dme-mir-2279- 12- and 20-way alignments

dme-mir-2279	chr2RHet:1322833-1322945 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 1322894-1322915
   star strand at position 1322858-1322879
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2RHet:1322818-1322960 -	TCCGATGACCCAT-------GGCGGGAGAGGATTATGAAA--------------GACAATTTGAAATTAAATATCTGTGTGTGAAATTATTTAAA------------AGATTAATTTCACGCGAAGATAT-----TTATTTTTACATTTGTCCCTATA---------------ATAACCGGGGTGCCAA-------C----ATACAT------------
droSim1	chr3R:467591-467699 -	TCCAATGGCCCAA-------GCCGGGAGAGGATTTGGAAA--------------GGCAATTTTAAATTAAATATCTGCGTGTGAAATTATTAAAA-TTCACCTATATTTTTTGG------------AAAC-T----TGCTTGTCCACTACACTACGGA--GTC---------------------------CCCA-----------TCTGCCCCGAGGCG
droSec1	super_60:6933-7052 +	CCAAG--GCGGG---AATACGGC----GGGGATCATGAAATGCAAATGC----------------------------------------------AGTGAGTTTAAAACTTTATTTTCCCGCAAAGATAT-----TTATTTTTACATTTGTCCCAAGA---------------ATAATCGGCGAACCAA-------C----ATATA-------------
droYak2	Unknown	TTCGGTAAATATT-------A------------------------------------------GG--------TTTGTATATA-------------GTtttTtTTTTTtTttGG------------TTtT-T----tTTTTgttTtttttTTtCTTGATTGTTACAACTTTGGTTAATCGGAGTGATATTCCAAGTTATACATAA--------------
droEre2	Unknown	TTCAATGACGCAAGGAATATGCGGGGAGCAAATTAAAATA--------------CATAACT-----TTATATATCTGTGCGGGAAATTAAAAAACAGTGAGTTAGATAATTTAGTGTCGTCAGCAGTTAT-----TTATTTCTACATTTGTCGCGGGGATAA------ACAGAGTAACCGGGGTCCCAA-------C----ATAA--------------
droAna3	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181143:1203866-1203907 +	TgtttgGtGt---------------------------------------------------------------------------------------------------TtTTTtTg--------ttTTgtttgtTTggtgttGttt----------------------------------------------------------tt------------
droVir3	Unknown	GTCATTGGCCCAT-------GACGGGGAAA---------CTGCAACTGCTGAGAATCTAAATCAGAGCACATGTTAATCCTAAATGTGATTAAAT------------GTATAGGTATCATCCCAGCCAGT-----TTATCCCTTCATTTATCCTCATA---------------ATAA------------------------------------------
droMoj3	scaffold_6474:62415-62475 +	ACGTT-----------------------------TTGAAA--------------GTTTCATTAAGATCGTATGTCTACAAAAGAAATTATTCAAC------------AAATAAATT-------------------------------------------------------------------------------------------------------
droGri2	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2RHet:1322818-1322960 -	NA	TCCGATGACCCATGGCGGGAGAGGATTATGAAAGAC-AA---TTTGAAA---------------TTAAATATCTGTGTGT----------------------------GAA-------------------------------------------------ATTATTTAAAAG----------------------------------------------ATTAATTTC---------------------------------------ACGCGA-----------------------------------------------------------AGATATTTATTT---TTACATTTGTCC---------------------------------------------------------------------CTATAATAACCGGGG---------------------T----------GCCA---ACATACAT
droSim1	chr2R:265657-265782 +	334	AGGCAATTTTC-------------------AA--------------------------------TTAAATATCTGTGTGT----------------------------GGA-------------------------------------------------ATTATTAAAAACAATGAG------------------------TTCAAAGG--------TTTAGTTTC---------------------------------------ACGTAA-----------------------------------------------------------AGATATTTATTTTGTTTAAATT-TTCC---------------------------------------------------------------------CTAGAATAACCAGTA---------------------T----------GCCG---ACATAA-A
droSec1	super_55:122657-122779 +	768	AAGTAAACTTA-------------------AAA-------------------------------TTATAAATATGTGTGT----------------------------GAAATTAAT---------------------------------------------------AAACGGTAAG------------------------TTCGAAAG--------TTTAGTTTC---------------------------------------ACGCGA-----------------------------------------------------------AAGTATTTATTT---TTACATTTGTCC---------------------------------------------------------------------ATAGAATAACCGGGG---------------------G----------GCCA---ACATAA-A
droYak2	chr2h_random:1837227-1837349 -	9623	AAGACAACTTA-------------------AAT-------------------------------TTTTATATCTGTGTGG----------------------------GAAATTAAG---------------------------------------------------AAACAGTGAG------------------------TTCGAAAA--------TTTAGTTTC---------------------------------------GTGTAA-----------------------------------------------------------AGTTATTTATTT---CTGCATTTGTCC---------------------------------------------------------------------CTAGAATAACCGAGG---------------------T----------CCCA---ACATAA-A
droEre2	scaffold_4845:21278391-21278511 +	1760	CTCCATAACTC-------------------AACTTA---------TCTT---------------AATCGGATTTTGAAGT----------------------------G---------GCATACCTCTAAATGTTTGTGG----------------TGCAATTATCTAAAAAACTGCA------------------------TTCAAA-------------------------------------------------------------TTT-----------------------------------------------------------AAAAATTTATTTTTTTTACATTTTTTT---------------------------------------------------------------------GT-----------------------------------------------------------A
droEug1	scf7180000409463:813252-813375 -	2987	TGACACAAATC-------------------GAGAGT--G---CACTGAGAAAAAGGCAGGGTAGCTACTTATCTGTAAGA----------------------------GGA-------------------------------------------------AAAACTTAAGAA-ATAAGTTCTTTTATGAAGTAATGAAATTT--------AT-TCATC---------------------------------------------------------------------------------------------------------------------------TT---TCACCTTTATTT---------------------------------------------------------------------CT-----------------------------------------------------------A
droBia1	scf7180000302069:1281651-1281776 -	1465	GGGAAGAAATT-------------------GAAGTGCAA---ATATGCA---------------AAACATATCTATGTAC----------------------------GAT-------------------------------------------------ATTATTTAAGTT--------------------------------------TT-TTTTT---------------------------------------------------------------------------------------------------------------------------TC---AAACTTCTATGC---------------------------------------------------------------------AG--TAGTTTCTGGGGTGCATCTTATAGTGCCCAGTT----------TCAT---AAAGACAT
droTak1	scf7180000414441:15526-15661 -	4072	TTTTATAATAC-------------------AAATTG-AA-------AAA-----------------TAAGACTTATTTGTCAATTTTTTTAAAAAAGTAACTCTTACTT--------GCGATCCCTGTAAATATTTCTATAAGTGTAATTTAAGGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACC---------------------------------------------------------------------CTATAACGAGTACAA---------------------T----------TCTT---ACATGCTT
droEle1	scf7180000486807:9902-10004 +	7	TGATCCATATC-------------------GGTAA--AT---TTATAAG---------------AAACTGACTTGAAAGC----------------------------GGA-------------------------------------------------AAATTTTATG------------------------------------------------------------------------------------------------------------------------------GAAATCCAATCAATATTATT---AAATTCATCAAAAGATATTTCTTC---T------------------------------------------------------------------------------------------------------------------------------------------GACA
droRho1	scf7180000767875:903-1047 +	542	TCGGAGCACCC-------------------GACTAT-AG---C---GTT-------------------C-TCTCTTGTTT----------------------------TGTATTAAG---------------------------------------------------AAAGGGTACA------------------------CTTTTAAA--------TTAAGTGTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------TGGAGAGTTCTGAATTTCTTAAGAGATATCATAAGTTCTTTGTAATAAGAGGTA---------------------TTTTAGCAG--TCAT---GTCTCTCA
droFic1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000298698:14727-14830 -	141	GAAAAACGAAG-------------------CAA----AA---CTAAAAA-----------------AA--ACATGTGTGT----------------------------GAC-------------------------------------------------ATCATTTTAAACATTAAA------------------------TTCAAA-------------------------------------------------------------ACA-----------------------------------------------------------AAACTTTGATTTGGCC------------------------------------------------------------------------------------AACACGTTTGG---------------------G----------CGCT---A-TAATAA
droAna3	scaffold_13334:5190-5293 +	526	AAAAAATTAGT-------------------AAAAAA-AA---TAATAAA---------------TAAAAAAAAATATGGT----------------------------GGG-------------------------------------------------ATTTTTTAAAAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATATTTTTT-------------------------------------------------------------------------------------ATATGGCAATTGGTA---------------------GTTAAATATTAGTCT---TTTTAAGA
droBip1	scf7180000395238:27783-27922 +	37	CGTCATGGCCA-------------------TATA----A---CGGCAGA---------------CGATGGTATGTA-------------------------------------------------------------TAA----------------TACAACTTTTCGATAAAA---------------------------------------------AAAATATATAAAATTTTTTACATTCAATTATTACAGTTTTAGACTTCACGCAA-----------------------------------------------------------ATCGTGGAGCTT---TTACATGTGCCC---------------------------------------------------------------------CTACA-------------------------------------------------------AT
dp4	Unknown_group_37:8363-8450 +	47	GGCAATGAGGT-------------------AGGAGG-GACAATTTTGTA---------------TTCTATAATTATCGTT----------------------------AGA-------------------------------------------------CCTACGCAAAGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATACATTTT---------------------------------------------------------------------------------------------ACTGCGG---------------------G----------TTGT---ATATT-TT
droPer1	super_5473:1216-1318 +	722	TATACGTGTGT-----------------------------------------------------------------AAGT----------------------------GGA-------------------------------------------------ACTATGCAGGGG----------------------------------------------AATGATTTC---------------------------------------ACATGAAGAAAGTCGATTCGCCTGTAC------------------CTA---------------------------TT---GC------ATTC---------------------------------------------------------------------CT--AA--GCTGAGG---------------------T-------TT-AAGC---TTTAACAT
droWil1	scaffold_180772:5217896-5218034 +	549	GCCGTTGACCA-------------------GTGGCG--G---CGCCAAA---------------GTGCACATATTCTTGT----------------------------CAG-------------------------------------------------A----------------------------------------------------------------------------------------------------------------GTTAGCTGGATAGTATGTTCCTGAAAATTCAATTAAAATTGAAAGAGGACTTGTTGCAATGAATTTTTT----TTTA----------------------------------------------------------------------------------------------------------------------ATATTTGTCTAGATTTCGACC
droVir3	scaffold_291:1622-1745 -	75	AAAGAATCATT-------------------AGATAA-AT---CTTTAAA---------------ATATAGATTTTTTTTT----------------------------A---------CCATATTTGTAATGATTT--------------------------------------------------------------------------------------TTGGA---------------------------------------TTGCGA-----------------------------------------------------------AATTTTTTATTT---AAATTGTTAATT---------------------------------------------------------------------ATATAATATATTAAA---------------------T----------ATTT---ATATATAT
droMoj3	scaffold_6473:7010400-7010528 +	210	AAAGACAAAAA-------------------AAAATA-AA-------ATA----------------AAAAA-------------------------------------------------------------------------AATAAACAAACAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGTGTAAAGAGTGCAATGCCAACAAATCATACGTAGATTTCTATATTTACATATGTAC------------ATAAATATATATATG---------------------T----------ATGC---ACATACAT
droGri2	scaffold_14906:12727535-12727642 +	4	TGCCGAGAAGG-------------------GAAAAC-GA---------------------------GAATACAATTTTGT----------------------------TAT-------------------------------------------------ATTATTTAATTT--------------------------------------ATCTTATC---------------------------------------------------------------------------------------------------------------------------TT---GTCCTTTTATTT---------------------------------------------------------------------GAAAGATAATTTGAA---------------------TTTGAATAAATTTAT---ATTTGTAT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TCCGATGACCCAT-------GGCGGGAGAGGATTATGAAA--------------GACAATTTGAAATTAAATATCTGTGTGTGAAATTATTTAAA------------AGATTAATTTCACGCGAAGATAT-----TTATTTTTACATTTGTCCCTATA---------------ATAACCGGGGTGCCAA-------C----ATACAT------------

Size

Hit Count

Total Norm

droSim1

TCCAATGGCCCAA-------GCCGGGAGAGGATTTGGAAA--------------GGCAATTTTAAATTAAATATCTGCGTGTGAAATTATTAAAA-TTCACCTATATTTTTTGG------------AAAC-T----TGCTTGTCCACTACACTACGGA--GTC---------------------------CCCA-----------TCTGCCCCGAGGCG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................CGAGAGAGGATTTGTAAA--------------.....................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50

droSec1

CCAAG--GCGGG---AATACGGC----GGGGATCATGAAATGCAAATGC----------------------------------------------AGTGAGTTTAAAACTTTATTTTCCCGCAAAGATAT-----TTATTTTTACATTTGTCCCAAGA---------------ATAATCGGCGAACCAA-------C----ATATA-------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....................................GAATGCAAAGGC----------------------------------------------AGTGAG......................................................................................................................	18	2	0.50	0.00	0.50	0.00
CCAAG--GCGGG---TAAACGGC----GG..............................................................................................................................................................................................	20	2	0.50	0.50	0.00	0.00
.......GCGGG---AATGGGGC----GGGGA...........................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50

droYak2

TTCGGTAAATATT-------A------------------------------------------GG--------TTTGTATATA-------------GTtttTtTTTTTtTttGG------------TTtT-T----tTTTTgttTtttttTTtCTTGATTGTTACAACTTTGGTTAATCGGAGTGATATTCCAAGTTATACATAA--------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..............................................................................................................................TTTT-T----TTTTTTTTTTTTTTTT...................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
...............................................................................................................................TTT-T----TTTTTTTTTTTTTTTTT..................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
..............................................................................................................................TTTT-T----TTTTTTTTTTTTTTTTT..................................................................	22	33	0.21	0.00	0.00	0.00	0.00	0.21
................................................................................................................................TT-T----TTTTTTTTTTTTTTTTT..................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
...............................................................................................................................TTT-T----TTTTTTTTTTTTTTTT...................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
..............................................................................................................................TTTT-T----TTTTTTTTTTTTTTT....................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
...............................................................................................................................TTT-T----TTTTTTTTTTTTTTT....................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
..............................................................................................................................TTTT-T----TTTTTTTTTTTTTT.....................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
.................................................................................................................................T-T----TTTTTTTTTTTTTTTTT..................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
................................................................................................................................TT-T----TTTTTTTTTTTTTTTT...................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
........................................................................................................TTTTTTTTGC------------TTTT-T----TTTGT..............................................................................	20	5	0.20	0.00	0.00	0.20	0.00	0.00
..................................................................................T-------------GTTTTTTTTTTTTTTTTG------------TTTT-T----T..................................................................................	25	4	0.25	0.25	0.00	0.00	0.00	0.00
.............................................................................................................TTTTG------------TTTT-T----TCTTTGTTTTTT.......................................................................	22	4	0.25	0.25	0.00	0.00	0.00	0.00
...............................................................................................................TTG------------TTTT-T----TTTTTGTTGTT........................................................................	19	5	0.20	0.00	0.00	0.20	0.00	0.00
................................................................................................................................TT-T----TTTTTGCTTTTTTTTGT..................................................................	20	5	0.20	0.00	0.00	0.20	0.00	0.00

droEre2

TTCAATGACGCAAGGAATATGCGGGGAGCAAATTAAAATA--------------CATAACT-----TTATATATCTGTGCGGGAAATTAAAAAACAGTGAGTTAGATAATTTAGTGTCGTCAGCAGTTAT-----TTATTTCTACATTTGTCGCGGGGATAA------ACAGAGTAACCGGGGTCCCAA-------C----ATAA--------------	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................GAGCAAATTAATATA--------------CGT..................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
.............................................................................................................................................CTACATTCGTGGCGGGGA............................................................	18	2	0.50	0.50	0.00	0.00	0.00

droAna3

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

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

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

TgtttgGtGt---------------------------------------------------------------------------------------------------TtTTTtTg--------ttTTgtttgtTTggtgttGttt----------------------------------------------------------tt------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.................................................................................................................TGTx--------TTTTGTTTGTGTGGTGT.............................................................................	20	1	8.00	0.00	7.00	1.00	0.00
...............................................................................................................TTTGTx--------TTTTGTTTGTGTGGTGT.............................................................................	22	1	7.00	0.00	6.00	1.00	0.00
.........T---------------------------------------------------------------------------------------------------TTTTTTTG--------TTGTGTGTGT....................................................................................	19	1	6.00	1.00	5.00	0.00	0.00
.................................................................................................................TGTx--------TTTTGTTTGTGTGGTGTTG...........................................................................	22	1	5.00	0.00	5.00	0.00	0.00
.....AGTGT---------------------------------------------------------------------------------------------------TGTTTTTG--------TTTTG.........................................................................................	18	1	3.00	0.00	3.00	0.00	0.00
...............................................................................................................TTTGTx--------TTTTGTTTGTGTGGTGTTG...........................................................................	24	1	3.00	0.00	3.00	0.00	0.00
.............................................................................................................TTTTTTTG--------TTGTGTGTGT....................................................................................	18	2	1.50	0.00	1.50	0.00	0.00
.................................................................................................................TGTx--------TTTTGTTTGTGTGGTGTT............................................................................	21	1	3.00	0.00	3.00	0.00	0.00
......GTxT---------------------------------------------------------------------------------------------------TTGTTTTG--------TTTTGCT.......................................................................................	18	1	2.00	0.00	1.00	0.00	1.00
.......TGx---------------------------------------------------------------------------------------------------TTTTTTTG--------TTTTGTGTGTT...................................................................................	21	1	2.00	0.00	0.00	2.00	0.00
..................................................................................................................GTx--------TTTTGTTTGTGTGGTGT.............................................................................	19	1	2.00	0.00	0.00	2.00	0.00
..................................................................................................................................TTTGTTAGGTGTTGTTT----------------------------------------------------------TT------------	19	1	2.00	0.00	0.00	0.00	2.00
..................................................................................................................TTG--------TGTAGTTTGTTTGGT...............................................................................	18	1	2.00	0.00	2.00	0.00	0.00
..............................................................................................................................TTTGTTTGTGTGGTGTTGG..........................................................................	19	1	2.00	0.00	0.00	2.00	0.00
................................................................................................................TTGTx--------TTTTGTTTGTGTGGTGT.............................................................................	21	1	2.00	0.00	2.00	0.00	0.00
.......TTT---------------------------------------------------------------------------------------------------TTTTTCTG--------TTTTGTTTG.....................................................................................	20	5	0.20	0.00	0.20	0.00	0.00
........GT---------------------------------------------------------------------------------------------------TGTTTTTG--------TTTTGTTT......................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
.............................................................................................................................................TTCTTT----------------------------------------------------------TT------------	18	49	0.02	0.00	0.02	0.00	0.00
...............................................................................................................TTTGTx--------TTTTGTTTGTGTGGTGTTGTT.........................................................................	26	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TTTTTTTG--------TTTTGTTTTTG...................................................................................	19	16	0.06	0.00	0.06	0.00	0.00
.............................................................................................................................TTTTTTTTGTGTGGTGTTG...........................................................................	19	1	1.00	0.00	1.00	0.00	0.00
......GTGT---------------------------------------------------------------------------------------------------TGTTGTTG--------TTTTGTT.......................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................TTTGTTTGTGTGGTGTTG...........................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TTGTTTTG--------TTTTGTTTGTTTG.................................................................................	21	2	0.50	0.00	0.00	0.50	0.00
................................................................................................................TTGTx--------TTTTGTTTGTGTGGTGTTGTTT----------------------------------------------------------..............	26	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................TCTTGTG--------xTTTGTTTGTTTGGTGT.............................................................................	23	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................TTTTTTG--------TTTTGTTTGGT...................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
..............................................................................................................TTTGTTG--------TTTTGTTTGGTTG.................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.........T---------------------------------------------------------------------------------------------------TTTTTTTT--------TTTTGTTTGTT...................................................................................	20	37	0.03	0.00	0.03	0.00	0.00
.............................................................................................................................TTTTGTTTGTGTGGTGTTGGT.........................................................................	21	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................T--------TTTTGTTTGTGTGGTGTTG...........................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................TTTGTTTATTTxGTGTTGT..........................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................TATTTTTT--------TTTTGTTTGTT...................................................................................	19	13	0.08	0.00	0.08	0.00	0.00
...............................................................................................................................TTGTTTGTTTGTTGTTATT.........................................................................	19	1	1.00	0.00	1.00	0.00	0.00
........GG---------------------------------------------------------------------------------------------------TTATTTTG--------TTTTGTTT......................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................TTTTG--------TTTTGTGTGTGTG.................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
..............................................................................................................................TTTGTTTGTTTGGTGGTGTG.........................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.......TTT---------------------------------------------------------------------------------------------------TTTTTTTG--------TTTTGCT.......................................................................................	18	17	0.06	0.00	0.06	0.00	0.00
................................................................................................................TTGTx--------TTTTGTTTGTGTGGTGTT............................................................................	22	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................TTTGTTGTTGTTG----------------------------------------------------------TT------------	18	6	0.17	0.00	0.17	0.00	0.00
...............................................................................................................................TTGTTTGTTTGTTGTTGTTG----------------------------------------------------------T.............	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................TTTTTTTG--------TTTTGTGTGTTTT.................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.......AGT---------------------------------------------------------------------------------------------------TTTTTTTG--------TTTCGTTTGTT...................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................GTTTGTTTGTTTGTTGTT............................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TTATTTTG--------TTTTGTTTCT....................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................TTATx--------CTTTGTTTGTTTGG................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........GT---------------------------------------------------------------------------------------------------TTATTCTG--------TTTTGTTTGT....................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................TTTTTG--------TTTTGTGTGTGTG.................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
.........G---------------------------------------------------------------------------------------------------TTTTTTTG--------TTTTGTGTGTTT..................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................TTTTTTAG--------ATTTGTTTGT....................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
.........T---------------------------------------------------------------------------------------------------TTTTTTTG--------TTTGGTTTGCT...................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........GT---------------------------------------------------------------------------------------------------TGTTTTTG--------TTTTGTTGG.....................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................TTGTTGTTGTTG----------------------------------------------------------TT------------	19	6	0.17	0.00	0.00	0.00	0.17
TGTTTTGTGT---------------------------------------------------------------------------------------------------TTTTTGTG--------TT............................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................................................TTGTTGTTGTTT----------------------------------------------------------TT------------	21	8	0.13	0.00	0.13	0.00	0.00

droVir3

GTCATTGGCCCAT-------GACGGGGAAA---------CTGCAACTGCTGAGAATCTAAATCAGAGCACATGTTAATCCTAAATGTGATTAAAT------------GTATAGGTATCATCCCAGCCAGT-----TTATCCCTTCATTTATCCTCATA---------------ATAA------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

ACGTT-----------------------------TTGAAA--------------GTTTCATTAAGATCGTATGTCTACAAAAGAAATTATTCAAC------------AAATAAATT-------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
....................................AAAA--------------GTTTCATGAAGATCGTA....................................................................................................................................................	21	2	4.00	4.00	0.00	0.00	0.00
......................................AA--------------GTTTCATGAAGATCGTACG..................................................................................................................................................	21	2	2.50	2.00	0.50	0.00	0.00
....................................GAAA--------------GTTTCATGAAGATCGTA....................................................................................................................................................	21	2	1.50	1.50	0.00	0.00	0.00
...................................TAAAA--------------GTTTCATGAAGATCGT.....................................................................................................................................................	21	2	1.50	1.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATGAAGATCGTACGT.................................................................................................................................................	25	2	1.00	1.00	0.00	0.00	0.00
.......................................A--------------GTTTCATGAAGATCGTACGT.................................................................................................................................................	21	2	1.00	1.00	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATTAAGATCATATGTT................................................................................................................................................	26	2	1.00	1.00	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATGAAGATCGTATGTCC...............................................................................................................................................	27	2	1.00	1.00	0.00	0.00	0.00
.......................................................TTTCATGAAGATCGTACGTCT...............................................................................................................................................	21	2	1.00	1.00	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATGAAGATCGT.....................................................................................................................................................	21	2	1.00	1.00	0.00	0.00	0.00
........................................................TTCATTAAGATTGTATGTC................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
.......................................A--------------GTTTCATTAAGATCTTCTGTCT...............................................................................................................................................	23	2	0.50	0.00	0.00	0.00	0.50
............................................................TTAAGATCGTGTGTCTACAAAAG........................................................................................................................................	23	2	0.50	0.00	0.00	0.00	0.50
.........................................................TCATGAAGATCGTATGTCCACAAAAG........................................................................................................................................	26	2	0.50	0.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATTAAGATTGTACGTCT...............................................................................................................................................	27	2	0.50	0.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATTAAGATCGTATGT.................................................................................................................................................	25	2	0.50	0.50	0.00	0.00	0.00
......................................AA--------------GTTTCATGAAGATCGTATGTCCA..............................................................................................................................................	25	2	0.50	0.50	0.00	0.00	0.00
........................................................TTCATGAAGATCGTACGTCTA..............................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
......................................AA--------------GTTTCATGAAGATCGTATG..................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
......................................................GTTTCATTAGGATCGTATGTC................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATTAAGATTGTATGTC................................................................................................................................................	26	2	0.50	0.00	0.00	0.00	0.50
.....................................AAA--------------GTTTCATTAGGATCGTATGTC................................................................................................................................................	24	2	0.50	0.50	0.00	0.00	0.00
..................................TTGAAA--------------GTTTCATTAAGATTGTATGTC................................................................................................................................................	27	2	0.50	0.00	0.00	0.00	0.50
.......................................................TTTCATGAAGATCGTATGTCC...............................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
..................................TTGAAA--------------GTTTCATTAAGATT.......................................................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
..GTT-----------------------------TTGAAA--------------GTTTCATTAAGATTGT.....................................................................................................................................................	25	2	0.50	0.50	0.00	0.00	0.00
...........................................................................TACAAGAGAAATTATTCAAC------------TAATAAAT........................................................................................................	28	2	0.50	0.50	0.00	0.00	0.00
..................................CTGAAA--------------GTTTCATGAAGATCGTATG..................................................................................................................................................	25	2	0.50	0.50	0.00	0.00	0.00
...........................................................................TACAAAAGAATTTATTCAAC------------AAATAAAT........................................................................................................	28	2	0.50	0.00	0.00	0.00	0.50
...................................TGAAA--------------GTTTCATGAAGATCGTA....................................................................................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
.......................................A--------------GTTTCATTAAGATCGTATGT.................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATTAAGATTGTATGC.................................................................................................................................................	25	2	0.50	0.00	0.00	0.00	0.50
...................................TGAAA--------------GTTTCATGAAGATCGTATGC.................................................................................................................................................	25	2	0.50	0.50	0.00	0.00	0.00
..............................................................AAGATCGTATGTCTACAAAAG........................................................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
......................................AA--------------GTTTCATTAAGATCGTATGTC................................................................................................................................................	23	2	0.50	0.00	0.50	0.00	0.00
...................................TAAAA--------------GTTTCATGAAGATCGTATG..................................................................................................................................................	24	2	0.50	0.50	0.00	0.00	0.00
...........................................................................TACAAAAGAAATTATTCAAC------------AAATAAAT........................................................................................................	28	2	0.50	0.50	0.00	0.00	0.00
....T-----------------------------CTGAAA--------------GTTTCATGAAGATC.......................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
........................................................TTCATGAAGATCGTATGTCC...............................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
...................................TGGAA--------------GTTTCATTAAGATCGTATGTC................................................................................................................................................	26	2	0.50	0.50	0.00	0.00	0.00
..........................................................CATTAAGATCGTATGTCTACAAAAGAATT....................................................................................................................................	29	2	0.50	0.50	0.00	0.00	0.00
...................................TAAAA--------------GTTTCATGAAGATCGTA....................................................................................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
.......................................................TTTCATTAAGATCGTATGTCTACAA...........................................................................................................................................	25	2	0.50	0.50	0.00	0.00	0.00
...........................................................ATGAAGATCGTATGTCCACAAA..........................................................................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
.......................................................TTTCATTAAGATTGTACGTCT...............................................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50
...................................TGAAA--------------GTTTCATGAAGATCGTATGT.................................................................................................................................................	25	2	0.50	0.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATTAAGATCATATGT.................................................................................................................................................	25	2	0.50	0.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATTAAGATCATATGTC................................................................................................................................................	26	2	0.50	0.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATGACGATCGTATGT.................................................................................................................................................	25	2	0.50	0.50	0.00	0.00	0.00
....T-----------------------------CTGGAA--------------GTTTCATTAAGATC.......................................................................................................................................................	21	2	0.50	0.00	0.00	0.50	0.00
........................................................TTCATTAAGATCGTATGCCTACAAAAGAA......................................................................................................................................	29	2	0.50	0.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATTAAGATTGTATG..................................................................................................................................................	24	2	0.50	0.00	0.00	0.00	0.50
...................................TGAAA--------------GTTTCATTAAGATTGTACGTC................................................................................................................................................	26	2	0.50	0.50	0.00	0.00	0.00
....................................GGAA--------------GTTTCATGAAGATCGTA....................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
...................................TGAAA--------------GTTTCATGAAGATCGTATG..................................................................................................................................................	24	2	0.50	0.50	0.00	0.00	0.00

droGri2

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

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