dme-mir-973- 12- and 20-way alignments

dme-mir-973	chrX:19445561-19445661 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 19445579-19445599
   star strand at position 19445623-19445644
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:19445546-19445676 +	AATATACTTCACTTTACCGTCGTCGACTTTTCGTGGTTGGTGGTTGAACTTCGATTTT-AAGTATTTAAATAAAA-------------TGAAATCTG-TTCATTCTCCGACACAAGAAGTTCACGCAAAGGAGCTGCAGCTGCGAA
droSim1	chrX:15011304-15011407 +	CG--------------------TATACTTTTCCGGGTTGGTGGTTGAACTTCGATTTT-AAGCATTTAAATAAGA--------------TAAATCTG-TTCATTCTTCGACCCAAAAAGTTCACGTGAAGAAGCAGCG------AA
droSec1	super_8:1727982-1728085 +	CG--------------------TATACTTTTCGGGGTTGGTGGTTGAACTTCGATTTT-AGGTATTTAAATAAGA--------------TAAATCTG-TTCATTCTTCGACCCAAAAAGTTCACGTGAAGAAGCAGCG------AG
droYak2	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4690:9682314-9682417 +	CG--------------------TCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTT-GAGTATTCAAATAAAA--------------TAAATCTG-TTCATTCCTCGACACAAGAAGTTGACGTGCAGGAGCGGCA------AA
droAna3	scaffold_13417:2478641-2478748 -	CA--------------------CCGACTCCTCGTGTTTGGCGATTGAACCTGGATTTT-TAATTTTCGAGTACGA--------------GAAATCTG-TTCATTCCTCGACACTAGTAGTTGGCGCGAC-ACTCAGCG-CACCAAA
dp4	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	CA--------------------TGGCCTTTTCGTGTTTGGTGATTGAACTTGGATTTTGTTCTATATAC-----ATATATAAAAATATGTAAATCTG-TTCATTCCTCGACACTAGAAGTTCATGTCAATAACCTGCA------CA
droVir3	Unknown	T-------------CATGGACATTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTT-TTTTATATAC-----A--------------CAAATCTG-TTCATTCCTCGACACTAGAAGTTTGCGTCAATAAGCTGCG-CATAAAT
droMoj3	scaffold_6328:2909118-2909204 -	C-----------------GGCTTTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTT-TAAAATATGAA---AA--------------GAAATCTG-TTCATTCCTCGACACTAAGAGTTTA-----------------------
droGri2	scaffold_15081:2051526-2051596 -	------------------GACATTTACTTTTTGTGTTGGGTGATTC-------------------------------------------------TGATTCACTTTTCGACACATCAAGTTCACCTCAATAAACTGCA--------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:19445546-19445676 +	NA	AATA----------T-ACTTC-------ACTTTAC---------------CGTCGTCGACTTTTCGTGGTTGGTGGT--------TGAACTTCGATTTTAA--GTATTTAAATA---------AAATGAAATCTGTTCATTCTCCGACACAAGAAGTTCAC-GCAAAGGA------GCTGC------------------AGCTGCGAA
droSim1	chrX:15011303-15011407 +	6	C-----------------------------------------------------GTATACTTTTCCGGGTTGGTGGT--------TGAACTTCGATTTTAA--GCATTTAAATA---------AGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCAC-GTGAAGAA------GCAGC------------------GAA------
droSec1	super_8:1727974-1728085 +	2	ACT----------------------------TC------------------AACGTATACTTTTCGGGGTTGGTGGT--------TGAACTTCGATTTTAG--GTATTTAAATA---------AGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCAC-GTGAAGAA------GCAGC------------------GAG------
droYak2	chr2L:20912127-20912226 -	56	ATTT----------C-G-----------ATTTG------------------AAATCGTAAAATTGGTG-------ATCCGGTATTTGAAATCGGAA-------GTATTT-TGTA---------AAACGGTAACTTTTTTCTGGCCGAAATGATAAGTTAAT-GC--------------------------------------------
droEre2	scaffold_4690:9682299-9682417 +	4	ACTA----------T-A--CC-------ATTTT------------------AACGTCGACTTTTCGTGGTTGGTGGC--------TGAACTTAGATTTTGA--GTATTCAAATA---------AAA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGAC-GTGCAGGA------GCGGC------------------AAA------
droEug1	scf7180000409109:6855-6998 -	2	AAGTCAAACTTTTAT-AAATCATTAAAGATTCC------------------AACGACGACTTCTCGTGTTTGGTGAC--------TGAACTTGGATTTTGA--ATATTTAAATA---------AAA-TAAATCTGTTCAATCCTCAACACGAGAAGTCGAC-GTAAATGA------CCAGC------------------AAACATAAA
droBia1	scf7180000302069:1157467-1157589 -	22	AATG----------A-ATTTG-------ATGTT------------------AACGCCGACTTTAGGTGTTTGGTGGC--------TGAACTTGGATTTTTA--ACAGTTGAATG---------TAT-TAAATCTGTTCATTCCTCAACACAAAAAGTTGAC-GTTAAGGC------CCAGC------------------ATA----AA
droTak1	scf7180000415169:850730-850846 -	24	AGTT----------T-A-----------ATTTT------------------AACGTCGACTTTTCGTGTTTGGGGGC--------TGAACTCTGATTTTTA--ATAATTGAATT---------AAG-TAAATCTGTTCATTCCTCGACACAAGAAGTTGGC-GTAAAGTA------ACAGC------------------GCA------
droEle1	scf7180000490751:1106831-1106973 +	1	AAAACGGTT----AT-A--CA-------ACTTA-GAATTATTTAATAGTATGACATCGACTTTTTGTGTTTGGCGGA--------TGAACTTAGATTTTTC--TTATTTGTA-A---------AAA-CAAATCTGTTCATTCCTCGACGCAAAAAGTTGATTGTTAAAAA------CCAGC------------------ACAC-----
droRho1	scf7180000761121:198723-198828 -	8	A---------------------------------------------------ACATCGACTTCTCGTGTTTGGCGTC--------TGAACTCAGATTCTTA--ACAGTTGTGTT---------AAATAAAATCTGTTCATTCCTCGACACAAGAAGTTGAC-GTTAAG-A------CCAGC------------------ATA------
droFic1	scf7180000454073:1723943-1724040 +	2	G---------------------------------------------------ACATTGACATCTCGTGTTTGGCGAA--------TGAGCTCGGATTTTTGTAGTATTTGAATA---------AGA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGAA-GTTGAT----------------------------------------
droKik1	scf7180000302517:1176199-1176317 +	1	AAAA----------ACACACA-------ATAT--------------------AAATTGACTTTTCGTGCTTGGCGAT--------TGAAGGTGGATTTGTG--ATTTTTAAGC----------AAT-TAAATCTGTTCAATCGTCAACACTAAAAGTTGAT-GTTATTTA------GCTTC------------------GAA------
droAna3	scaffold_13417:2478622-2478750 -	3	G---------------------------------------------------ACACCGACTCCTCGTGTTTGGCGAT--------TGAACCTGGATTTTTA--ATTTTCGAGTA---------CGA-GAAATCTGTTCATTCCTCGACACTAGTAGTTGGC-GCGACA-C------TCAGCGCACCAAACATGAACCGCGGCTCAAAT
droBip1	scf7180000395874:49685-49789 -	3	--------------------------------------------------------CGACTTCTCGTGTTAGGCGAT--------TGAACCTGGATTT-AA--ATTTTCGAGTA---------CGA-GAAATCTGTTCAATCCTCGACACTAGCAGTTGGC-GCGACCG-------ACTGC------------------GCATAAAAA
dp4	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7946449-7946592 +	1	AAAA----------T-ATATCGGGAATATTGTC------------------GACATGGCCTTTTCGTGTTTGGTGAT--------TGAACTTGGATTTTGT-TCTATATACATATATAAAAATATG-TAAATCTGTTCATTCCTCGACACTAGAAGTTCAT-GTCAATAACTTCATTTCCTGC----------------A--------
droVir3	scaffold_13042:918337-918453 -	9	AGAA----------C-AGTTA-------AAATCAT--------------CGGACATTCACTTTTCGTGTTCGATGTT--------TGAACTTGGATTTTTT--TTATAT--------------ACA-CAAATCTGTTCATTCCTCGACACTAGAAGTTTGC-GTCAATAA------GCTGC---------------------------
droMoj3	scaffold_6328:2909116-2909204 -	4	C--------------------------------------------------GGCTTTCACTTTTCGTGTTCGATGTT--------TGAACTTGGATTTTTA--AAATATGA------------AAA-GAAATCTGTTCATTCCTCGACACTAAGAGTTTAG-G---------------------------------------------
droGri2	scaffold_15081:2051526-2051596 -	6	G---------------------------------------------------ACATTTACTTTTTGTGTTGGGTGAT--------TC---------------------------------------------TGATTCACTTTTCGACACATCAAGTTCAC-CTCAATAA------ACTGC------------------A--------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

AATATACTTCACTTTACCGTCGTCGACTTTTCGTGGTTGGTGGTTGAACTTCGATTTT-AAGTATTTAAATAAAA-------------TGAAATCTG-TTCATTCTCCGACACAAGAAGTTCACGCAAAGGAGCTGCAGCTGCGAA

Size

Hit Count

Total Norm

droSim1

CG--------------------TATACTTTTCCGGGTTGGTGGTTGAACTTCGATTTT-AAGCATTTAAATAAGA--------------TAAATCTG-TTCATTCTTCGACCCAAAAAGTTCACGTGAAGAAGCAGCG------AA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................................................................................TCTG-TTCATTCTTCGACCCAAA..............................	22	1	276.00	0.00	3.00	272.00	1.00
.............................................................................................TCTG-TTCATTCTTCGACCCAA...............................	21	1	207.00	0.00	7.00	200.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCA................................	20	1	83.00	0.00	17.00	66.00	0.00
............................................................................................ATCTG-TTCATTCTTCGACCCA................................	21	1	15.00	0.00	0.00	15.00	0.00
...........................................................................................AATCTG-TTCATTCTTCGACCC.................................	21	1	12.00	0.00	1.00	11.00	0.00
...........................................................................................AATCTG-TTCATTCTTCGACCCA................................	22	1	12.00	0.00	0.00	12.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCAAAA.............................	23	1	12.00	0.00	0.00	12.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCC.................................	19	1	10.00	0.00	1.00	9.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACC..................................	18	1	9.00	0.00	3.00	6.00	0.00
............................................................................................ATCTG-TTCATTCTTCGACCCAA...............................	22	1	7.00	0.00	0.00	7.00	0.00
............................................................................................ATCTG-TTCATTCTTCGACCCAAA..............................	23	1	5.00	0.00	0.00	5.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCAG...............................	21	1	4.00	0.00	0.00	4.00	0.00
...........................................................................................AATCTG-TTCATTCTTCGACCCT................................	22	1	4.00	0.00	0.00	2.00	2.00
.............................................................................................TCTG-TTCATTCTTCGACCCG................................	20	1	3.00	0.00	0.00	3.00	0.00
............................................................................................ATCTG-TTCATTCTTCGACCC.................................	20	1	3.00	0.00	0.00	3.00	0.00
............................................................................................ATCTG-TTCATTCTTCGACC..................................	19	1	3.00	0.00	1.00	2.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCAAT..............................	22	1	2.00	0.00	0.00	2.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCT................................	20	1	2.00	0.00	0.00	2.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCACC..............................	22	1	2.00	0.00	0.00	2.00	0.00
...........................................................................................AATCTG-TTCATTCTTCGACCCAA...............................	23	1	2.00	0.00	0.00	2.00	0.00
...........................................................................................AATCTG-TTCATTCTTCGAC...................................	19	1	2.00	0.00	0.00	2.00	0.00
............................................................................................ATCTG-TTCATTCTTCAACCCA................................	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTATTCGACCC.................................	19	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCAAG..............................	22	1	1.00	0.00	0.00	1.00	0.00
............................................................................................ATCTG-TTCATTCTTCGACCAAA...............................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCCAA..............................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTGATTCTTCGACCCAAA..............................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCTTCTACCCAAA..............................	22	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................AATCTG-TTCATTCTTCGACTC.................................	21	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................AGTCTG-TTCATTCTTCGACCC.................................	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCTTCCACCCAAA..............................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTT-TTCATTCTTCGACCCAAA..............................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCGG-TTCATTCTTCGACCCA................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TTTG-TTCATTCTTCGACCCAA...............................	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-ATCATTCTTCGACCCAAA..............................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCTTCGGCCCAAA..............................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TATG-TTCATTCTTCGACCCAAA..............................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCCG-TTCATTCTTCGACCCAAA..............................	22	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................AATCTG-TTCATTCTTCGACC..................................	20	1	1.00	0.00	0.00	1.00	0.00
...............................TCGCGTTGGTGGTTGAACTTC..............................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................CTG-TTCATTCTTCGACCCAA...............................	20	1	1.00	0.00	0.00	1.00	0.00
............................................................................................ATCTG-TTCATTCTTCGACCCT................................	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCTTCCACCCA................................	20	1	1.00	0.00	0.00	1.00	0.00
............................................................................................ATCCG-TTCATTCTTCGACCCA................................	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCAC...............................	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACCCAAAGA............................	24	1	1.00	0.00	0.00	1.00	0.00

droSec1

CG--------------------TATACTTTTCGGGGTTGGTGGTTGAACTTCGATTTT-AGGTATTTAAATAAGA--------------TAAATCTG-TTCATTCTTCGACCCAAAAAGTTCACGTGAAGAAGCAGCG------AG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
............................................................................................ATCTG-TTCATTCTTCGACCCAA...............................	22	1	6.00	3.00	1.00	2.00
.............................................................................................TCTG-TTCATTCTTCGACCCAA...............................	21	1	3.00	2.00	1.00	0.00
............................................................................................ATCTG-TTCATTCTTCGACCCA................................	21	1	2.00	1.00	1.00	0.00
..................................................................................................TTCATTCTTCGACCCAAAAAGT..........................	22	1	1.00	1.00	0.00	0.00
................................GGGGTTGGTGGTTGAACTTCGA............................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTCGGGGTCGGTGGTTCAA..................................................................................................	19	1	1.00	1.00	0.00	0.00
...............................CGGGGTTGGTGGTTGAACTTCGATT..........................................................................................	25	1	1.00	0.00	1.00	0.00
.......................................................................................................TATTCGACCCAATAAGTT.........................	18	2	0.50	0.00	0.00	0.50
.............................................................................................TCTG-TTCATTCTTCGACCCAAA..............................	22	1	1.00	0.00	1.00	0.00
................................GGGGTTGGTGGTTGAACTTCG.............................................................................................	21	1	1.00	1.00	0.00	0.00
............................................................................................ATCTG-TTCATTCTTCGACCCAAA..............................	23	1	1.00	1.00	0.00	0.00

droYak2

--------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

CG--------------------TCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTT-GAGTATTCAAATAAAA--------------TAAATCTG-TTCATTCCTCGACACAAGAAGTTGACGTGCAGGAGCGGCA------AA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.............................................................................................TCTG-TTCATTCCTCGACACAAGT.............................	23	1	6.00	0.00	1.00	0.00	5.00
.............................................................................................TCTG-TTCATTCCTCGACACAAG..............................	22	1	5.00	0.00	1.00	0.00	4.00
.............................................................................................TCTG-TTCATTCCTCGACACA................................	20	1	2.00	0.00	1.00	0.00	1.00
.............................................................................................TCTG-TTCATTCCTCGACACAA...............................	21	1	2.00	0.00	0.00	0.00	2.00
...............................CGTGGTTGGTGGCTGAACTTAGA............................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TCTG-CTCATTCCTCGACACAAG..............................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................CAGGGAGTTGACGTGCAGG...............	19	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGGCACAAGT.............................	23	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TCTG-TCCATTCCTCGACACAAG..............................	22	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TCTG-TTCATTCCTCGACACTAG..............................	22	1	1.00	0.00	0.00	1.00	0.00

droAna3

CA--------------------CCGACTCCTCGTGTTTGGCGATTGAACCTGGATTTT-TAATTTTCGAGTACGA--------------GAAATCTG-TTCATTCCTCGACACTAGTAGTTGGCGCGAC-ACTCAGCG-CACCAAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.............................................................................................TCTG-TTCATTCCTCGACACTAG..............................	22	1	13.00	9.00	2.00	2.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGT.............................	23	1	6.00	4.00	2.00	0.00	0.00
...............................CGTGTTTGGCGATTGAACCTGG.............................................................................................	22	1	5.00	5.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTA...............................	21	1	4.00	4.00	0.00	0.00	0.00
...............................CGTGTTTGGCGATTGAACCTGGAT...........................................................................................	24	1	2.00	2.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCAATCCTCGACACTAG..............................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................CCTG-TTCATTCCTCGACACTAGT.............................	23	1	1.00	1.00	0.00	0.00	0.00
...............................CGTGTTTGGCGATTGAACCTGGAA...........................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................CTG-TTCATTCCTCGACACTAGT.............................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................CTG-TTCATTCCTCGACACTAG..............................	21	1	1.00	0.00	0.00	1.00	0.00
...............................CGTGTTTGGCGATTGAACCTGGATT..........................................................................................	25	1	1.00	0.00	0.00	1.00	0.00
...............................CGTGTTTGGCGATTGAACCTGGT............................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACT................................	20	1	1.00	0.00	1.00	0.00	0.00
.................................TGTTTGGCGCTTGAACCTGGTTT..........................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
............................................................................................CTCTG-TTCATTCCTCGACACTAG..............................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................ATG-TTCATTCCTCGACACTAG..............................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................CTG-TTCAGTCCTCGACACTAGT.............................	22	1	1.00	0.00	0.00	1.00	0.00
.................................TGTTTGGCGATTGAACCTGGA............................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TCTG-TCCATTCCTCCACACTAG..............................	22	1	1.00	0.00	0.00	1.00	0.00
..................................GTTTGGCTATGGAACCTGGATT..........................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.................................TGTTTGGCGATTGAACCTGGATT..........................................................................................	23	1	1.00	1.00	0.00	0.00	0.00

dp4

--------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

--------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

CA--------------------TGGCCTTTTCGTGTTTGGTGATTGAACTTGGATTTTGTTCTATATAC-----ATATATAAAAATATGTAAATCTG-TTCATTCCTCGACACTAGAAGTTCATGTCAATAACCTGCA------CA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........................TTTTCGTGTTTGGTGATTGAACT................................................................................................	23	1	64.00	30.00	0.00	1.00	33.00
...........................TTTTCGTGTTTGGTGATTGAAC.................................................................................................	22	1	30.00	29.00	0.00	0.00	1.00
.............................................................................................TCTG-TTCATTCCTCGACACTAG..............................	22	1	23.00	0.00	0.00	0.00	23.00
..................................................................................................TTCATTCCTCGACACTAGAAGT..........................	22	1	20.00	20.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGA.............................	23	1	13.00	0.00	0.00	0.00	13.00
...........................TTTTCGTGTTTGGTGATTGAA..................................................................................................	21	1	9.00	6.00	0.00	0.00	3.00
.............................................................................................TCTG-TTCATTCCTCGACACT................................	20	1	5.00	0.00	0.00	0.00	5.00
...........................TTTTCGTGTTTGGTGATTGA...................................................................................................	20	1	5.00	5.00	0.00	0.00	0.00
............................TTTCGTGTTTGGTGATTGAACT................................................................................................	22	1	2.00	1.00	0.00	0.00	1.00
...........................TTTTCGTGTTTGTTGATTGAACT................................................................................................	23	1	2.00	0.00	0.00	0.00	2.00
...............................CGTGTTTGGTGATTGAACTTGGATT..........................................................................................	25	1	2.00	0.00	1.00	1.00	0.00
...........................TTTTCGTGTTTGGTGATTGAACTT...............................................................................................	24	1	2.00	0.00	0.00	0.00	2.00
.............................................................................................TCTG-TTCATTCCTCGACACTA...............................	21	1	2.00	1.00	0.00	0.00	1.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGG.............................	23	1	2.00	0.00	0.00	0.00	2.00
.............................................................................................TCTG-TTCATTCCTCGGCACTAG..............................	22	1	1.00	0.00	0.00	0.00	1.00
........................................................CTGxTCTATATAC-----ATATATA.................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................CGTGTTTGGTGATTGAACTTGGATC..........................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TCCG-TTCATTCCTCGACACTAG..............................	22	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................TTCATTCCTCGACACTAGAAGTT.........................	23	1	1.00	1.00	0.00	0.00	0.00
.................................................................ATAC-----ATATATAAAACTGTGT........................................................	20	1	1.00	0.00	1.00	0.00	0.00
...........................TTTTCGTGTTTGCTGATTGAAC.................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGC.............................	23	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TCTG-TTCATTCCTCGACAC.................................	19	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TCTx-TTCATTCCTCGACACTAG..............................	21	1	1.00	0.00	0.00	0.00	1.00
...............................CGTGTTTGGCGATTGAACTTGGATT..........................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
...........................TTTTCGTGTTTGGTTATTGAACT................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGT.............................	23	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TCTG-TTCATTCCTCTACACTAG..............................	22	1	1.00	0.00	0.00	0.00	1.00
...........................TTTTCGTGTTTGTTGATTGAA..................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................TTCATTCCTCGACACTAGAAG...........................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................ATATAT-----ATATATAAAAGTAT..........................................................	20	2	0.50	0.00	0.50	0.00	0.00

droVir3

T-------------CATGGACATTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTT-TTTTATATAC-----A--------------CAAATCTG-TTCATTCCTCGACACTAGAAGTTTGCGTCAATAAGCTGCG-CATAAAT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.............................................................................................TCTG-TTCATTCCTCGACACTAG..............................	22	1	293.00	12.00	1.00	1.00	276.00	3.00
.............................................................................................TCTG-TTCATTCCTCGACACT................................	20	1	257.00	1.00	0.00	0.00	247.00	9.00
............................................................................................ATCTG-TTCATTCCTCGACACT................................	21	1	134.00	9.00	0.00	0.00	123.00	2.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGTC............................	24	1	58.00	10.00	0.00	0.00	48.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGA.............................	23	1	53.00	0.00	0.00	0.00	52.00	1.00
.............................................................................................TCTG-TTCATTCCTCGACACC................................	20	1	39.00	0.00	0.00	0.00	38.00	1.00
.............................................................................................TCTG-TTCATTCCTCGACACTA...............................	21	1	27.00	2.00	0.00	0.00	24.00	1.00
............................................................................................ATCTG-TTCATTCCTCGACACTAG..............................	23	1	20.00	7.00	0.00	0.00	13.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGG.............................	23	1	11.00	0.00	0.00	0.00	11.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACG................................	20	1	10.00	0.00	0.00	0.00	10.00	0.00
............................................................................................ATCTG-TTCATTCCTCGACACC................................	21	1	10.00	0.00	0.00	0.00	10.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTGG..............................	22	1	10.00	0.00	0.00	0.00	10.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACAC.................................	19	1	7.00	0.00	0.00	0.00	7.00	0.00
.............................................................................................TCTT-TTCATTCCTCGACACTAG..............................	22	1	6.00	0.00	0.00	0.00	5.00	1.00
............................................................................................ATCTG-TTCATTCCTCGACACTAGTC............................	25	1	5.00	5.00	0.00	0.00	0.00	0.00
.............................................................................................TCTx-TTCATTCCTCGACACTAG..............................	21	1	4.00	0.00	0.00	0.00	4.00	0.00
.............................................................................................TCTG-TTCATTCCTCTACACTAG..............................	22	1	4.00	0.00	0.00	0.00	4.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACA..................................	18	1	4.00	0.00	0.00	0.00	4.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGT.............................	23	1	3.00	0.00	0.00	0.00	3.00	0.00
.............................................................................................TCTG-TTCATTCCTxxACACTAG..............................	20	1	3.00	0.00	0.00	0.00	3.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACC..................................	18	1	3.00	0.00	0.00	0.00	3.00	0.00
............................................................................................ATCTG-TTCATTCCTCGACACTA...............................	22	1	2.00	1.00	0.00	0.00	1.00	0.00
..........................................TTTGAAAATGGATTTT-TTT....................................................................................	19	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTG...............................	21	1	2.00	0.00	0.00	0.00	2.00	0.00
............................................................................................ATCTG-TTCATTCCTCGACACG................................	21	1	2.00	0.00	0.00	0.00	2.00	0.00
............................................................................................ATCTG-TTCATTCCTCGACACTGG..............................	23	1	2.00	0.00	0.00	0.00	2.00	0.00
............................................................................................ATCTG-TTCATTCCTCGACAC.................................	20	1	2.00	0.00	0.00	0.00	2.00	0.00
............................................................................................ATCTG-TTCATTCCTCGACA..................................	19	1	2.00	0.00	0.00	0.00	2.00	0.00
............................................................................................ATCTG-TTCCTTCCTCGACACT................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATCTG-TTCATTCCTCTACACT................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................CGTGTTCGATGTTTGAACTTGGATTT.........................................................................................	26	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................................................................CCTG-TTCATTCCTCGACACT................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGC.............................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCACTCCTCGACAC.................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................CTG-TTCATTCCTCGACACTAGTC............................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................ATCTG-TTCATTCCTCTACACTC...............................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCCTTGACACTAG..............................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................CGTGTTCGATGTTTGAACT................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................CGTGTTCGATGTTTGAACTTGGATTTC-C......................................................................................	28	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTT-TTCATTCCTCGACACT................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................GCTG-TTCATTCCTCGACACTAG..............................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................ATCTG-TTCATTCCTCGAC...................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................TC-TTCATTCCTCGACACTAGA.............................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-GTCATTCCTCGACACT................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................CTG-TTCATTCCTCGACACT................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCCTCxACACTAG..............................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACCC.................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................TTTTTGAAGTTGGATTTT-TT.....................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAGCC............................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................TG-TTCATTCCTCGACACTA...............................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................ATCTG-TTCCTTCCTCGACACTAGG.............................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATCTG-TTTATTCCTCGACACTAG..............................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................................................................TCTT-TTCATTCCTCGACACTA...............................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATCTx-TTCATTCCTCGACACTAG..............................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTC...............................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATCTG-TTCCTTCCTCGACACC................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATCTG-TTCCTTCCTCGACACTAG..............................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATCTG-TTCATTCCTCAACACTAG..............................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCCTCTACACTAGA.............................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTCGA.............................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCTTCGACACTAG..............................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATCTT-TTCATTCCTCGACACT................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TCTG-TTCATTCCTCGGCACTAG..............................	22	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

C-----------------GGCTTTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTT-TAAAATATGAA---AA--------------GAAATCTG-TTCATTCCTCGACACTAAGAGTTTA-----------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.............................................................................................TCTG-TTCATTCCTCGACACTA...............................	21	1	14.00	14.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACT................................	20	1	6.00	5.00	0.00	1.00	0.00
...............................CGTGTTCGATGTTTGAACTTGGATTT.........................................................................................	26	1	4.00	4.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAA..............................	22	1	4.00	4.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAT..............................	22	1	3.00	3.00	0.00	0.00	0.00
...............................CGTGTTCGATGTTTGAACTTGGATT..........................................................................................	25	1	3.00	3.00	0.00	0.00	0.00
...............................CGTGTTCGATGTTTGAACTTGGATC..........................................................................................	25	1	2.00	2.00	0.00	0.00	0.00
............................................................................................ATCTG-TTCATTCCTCGACACT................................	21	1	2.00	2.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTAAT.............................	23	1	2.00	1.00	0.00	1.00	0.00
...............................CGTGTTCGATGTTTGAACTTGGATTTC-.......................................................................................	27	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATCTG-TTCATTCCTCTACACT................................	21	1	1.00	0.00	0.00	1.00	0.00
...............................CGTGTTCGATGTTTGAACTTGGATTTT-C......................................................................................	28	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATCTG-TTCATTCCTCGACACTA...............................	22	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATCTG-TTCATTCCTCGACACTAA..............................	23	1	1.00	0.00	0.00	1.00	0.00
...............................CGTGTTCGATGTTTGAACTTGGATTC.........................................................................................	26	1	1.00	1.00	0.00	0.00	0.00
...............................CGTGTTCGATGTTTTAACTTGGATTT.........................................................................................	26	1	1.00	1.00	0.00	0.00	0.00
...............................CGTGTTCGATGTTTGGACTTGGATT..........................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TCTG-TTCATTCCTCGACACTACC.............................	23	1	1.00	1.00	0.00	0.00	0.00
...............................CGTGTTCGATGTTTGAACTTGGTTTT.........................................................................................	26	1	1.00	0.00	1.00	0.00	0.00

droGri2

------------------GACATTTACTTTTTGTGTTGGGTGATTC-------------------------------------------------TGATTCACTTTTCGACACATCAAGTTCACCTCAATAAACTGCA--------	Size	Hit Count	Total Norm	V109 Male body
......................TTTACTTTTTGTGTTAGGAGA.......................................................................................................	21	1	1.00	1.00

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image				None			None	None
UNAFold Image				None			None	None

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															None	None
UNAFold Image															None	None