dme-mir-2496- 12- and 20-way alignments

dme-mir-2496	chrX:1904333-1904450 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 1904344-1904366
   star strand at position 1904418-1904439
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:1904318-1904465 +	AAGAG-------------------------------------------------------------------------------------------------------------------CGCA---AAATGAGTGCGCC--G--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGCGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGCGGGGCACTCACACACGCATATTCAGCCGCACATCTG-------------------------------GGAAAA-----TGGG
droSim1	chrX:1343126-1343273 +	AAGAG-------------------------------------------------------------------------------------------------------------------CGCG---AAATGAGTGCGCC--G--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCGGGGCACACACACACGCATATTCAGCCGCACATCTG-------------------------------GGAAAA-----TGGG
droSec1	super_10:1689518-1689665 +	AAGAG-------------------------------------------------------------------------------------------------------------------CGCA---AAATGATTGCGCC--T--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCGGGGCACTCACACACGCATATTCAGCCGCACATCTG-------------------------------GGAAAA-----TGGG
droYak2	chrX:6422544-6422691 -	AAGAG-------------------------------------------------------------------------------------------------------------------CGCA---AAATGTGTGCGCC--G--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATCGGGGGGCACTCACACACGCACATACAGCCGCACATCTG-------------------------------GGAAAA-----TGGG
droEre2	scaffold_4644:1874871-1875018 +	AAGAG-------------------------------------------------------------------------------------------------------------------CGCA---AAATGTGTGCGCC--G--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGGGGGGCACTTACACACGCACATACAGCCGCACATCTG-------------------------------GGAAAA-----TGGG
droAna3	scaffold_12929:1897900-1898023 +	GAGAG-------------------------------------------------------------------------------------------------------------------AGCA---------GTTT--------GCATGTGTGCGAT--TTT-GTGGT-CATAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCGAATTGGGGGGGGGGGGGG-------------CCATACAAGCT-------------------------------GGAAAA-----TAGG
dp4	chrXL_group1a:2576133-2576311 +	agggagagatagagagagagaATAATGGAG------------------------------------------------------------------------------------------TGCTG--GTGTATATGTACCTACATATGTACGTGTGGT--TGA-GTACC-CATAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTGTGTTGGGCGGCACACACACCAGCGCCATTGGCTTTTCA-----------------------------CAGGGCGAGAAG-----TAAG
droPer1	super_28:1013170-1013344 +	agggagagatagagagagagaATAATGGAG------------------------------------------------------------------------------------------TGCTG--GTGTATATGTACC--T--ATGTACGTGTGGT--TGA-GTACC-CATAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTGTGTTGGGCGGCACACACACCAGCGCCATTGGCTTTTCA-----------------------------CAGGGCGAGAAG-----TAAG
droWil1	scaffold_181096:6994274-6994470 -	aggaagaaagacagaggccaaaagagacagtgcgatagagagaggtagagagaacgtacagagagagCTTGTTCTGGTTTGTAACTAATTTTCCCCCTCAAATGTAAGCATTTCGAATGC---ATGTGT----------------GTGTA-----------------------------------------------------------------------------CGTGTAATCACACACGCACACAAATA---------------CCACGTCATTACGATTTCCACATGGC-GAAAATTGTGTGAG
droVir3	scaffold_12928:6459245-6459266 +	GC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTATTTCTG-------------------------------TGCAAG-----TGTG
droMoj3	scaffold_6473:2945642-2945806 -	AGCAGTTCGTGCACATGCTta--------------------------------------------------------------------------------------------------t---atgtatatgtacacaca--a--atatactcatgtg--tatgagtatgtgtaaaatgcatattcaaatgttaaat-------------------------------gtgcttttacatatagatatgtatgcgtatatTAAAAATACAAAGGTACTTGGCTTTTCTCATGGC-GAAAA-----TAAA
droGri2	scaffold_14853:1363850-1364011 +	AACAGTTCGTACACACATGC-----------------------------------------------------------------------------------------TTATtgcatgt---atgtatgtgtgtatgtg--a--gtatgtatgtgtgcatatgaacatgt----at-acatatatgcatgtaAAAT-------------------------------G----CTTGCATGTGGCTGTGTGCG-----GTACAAAATACAAAGGCATTTGGCTTTTCTCATGGC-GAAAC-----TGAA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:1904318-1904465 +	NA	AAGAGC-GC------AAAAT-------------G-------------------AGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGCGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGCG-------GGG--------CACTCACACA----------------CGCATATTCAGCCGCACATCTGGGAAAA------------------------TGGG
droSim1	chrX:1343126-1343273 +	2	AAGAGC-GC------GAAAT-------------G-------------------AGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCG--AATTGCG-------GGG--------CACACACACA----------------CGCATATTCAGCCGCACATCTGGGAAAA------------------------TGGG
droSec1	super_10:1689518-1689665 +	2	AAGAGC-GC------AAAAT-------------G-------------------ATTGCG--CCTGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCG--AATTGCG-------GGG--------CACTCACACA----------------CGCATATTCAGCCGCACATCTGGGAAAA------------------------TGGG
droYak2	chrX:6422544-6422691 -	1	AAGAGC-GC------AAAAT-------------G-------------------TGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATCGGG-------GGG--------CACTCACACA----------------CGCACATACAGCCGCACATCTGGGAAAA------------------------TGGG
droEre2	scaffold_4644:1874871-1875018 +	1	AAGAGC-GC------AAAAT-------------G-------------------TGTGCG--CCGGTG--TGCGTGT--G--T-------GAG----AGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACTTACACA----------------CGCACATACAGCCGCACATCTGGGAAAA------------------------TGGG
droEug1	scf7180000409182:447470-447608 +	1	AACAGC-GA------AAAAT-------------G-T---TT-------GCGT------------ATG--TG----T--G--T-------GAG----GGGCC--A---TAAAAGCCTTGTTTGCGCGTGGAATTTAACTGTTTTTTCGCCGTCTGCT--GGTTCGG-------GGGGTGGGGAGCACGTACA------------------------CTCAACCGCACATCTGGGAAAA------------------------TGGG
droBia1	scf7180000301760:4508970-4509126 +	1	GACAGC-GC------AAATT-------------G-------------------TGTGCG--CTCGTGTGTGCGTGTG----TGT-----GTGTGCGGGGCC--G---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCC--AATTGGG-------GGG--------CACTCACACAG------------AGGCACACGCACAGTCACACACCTGGGAAAA------------------------TGGG
droTak1	scf7180000415211:36485-36643 -	1	GACGGC-GC------AAA-----------------T---GTGCCATGTGTGTGTGTGCG--CTGGTG--TGCGTGT--G--C-------G------GGGCC--G---CAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACTCACACAG------------ACGCGCACACACAGCCGCACACCTGGGAAAA------------------------TGGG
droEle1	scf7180000491001:1416804-1416930 +	1	GAGAGC-GC------AAAAA-------------A-T---GT-------GGCT------------GTG--TG-------------------TG----TGGCC--A---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCA--AATTGGG-------GGG--------CACTAACACA------------------------CAGCCGTACACCTGGGAAAA------------------------TGGG
droRho1	scf7180000777610:12722-12848 -	1	AAGAGC-GC------AAAAA-------------A-T---GT-------GGCT------------GTG--TG-------------------TG----TGGCC--A---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACTCACACA------------------------CAGCCACACACCTGGGAAAA------------------------TGGG
droFic1	scf7180000454072:3017522-3017650 +	1	GAGAGC-GC------AAAAT-------------G------G-------GACT--GT--------GTG--TGCGTGT---------------G----TGGCC--A---AAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTTTCGCCGTCTGCG--AATTGGG-------GGG--------AACACACA--------------------------CAGCTGCACACCTGGGAAAA------------------------TGGG
droKik1	scf7180000302610:169951-170123 +	1	AAAGGCGGAGAGCGCCGCAG-------------A-T---GT-------GCCA------------GTG--TGTGAGT--GTGTCTGTGTTGAG----TGGCC--A---TAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCG--AATTGGG-------GGG--------CACACACACAACCACACCAACCTA--CACGCACACACCGGCGCACCTGGGAAAA------------------------TGGG
droAna3	scaffold_12929:1897894-1898023 +	1	AAGGGG-GA------GAGAG-------------C---------AGTTTGCAT------------GTG--TGCGATT--T-----------TG----TGGTC--A---TAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCG--AATTGGG-------GGG--------GGGGG-----------------------------GGGCCATACAAGCTGGAAAA------------------------TAGG
droBip1	scf7180000396543:357925-358040 +	2	GGGGGA-AT----------A-------------G-T---TT-------GCAT------------GTG--TGCGATT--T-----------TG----TGGTC--A---TAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCG--AATTGGG-------GGG--------C-------------------------------------CATACAAGCTGGAAAA------------------------TAGG
dp4	chrXL_group1a:2576130-2576311 +	1	AAGAGG-GA------GAGATAGAGAGAGAGAATAATGGAG---TGCTGGTGTATATGTACCTACATATGTACGTGTGGT--T-------GAG----TACCC--A---TAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTG--TGTTGGG-------CGG--------CACACACACC----------------AGCGCCATTGGCTTTTCACAGGGCGA----------------------GAAGTAAG
droPer1	super_28:1013167-1013344 +	1	AAGAGG-GA------GAGATAGAGAGAGAGAATAATGGAG---TGCTGGTGTATATGTA--CCTATG--TACGTGTGGT--T-------GAG----TACCC--A---TAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTG--TGTTGGG-------CGG--------CACACACACC----------------AGCGCCATTGGCTTTTCACAGGGCGA----------------------GAAGTAAG
droWil1	scaffold_181096:6994288-6994457 -	4	GAGGCC-AA------AAGAG---A---------C-------------------AGTGCG--ATAGAG--AGAGGTA-------------GAG----AGAACGTACA-GAGAGAGCTTGTTCTGGTTTGTAACTAA-TTTTCCCC--CTCAAATGTAAGCATTTCGAATGCATGTG--------TGTGTACGTG------------------------TAATCACACACGCACACAAATACCACGTCATTACGATTTCCACATGGC
droVir3	scaffold_12928:6459245-6459266 +	1	GC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTATTTCTGTGCAAG------------------------TGTG
droMoj3	Unknown	NA	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15203:11679615-11679698 +	1	-------------------------------------------------------------------------------------------------------------------TTGTTTTCGCTTTTCATTT---TGTTTTACGATTAACTGTA--AACTGCA-------GCC--------GGC-----CA----------------ACCATTTTCGA---GCCCACTGGCAA----------------------AGAATGGG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

AAGAG-------------------------------------------------------------------------------------------------------------------CGCA---AAATGAGTGCGCC--G--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGCGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGCGGGGCACTCACACACGCATATTCAGCCGCACATCTG-------------------------------GGAAAA-----TGGG

Size

Hit Count

Total Norm

droSim1

AAGAG-------------------------------------------------------------------------------------------------------------------CGCG---AAATGAGTGCGCC--G--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCGGGGCACACACACACGCATATTCAGCCGCACATCTG-------------------------------GGAAAA-----TGGG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................................................................................................................................................................................ACACACACACGCATACTG...........................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................TGTGTGCGTC--G--GTGTGCGT............................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droSec1

AAGAG-------------------------------------------------------------------------------------------------------------------CGCA---AAATGATTGCGCC--T--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCGGGGCACTCACACACGCATATTCAGCCGCACATCTG-------------------------------GGAAAA-----TGGG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................................................................................................................GC--T--GTGTGCGTGTGTG--TG...................................................................................................................................................	18	2	0.50	0.00	0.00	0.50
......................................................................................................................................TGCGCC--T--GTGTGCGTGTGAG--C....................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
.....................................................................................................................................GTGCGCC--T--GTGTGTGTGTG.........................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
...................................................................................................................................................GTGCGTGTGTG--AGAGGCCAT-CGTA.......................................................................................................................................	24	1	1.00	1.00	0.00	0.00
..............................................................................................................................................T--GTGTGCGTGCGTG--CGAG.................................................................................................................................................	18	2	0.50	0.00	0.00	0.50
....................................................................................................................................................................................TTGTTTGCGTGTGTAATG...............................................................................................................	18	1	1.00	1.00	0.00	0.00
.....................................................................................................................................TTGCGGG--T--GTGTGCGTGTGT........................................................................................................................................................	20	1	1.00	0.00	1.00	0.00
.................................................................................................................................ATGACTGCGTC--T--GTGTGCG.............................................................................................................................................................	19	1	1.00	0.00	0.00	1.00
............................................................................................................................................................................................GTGTGGAATTTGATTGTT.......................................................................................................	18	1	1.00	0.00	1.00	0.00
......................................................................................................................................TGCGCC--A--GTGTGTGTGTG.........................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
...................................................................................................................................................................................................................GCCGTCTxCGAGTTGCGGG...............................................................................	18	1	1.00	0.00	0.00	1.00
....................................................................................................................................................TGCGTGTGTG--AGAGGCCA.............................................................................................................................................	18	1	1.00	0.00	0.00	1.00
.........................................................................................................................................GCC--T--GTGTGCGTGTGTG--TGTGG................................................................................................................................................	22	1	1.00	0.00	1.00	0.00
........................................................................................................................................CGCC--T--GTGTGTGTGCGTG--.....................................................................................................................................................	18	2	0.50	0.00	0.00	0.50
......................................................................................................................................TGTGCA--T--GTGTGCGTGTGT........................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
..............................................................................................................................................T--GTGTGTGTGTGTG--TGAGG................................................................................................................................................	19	4	0.25	0.00	0.25	0.00
....................................................................................................................................................TGCGTGTGTG--AGAGGCCAT-CGT........................................................................................................................................	22	1	1.00	0.00	1.00	0.00

droYak2

AAGAG-------------------------------------------------------------------------------------------------------------------CGCA---AAATGTGTGCGCC--G--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATCGGGGGGCACTCACACACGCACATACAGCCGCACATCTG-------------------------------GGAAAA-----TGGG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................................................................................................................CGCC--G--GTGTGAGTATGTG--.....................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
...................................................................................................................................................GTGCGTGTGTG--AGAGGCAA.............................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................................CG--A--GTGTGCGTGTGTG--.....................................................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................................................................TGCGCC--G--GTGTGCGTGTGTG--.....................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................................................................................GTGTGCGTGTGCG--AGCGGC...............................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................................................................G--CTGTGCGTGTGTG--ACAG.................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.................................................................................................................................................GTGTGCGTGTGTG--CGCG.................................................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................AATTTGTGCGCC--T--GTGTGC..............................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................................................C--GTGTGCGTGTGTC--AGAGGC...............................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................................................................................GTGTGCGTGTGTG--GGGG.................................................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................................................GACTGCGAATCTGGGGG..............................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................................................................GTGCGxC--G--GCGTGCGTGTGTG--.....................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AAGAG-------------------------------------------------------------------------------------------------------------------CGCA---AAATGTGTGCGCC--G--GTGTGCGTGTGTG--AGAGGCCAT-CGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGGGGGGCACTTACACACGCACATACAGCCGCACATCTG-------------------------------GGAAAA-----TGGG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..................................................................................................................................TGTGTGCGCC--A--GTGTGTGT............................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................GTGTGCGTGTGTG--AGAGGCCA.............................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................GTGTGTGCC--T--GTGTGCGTGTGTG--.....................................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................TTGTGCGTGTGTC--AGAGGC...............................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
..................................................................................................................................TGTGTGCGCC--G--GTGTGCGTGTG.........................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droAna3

GAGAG-------------------------------------------------------------------------------------------------------------------AGCA---------GTTT--------GCATGTGTGCGAT--TTT-GTGGT-CATAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCGAATTGGGGGGGGGGGGGG-------------CCATACAAGCT-------------------------------GGAAAA-----TAGG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............................................................................................................................................................................................................................TTGGGGGGGAGGGGGG-------------C........................................................	17	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................AGAGGGGGGGGGGGGGG-------------C........................................................	18	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................ATTGGGAGGGGGGGGGG-------------C........................................................	18	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................................................................GTGGGGGAGGGGGGGG-------------.........................................................	16	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................TGGT-CATAATAGCTTTGTTCG..........................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................................................................................................AATCGGGTGGGGGGGGGG-------------.........................................................	18	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................TTTTTCTGTTTTCTAGCCGT.............................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................................................................................TTGGGGGGGGAGGGG-------------CCA......................................................	18	1	1.00	0.00	0.00	1.00	0.00

dp4

agggagagatagagagagagaATAATGGAG------------------------------------------------------------------------------------------TGCTG--GTGTATATGTACCTACATATGTACGTGTGGT--TGA-GTACC-CATAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTGTGTTGGGCGGCACACACACCAGCGCCATTGGCTTTTCA-----------------------------CAGGGCGAGAAG-----TAAG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...GAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	8	0.88	0.25	0.63	0.00	0.00
.GAGAGAGAGAGAGAGAGA..................................................................................................................................................................................................................................................................................................	18	8	0.88	0.25	0.63	0.00	0.00
AGAGAGAGAGAGAGAGAGA..................................................................................................................................................................................................................................................................................................	19	6	0.67	0.33	0.33	0.00	0.00
..AGAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	19	6	0.67	0.33	0.33	0.00	0.00
....AGAGAAAGAGAGAGAGAG...............................................................................................................................................................................................................................................................................................	18	3	0.67	0.67	0.00	0.00	0.00
....AGAGAGAGAGAGAGAGAG...............................................................................................................................................................................................................................................................................................	18	9	0.22	0.22	0.00	0.00	0.00
.GCGAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
..AGAGAGAGAGAGAGAGAG.................................................................................................................................................................................................................................................................................................	18	9	0.22	0.22	0.00	0.00	0.00
AGAGAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	21	1	2.00	2.00	0.00	0.00	0.00
AGAGAGAGAGAGAGAGAG...................................................................................................................................................................................................................................................................................................	18	9	0.22	0.22	0.00	0.00	0.00
...CAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
...GAGAGACAGAGAGAGAGG................................................................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
..AGAGAGAGAGAGAGAGAGAA...............................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...GAGAGAAAGAGAGAGATA................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
...GAGAGAGAGAGATAGAGA................................................................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
...GAGAGAGAGAGAGAGGGA................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...GAGAGAGTGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...GAAAGACAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
....AGAGATAAAGAGAGAGAG...............................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
....AGAGAAAGAGAGAGAGATT..............................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...GAGAGACAGAGAGAGAGC................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.......................AATGGAG------------------------------------------------------------------------------------------TGCCG--GTGAAT................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..AGAGAGATAGAGGGAGAG.................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...GATAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.....GAGATAGAGAGAGAGGAA..............................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
AGGGAGAGAGAGAGAGAGA..................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
....AGAGAGAGAGAGAGAGAA...............................................................................................................................................................................................................................................................................................	18	4	0.25	0.25	0.00	0.00	0.00
...GAGAGAGAGAGAGGGAGA................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.GAGAGAGACAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....AGAGAAAGAGAGAGAGAAAA.............................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...GAGAGATAGCGAGAGAGA................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

agggagagatagagagagagaATAATGGAG------------------------------------------------------------------------------------------TGCTG--GTGTATATGTACC--T--ATGTACGTGTGGT--TGA-GTACC-CATAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTGTGTTGGGCGGCACACACACCAGCGCCATTGGCTTTTCA-----------------------------CAGGGCGAGAAG-----TAAG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...GAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	8	6.00	4.00	1.75	0.00	0.00	0.25
...GAGAGAGAGAGAGGGAGA................................................................................................................................................................................................................................................................................................	18	8	0.63	0.50	0.13	0.00	0.00	0.00
...GAGAGATAGATCGAGAGA................................................................................................................................................................................................................................................................................................	18	1	5.00	0.00	0.00	0.00	0.00	5.00
...GAGAGAGAGAAAGAGAGA................................................................................................................................................................................................................................................................................................	18	8	0.50	0.50	0.00	0.00	0.00	0.00
...GAGAGAGAGAGAGAGAGG................................................................................................................................................................................................................................................................................................	18	14	0.21	0.21	0.00	0.00	0.00	0.00
...GTGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	11	0.18	0.18	0.00	0.00	0.00	0.00
.GAGAGAGAAAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	20	7	0.29	0.14	0.14	0.00	0.00	0.00
...GACAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	10	0.20	0.20	0.00	0.00	0.00	0.00
...GAGAGAAAGAGAGAGAGAC...............................................................................................................................................................................................................................................................................................	19	4	0.50	0.00	0.00	0.00	0.00	0.50
...GAGAGAGAGAGAGAGAGAAA..............................................................................................................................................................................................................................................................................................	20	8	0.25	0.13	0.00	0.00	0.13	0.00
...GAGGGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	11	0.18	0.18	0.00	0.00	0.00	0.00
...GACAGACAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	6	0.33	0.00	0.17	0.00	0.00	0.17
.GTGAGAGAGAGAGAGAGA..................................................................................................................................................................................................................................................................................................	18	11	0.18	0.18	0.00	0.00	0.00	0.00
...TAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	12	0.17	0.08	0.08	0.00	0.00	0.00
...GAGAGAGAGAGATAGAGA................................................................................................................................................................................................................................................................................................	18	11	0.18	0.09	0.00	0.00	0.09	0.00
...GAGAGAAAAAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	4	0.50	0.50	0.00	0.00	0.00	0.00
..TGAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	19	9	0.22	0.11	0.00	0.00	0.11	0.00
...GAGAGAGAGAGGGAGAGA................................................................................................................................................................................................................................................................................................	18	9	0.11	0.11	0.00	0.00	0.00	0.00
.GGGAGACAGAGAGAGAGAG.................................................................................................................................................................................................................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00	0.00
ATGGAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	21	3	0.33	0.33	0.00	0.00	0.00	0.00
...GAGAGAGAGAGAGAGGGA................................................................................................................................................................................................................................................................................................	18	9	0.11	0.11	0.00	0.00	0.00	0.00
...GAGAGAGAGAGAAAGAGA................................................................................................................................................................................................................................................................................................	18	11	0.09	0.09	0.00	0.00	0.00	0.00
.GAGAGAGxGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	19	12	0.08	0.08	0.00	0.00	0.00	0.00
....................................................................................................................................................................................................................GTGCTCTTGTGTCGGGCG...............................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..AGAGAGACAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	19	8	0.13	0.13	0.00	0.00	0.00	0.00
...GATAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	10	0.10	0.10	0.00	0.00	0.00	0.00
.....GAGATAGAGAGAGAGAGA..............................................................................................................................................................................................................................................................................................	18	9	0.11	0.11	0.00	0.00	0.00	0.00
AGATAGAGATAGAGAGAGA..................................................................................................................................................................................................................................................................................................	19	3	0.33	0.33	0.00	0.00	0.00	0.00
....................................................................................................................................................AACGTGTGGT--TGA-GTGCC-...........................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...GAGAGTTAGAGAGAGAGAG...............................................................................................................................................................................................................................................................................................	19	4	0.25	0.25	0.00	0.00	0.00	0.00
...GAGAGACAGAGAAAGAGA................................................................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00	0.00
...GAGAGATAGAGAGAGAGGG...............................................................................................................................................................................................................................................................................................	19	4	0.25	0.25	0.00	0.00	0.00	0.00
...GAGACAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	10	0.10	0.10	0.00	0.00	0.00	0.00
...GAGAGATAGAGAGAGAGG................................................................................................................................................................................................................................................................................................	18	6	0.17	0.17	0.00	0.00	0.00	0.00
...GAGAGATAGAGAGAGAGAGA..............................................................................................................................................................................................................................................................................................	20	7	0.14	0.14	0.00	0.00	0.00	0.00
...GAGATAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	9	0.11	0.11	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................GTTTCTTCGGTGTTCTTC........................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...GAGAGATAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	4	0.25	0.25	0.00	0.00	0.00	0.00
...GAGAGGGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	10	0.10	0.10	0.00	0.00	0.00	0.00
..AGAGAGATAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	19	7	0.14	0.14	0.00	0.00	0.00	0.00
............................................................................................................................G--GTGTATATGTACA--T--GTGT................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
...AAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	14	0.07	0.00	0.07	0.00	0.00	0.00
....................................................................................................................................................................................................................................CGGCACCCACAxCAGCGCC..............................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.....GAGATAGATCGAGAGAAT..............................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.GAGAGAGTTAGAGAGAGA..................................................................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00	0.00
....ACAGATAGAGAGAGAGAAT..............................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
...GAGAGAGAGATAGAGAGAA...............................................................................................................................................................................................................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00	0.00
...GAGAAAAAGAGAGAGAGA................................................................................................................................................................................................................................................................................................	18	5	0.20	0.20	0.00	0.00	0.00	0.00
...GAGAGAGAGATAGAGAGA................................................................................................................................................................................................................................................................................................	18	11	0.09	0.09	0.00	0.00	0.00	0.00

droWil1

aggaagaaagacagaggccaaaagagacagtgcgatagagagaggtagagagaacgtacagagagagCTTGTTCTGGTTTGTAACTAATTTTCCCCCTCAAATGTAAGCATTTCGAATGC---ATGTGT----------------GTGTA-----------------------------------------------------------------------------CGTGTAATCACACACGCACACAAATA---------------CCACGTCATTACGATTTCCACATGGC-GAAAATTGTGTGAG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................AAGAGAGAGAGCGATAGA..............................................................................................................................................................................................................................................................................	18	2	2.50	2.50	0.00	0.00	0.00
.................................GATAGAGAGAGAGAGAGA..................................................................................................................................................................................................................................................................	18	7	0.57	0.29	0.29	0.00	0.00
....................AAAGAGAGAGAGCGATAGA..............................................................................................................................................................................................................................................................................	19	2	2.00	2.00	0.00	0.00	0.00
.................................GATAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................	20	6	0.33	0.33	0.00	0.00	0.00
.....................................................................................................................TGT---ATGTGT----------------GTGTA-----------------------------------------------------------------------------TGTGTA............................................................................	20	2	1.00	0.50	0.50	0.00	0.00
.........................GACAGAGAGATAGAGAGA..........................................................................................................................................................................................................................................................................	18	4	0.50	0.00	0.50	0.00	0.00
........................AGACAGTGAGAGAGAGAGA..........................................................................................................................................................................................................................................................................	19	4	0.25	0.25	0.00	0.00	0.00
...........................................................................................................GCTTTTCGAATGT---ATGTG.....................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................AAGAGAAAGTGCGAAAGA..............................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...................................AAGAGAGAGGTGGAGAGAA...............................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................GACAGAGCGATAGAGAGA..........................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.........................GATAGAGCGATAGAGAGA..........................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................GAGAAAGTGCGACAGAGAGA..........................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................ATGA---ATGTGT----------------GTGTA-----------------------------------------------------------------------------TGT...............................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.......................GAGACAGAGAGATAGAGA............................................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
.................................GAAAGAGAGAGGxAGAGAGA................................................................................................................................................................................................................................................................	19	6	0.17	0.17	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................CACATGAC-GATAATTGTGT...	19	1	1.00	0.00	1.00	0.00	0.00
...................................TAGAGAGAGAGAGAGAGA................................................................................................................................................................................................................................................................	18	6	0.17	0.17	0.00	0.00	0.00
..................................AGAGAGAGAGGGAGAGAGA................................................................................................................................................................................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00
...........................................................................................................................................................................................................................................CACACACACACACACATA---------------C........................................	19	41	0.02	0.00	0.02	0.00	0.00
..................................ATAGAAAGAGGTAGAGGGA................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................AGAGAGAGGxAGAGAGAGC..............................................................................................................................................................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
.....................................................................................................................TGT---ATGTGT----------------GTGTA-----------------------------------------------------------------------------TGTGT.............................................................................	19	17	0.06	0.06	0.00	0.00	0.00
.......................GAGAAAGTGCGACAGAGAGAG.........................................................................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.................................GAGAGAGAGAGGGAGAGA..................................................................................................................................................................................................................................................................	18	6	0.17	0.17	0.00	0.00	0.00
...................................GAGAGAGAGGTAGGGAGA................................................................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.................................GAGAGAGAGAGGGAGAGAGA................................................................................................................................................................................................................................................................	20	4	0.25	0.00	0.25	0.00	0.00
..........................ACAGTGTGAGAGAGAGAG.........................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..................................ATAGAGAGAGGGAGTGAGA................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........GACAGAxGCAAAAAGAGACA........................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................................AAGAGAGAGGGAGAGAGA................................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
.....................................................................................................................TGC---AAGTGT----------------GTGTG-----------------------------------------------------------------------------CGTGT.............................................................................	19	1	1.00	0.00	1.00	0.00	0.00
....................AAAGAGAAAGTGCGAAAGA..............................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................CACACACGCACACAAACA---------------CT.......................................	20	4	0.25	0.00	0.25	0.00	0.00
....................................................................................................................ATGC---GTGTGT----------------GTGTA-----------------------------------------------------------------------------CGTGTC............................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.................................GAAAGAGAGAGGGAGAGA..................................................................................................................................................................................................................................................................	18	4	0.25	0.25	0.00	0.00	0.00
....................AAAGAGAAAGTGCGAAAGAGAGA..........................................................................................................................................................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
......................AGAGAGAGAGCGATAGAGA............................................................................................................................................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
.............................GTGCGACAGAGAGAGGGAGA....................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..................................AAAGAGAGAGATAGAGAGA................................................................................................................................................................................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
...........................................................................................................................ATGTGT----------------GTGTG-----------------------------------------------------------------------------CGTGTAAA..........................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................TGT---ATGTGT----------------GTGTG-----------------------------------------------------------------------------CGTGT.............................................................................	19	18	0.06	0.06	0.00	0.00	0.00
......................AGAGAGAGAGCGATAGAGAG...........................................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.................................GATAGAGAGAGATAGAGAG.................................................................................................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
.................................GATAGAGAGAGGTAGAGAGA................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droVir3

GC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTATTTCTG-------------------------------TGCAAG-----TGTG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

AGCAGTTCGTGCACATGCTta--------------------------------------------------------------------------------------------------t---atgtatatgtacacaca--a--atatactcatgtg--tatgagtatgtgtaaaatgcatattcaaatgttaaat-------------------------------gtgcttttacatatagatatgtatgcgtatatTAAAAATACAAAGGTACTTGGCTTTTCTCATGGC-GAAAA-----TAAA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
........................................................................................................................................................CATGTG--TGTGTGTATGTGT........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
AGCAGGGCGTGCACATGCT..................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................TAATGTG--TATGTGTATGTG.........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droGri2

AACAGTTCGTACACACATGC-----------------------------------------------------------------------------------------TTATtgcatgt---atgtatgtgtgtatgtg--a--gtatgtatgtgtgcatatgaacatgt----at-acatatatgcatgtaAAAT-------------------------------G----CTTGCATGTGGCTGTGTGCG-----GTACAAAATACAAAGGCATTTGGCTTTTCTCATGGC-GAAAC-----TGAA	Size	Hit Count	Total Norm	V109 Male body
....................................................................................................................................TGTATTTG--T--GTATGTATGTGT........................................................................................................................................................	21	1	1.00	1.00
...........................................................................................................................ATGTGTGTGTGTGTGTG--A--GTA.................................................................................................................................................................	21	2	0.50	0.50
.................................................................................................................TGCATGT---GTGTGTGTGTGTATG...........................................................................................................................................................................	22	2	0.50	0.50
.........................................................................................................................................GTG--T--GTGTGTATGTGTGCA.....................................................................................................................................................	19	4	0.25	0.25
....................................................................................................................................TATATGTG--A--GTGTGTATGTGT........................................................................................................................................................	21	1	1.00	1.00
...................................................................................................................TATGT---ATGTATGTTTGTATGT..........................................................................................................................................................................	21	1	1.00	1.00
...........................................................................................................................ATGTATATGTGTATGTG--C--G...................................................................................................................................................................	19	1	1.00	1.00
...............................................................................................................................ATGTGTGTGTGTG--A--GTGTGT..............................................................................................................................................................	20	24	0.04	0.04
..............................................................................................................................TATGTATTTATGTG--A--GTATGT..............................................................................................................................................................	21	1	1.00	1.00
......................................................................................................................GT---ATGTGTGTGTGTGTGTG--.......................................................................................................................................................................	19	49	0.02	0.02
...........................................................................................................................ATATATGTGTGTATGTG--T--G...................................................................................................................................................................	19	1	1.00	1.00

12-way Secondary Structure

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