.00
...................................................AGCAGCAGCAGCAGCGGCA........................................................................................................	19	6	0.17	0.00	0.00	0.17	0.00
...........................................GCGGCGGCAGCGGCAGCATCAC.............................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................................GCAGCAGCAGCGGCAGCGGCA..................................................................................................	21	3	0.33	0.33	0.00	0.00	0.00
....................................................GCAGCAGCAGCAGCGGCCGC......................................................................................................	20	5	0.20	0.00	0.20	0.00	0.00
..............................................................CAGCGGCAGCGGCACTGGC.............................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................................CAGCAGCAGCGGCGGCAGCGGGAGC..................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
.....................................GCAGCAGCAGCGGCAGCGGCA....................................................................................................................	21	3	0.33	0.33	0.00	0.00	0.00
.....................................GCAGCGGCGGCGGCAGCGGCA....................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
....................................AGCAGCAGCGGCGGCGGC........................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
............................................CAGCAGCAGCGGCAGCAGCAGC............................................................................................................	22	4	0.25	0.25	0.00	0.00	0.00
..............................................................CAGCGGGTGCCGCGCTGGC.............................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...........................................GCGGCGGCCGCGGCAGCGGC...............................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.....................................GCAGCGGCGGCGGCAGCGTCAGC..................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.................................................GCAGCAGCAGCAGCAGCGGCTT.......................................................................................................	22	2	0.50	0.00	0.50	0.00	0.00
......ATGGACGCCAACAGC---------ATC.............................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................CGACAGCxGCAGCAGCAGC............................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.................................................GAAGTGGCAGCAGCAGCGGC.........................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................T	21	3	0.33	0.00	0.33	0.00	0.00
.................................................GCAGCAGCAGCAGCAGCGGCA........................................................................................................	21	6	0.17	0.17	0.00	0.00	0.00
........................................................CAGCAGCAGCGGCGGCAGC...................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
................................................AGCAGCGGCAGCAGCAGCGCC.........................................................................................................	21	2	0.50	0.00	0.00	0.50	0.00
..........................................................................................................................................................................TTCT	21	33	0.03	0.00	0.00	0.00	0.03
...................................................AGCAGCAGCAGCAGCGGCGG.......................................................................................................	20	4	0.25	0.00	0.25	0.00	0.00
.....................................GCAGCAGCTGCGGCAGCGGC.....................................................................................................................	20	2	0.50	0.00	0.00	0.50	0.00
...................................CAGCAGCAGCGGCGGCAGC........................................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
......................................................GGCAGCAGCAGCGTCGGC......................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................AGCAGCAGCGGCGGCGGC...................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
............................................CGGCGGTAGCAGCAGCAGCAGC............................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................CT	18	45	0.02	0.00	0.00	0.02	0.00
..............................................GCGGCGGCGGCAGCATCAGC............................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................GCGGCAGCAGCAGCAGCGGCC.....................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
...........................................GCAGCGGCAGCAGCAGCAGCA..............................................................................................................	21	5	0.20	0.00	0.20	0.00	0.00
....................................AGCAGCAGCGGCGGCGGCGGC.....................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................GCAGCAGCGGCAGCGGCAGCA.................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00

dp4

CGACAGTTGGACACCAACGCCAACGCCCACACCATCGCCAGAGGCGGCGGCAACGGCAGTAGTA------------GCGGCATTCAGACGATTCGTGC---------TGCCACTGCTGATG------CCGTTGTCTCCGC------TGCTC-----T-------------GGTT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
................................................................................................................CTGCTGCTG------CCGTTGTCGCCG...................................	21	1	1.00	1.00	0.00	0.00	0.00
.......................CACCCACACCGTCGCCAG.....................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................CAGCGGCGGCGGCAATGGC.....................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.................................................................................ATTCAGTCGATTCGCGC---------TGC................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

CGACAGTTGGACACCAACGCCAACGCCCACACCATCGCCAGAGGCGGCGGCAACGGCAGTAGTA------------GCGGCATTCAGACGATTCGTGC---------TGCCACTGCTGATG------CCGTTGTCTCCGT------TGCTC-----T-------------GGAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................CACCCACACCGTCGCCAG.....................................................................................................................................	18	1	30.00	0.00	0.00	0.00	0.00	30.00
...................................................................................................................CTGATG------GCGTTGACTCCGT------............................	19	1	8.00	2.00	1.00	0.00	0.00	5.00
................................................................................CATTCAGTCGATTCGCGC---------T..................................................................	19	1	4.00	0.00	0.00	0.00	0.00	4.00
.................................................................................ATTCAGTCGATTCGCGC---------TGC................................................................	20	1	2.00	0.00	0.00	0.00	0.00	2.00
..................................................CAACAGCAGTAGTA------------GCAGC.............................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
..................................................................................TTCAGTCGATTCGCGC---------TG.................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................CATTCAGTCGATTCGCGC---------...................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.................................................GCAACAGCAGTAGTA------------GTGGC.............................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

GGACAATTGGACGCC---------------GTCTCcagcagcggcggcggcagcggcagcagca------gccgcaCTGGCGAGCAGCAAGTTGTTGACTc------cgccgctgctgctg------ccgttgccgctga------cgcagacgctactgttggtcatattgtt	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...................................................AGCAGCAGCAGCA------GCAGCA..................................................................................................	19	3	2.33	0.00	2.00	0.33	0.00
.................................................GCAGCAGCAGCAGCA------GCAGCA..................................................................................................	21	1	4.00	0.00	4.00	0.00	0.00
...................................................................................................................CTGCTG------CCGATGCTGCTG...................................	18	1	4.00	0.00	0.00	0.00	4.00
..................................................CAGCAGCAGCAGCA------GCAGCA..................................................................................................	20	1	4.00	0.00	3.00	1.00	0.00
.................................................GCAGCAGCAGCAGCA------GCAGC...................................................................................................	20	3	1.33	0.00	1.33	0.00	0.00
..............................................GCAGCAGCAGCAGCAGCA------GC......................................................................................................	20	3	1.33	0.00	1.33	0.00	0.00
.................................................GCAGCAGCAGCAGCA------GCGGCA..................................................................................................	21	1	3.00	1.00	2.00	0.00	0.00
....................................AGCAACAGCGGCGGCAGCGGC.....................................................................................................................	21	1	3.00	1.00	2.00	0.00	0.00
.......................................AGCAGCGGCGGCAGCGGCAGT..................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
..................................GCAGCAGCAGCGGCGGCAGC........................................................................................................................	20	1	3.00	0.00	3.00	0.00	0.00

droVir3

CGACAATTGACCGCA---------------ATCGCCAGTGGCAGCGACAGCGG---CAGCTGCAGCAGTCGCCGAATTGCCAAGTAGCAAGTTATTAA---------Cgccgctgctgctgctgctgccgttacctccgg------cgcc------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
................................................................................................................CTGCTGCTGCTGCTGCTG............................................	18	6	0.67	0.00	0.00	0.00	0.17	0.50
.............................................................................................................CTGCTGCTGCTGCTGCTGCTG............................................	21	3	1.33	0.00	0.00	0.00	0.00	1.33
.............................................................................................................CTGCTGCTGCTGCTGCTG...............................................	18	6	0.67	0.00	0.00	0.00	0.17	0.50
..............................................................................................................CGCTGCTGCTGGGGCTGC..............................................	18	1	3.00	0.00	0.00	0.00	2.00	1.00
........................................GCAGCCACTGCGG---CAGCTG................................................................................................................	19	1	2.00	0.00	0.00	0.00	2.00	0.00
..............................................................................................................TGCTGCTGCTGCTGCTGCTG............................................	20	4	0.50	0.00	0.00	0.00	0.25	0.25
.............................................................................................................CCGCTGCCGCTGCCGCTG...............................................	18	4	0.50	0.00	0.00	0.00	0.00	0.50
................................................................................................................CTGCTGCTGCTACTGCTG............................................	18	3	0.67	0.00	0.00	0.00	0.33	0.33
...........................................................................................................TGCTGCTGCTGCTGCTGCTG...............................................	20	4	0.50	0.00	0.00	0.00	0.25	0.25
.............................................................................................................CTGCTGCTGCTACTGCTG...............................................	18	3	0.67	0.00	0.00	0.00	0.33	0.33
................................................................................................................CTGCTGCTGCTGATGCTG............................................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
................................................................................................................CTGCTGCTGGTGCTGGCG............................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................CTGCTGCTGCTGATGCTG...............................................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
...........................................................................................................TGCCGTTGCTGCTGCTGCTG...............................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................................................GCTGCCGGTGCTGCTGCC.............................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
.............................................................................................................CTGCTGCTGTTGCTGCTG...............................................	18	6	0.17	0.00	0.00	0.00	0.00	0.17
........................................GCAGCGACGGCGG---CAGCAGC...............................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................................................GCTGTTGCTGCTGCTGCTG............................................	19	6	0.17	0.00	0.00	0.00	0.00	0.17
............................................................................................................GCTGTTGCTGCTGCTGCTG...............................................	19	6	0.17	0.00	0.00	0.00	0.00	0.17
.................................................................................................C---------TGCCGCTGCTGCTGCTGCTG...............................................	21	3	0.33	0.00	0.00	0.00	0.00	0.33
..........................................................GCAGCAGCAGTCGCCGCA..................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................................................TGCTGCAGCTGCTGACGTT..........................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................CTGCTGCTGTTGCTGCTG............................................	18	6	0.17	0.00	0.00	0.00	0.00	0.17
............................................................................................................GCTGCTGCCGCTGCTGCTG...............................................	19	3	0.33	0.00	0.00	0.00	0.00	0.33
........................................GCAGCGGCAGCGG---CAGCAGCAGCA...........................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................GATGCTGCTGCTGCxGCCGTT..........................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................GCTGCTGCCGCTGCTGCTG............................................	19	3	0.33	0.00	0.00	0.00	0.00	0.33
..................................GCAGTGGCAGCGGCAGCGG---C.....................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................AAGCGACAGCGG---CAGCAGCAGC............................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................................................................................CTGCTGCTGCTGCTGCTGCTGT...........................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................CTGCTGTTGCTGCTGCTGC..............................................	19	3	0.33	0.00	0.00	0.00	0.00	0.33
.............................................................................................................CCTCTTCTGCTGCTGCTGC..............................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................................GCTGCTGCTGCTGCGGCTG...............................................	19	2	0.50	0.00	0.00	0.00	0.50	0.00
...............................................................................................................GCTGCTGCTGCTGCGGCTG............................................	19	2	0.50	0.00	0.00	0.00	0.50	0.00
...............................................................................................................GCTGCTGCCGGTGCTGCC.............................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
.................................................................................................................TGCTGCTGCTGCTACCGAT..........................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

CGACAATTGACCGCA---------------ATCGCCAGTGGCAGCGACAGCGG---CAGCTGCAGCAGTCGCCGAATTGCCAAGTAGCAAGTTATTAA---------Cgccgctgctgctgctgctgccgttacctccgg------cgcc------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.............................................................................................................CTGCTGCTGCTGCTGATG...............................................	18	9	0.11	0.00	0.00	0.00	0.11
..............................................................................................................CGCTGCGGCTGCTGCTGCCGTT..........................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................AGAGGCAGxGACAGCGG---CA....................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................GCAGCGACAGCGG---CAGAGGC...............................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..........................................AGCAACAGCGG---CAGCAGCAGC............................................................................................................	21	4	0.25	0.00	0.00	0.25	0.00
............................................CGACAGAGG---CAGCAGCAGCA...........................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
................................................................................................................CTGCTGCTGCTGCTGATG............................................	18	9	0.11	0.00	0.00	0.00	0.11
...........................................GCGACAGCGG---CAGAGGCAG.............................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
.............................................................................................................CTGCTGCTGCTGCTGCTGCTGT...........................................	22	4	0.25	0.00	0.00	0.00	0.25
.....................................GAGGCAGCGGCAGCGG---CA....................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
............................................CAACAGCGG---CAGCAGCAGC............................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
....................................................G---CAGCTGCAGAAGTCGGC.....................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................CTGCTGCTGCTGCTGCTGTTGC........................................	22	4	0.25	0.00	0.00	0.00	0.25
........................................GCAGCGGCAGCGG---CAGCGGC...............................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00

droGri2

CGTCAATTGACCGCA---------------ATCGTCAGGGGCAGCGACAGCGG---CAGTTGCAACAGTCGCCGAATTGCCAAGTAGCAAgttattaacgccgctgctgctgctgctgctg------ccgttacctccgg------cgcc------------------------	Size	Hit Count	Total Norm	V109 Male body
......................................................................................................GCTGTTGCTGCTGCTGTTG------...............................................	19	1	1.00	1.00
...........................................................................................................TGCTGCTGCTGCTG------CCGTCA.........................................	20	1	1.00	1.00
................................................................................................CACxCCGCTGCTGCTGCTGCT.........................................................	20	1	1.00	1.00
.......................................................................................................CTGCTGCTGCTGCTGCCG------TC.............................................	20	2	0.50	0.50
..........................................................................................................CTGCTGCTGCTGCTG------CCGTC..........................................	20	2	0.50	0.50

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