sblock26534- 12- and 20-way alignments

sblock26534	chr2L:12284769-12284877 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 12284832-12284853
   star strand at position 12284794-12284816
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:12284754-12284892 +	AAAAGT---------TCCTTG-CGC-CAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GGACA-----ACCCTCTGATTGGTTTTCTTTTTGATT------------TT--CGTTCGCCATAGGTATTGTTATTCTTGA------------------------------------TTCT---------------------------TTGAC-------------------------T-GCGTTCTA
droSim1	chr2L:12084763-12084872 +	AAAAGT---------TCCTTG-CGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GGACA-----ACCCTCTGAT-------------------------------------------AGATATTGTTATTCTTGA------------------------------------TTCT---------------------------TTGAC-------------------------T-GCGTTGTA
droSec1	super_16:474625-474734 +	AAAAGT---------TCCTTG-CGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GGACA-----ACCCTGTGAT-------------------------------------------AGATATTGTTATTCTTGA------------------------------------TTCT---------------------------TGGAC-------------------------T-GCGGTGTA
droYak2	chr2L:8714891-8715022 +	AAAAGT---------TCTTTT-CGC-AAAAG--TGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GGACA-----ACCCTCAGATTGGTTTACTTTT-----------------CT--CCTTTGCCATAGGTTTTGTTATTCTCGA------------------------------------TTCT---------------------------TCGAC-------------------------T-GCCTTGTA
droEre2	scaffold_4929:13133063-13133194 -	AACAGT---------TCTTTT-CGC-AAAAG--TGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GAACA-----ACCCTCAGATTGGTTTTCTTTT-----------------GC--CCCTTGCCATAGGTATAGTTATTCTCGA------------------------------------TTCC---------------------------TTGAC-------------------------T-GCGTTGTA
droAna3	scaffold_12916:13110146-13110270 -	ACCCGT---------T--TGCCTGC-AAAAG--TGTTGCATACTTTTTGGCAGGCTAACG---------------------GG------GGACAGACCTCCCCTGCGATTGGTTTTCTTCT-----------------CTTTCATC------CGCCATTGTTATTCCTGA------------------------------------TTCG---------------------------GAGAG-------------------------TCGCATTCGA
dp4	chr4_group3:5836352-5836518 -	TGGAGT-------------GT-CGC-AAAAG--TGTTGCATACTTTTTGGCAGGCAGCAAT-G------------------CTAAAGA-GGGCAG----AGCCTTTGATTGGTTTTTCTTTGGGCTCGGGGCTCCCACGT--TCTGTGGCATTGCTATTGTTATTCCTGGCAGACCGAGAGAGAGAGAG--AGCAGGCTT--------------------------------------GGCC-------------------------T--TCTTCTT
droPer1	super_1:7324752-7324920 -	TGGAGT-------------GT-CGC-AAAAG--TGTTGCATACTTTTTGGCAGGCAGCAAT-G------------------CTAAAGA-GGACAG----AGCCTTTGATTGGTTTTTCCTTGGGCTCGGGGCTCCCACGT--TCTTTGGCATTGCTATTGTTATTCCTGGCAGACCGAGAGAGAGAGAGACAGCAGGCAT--------------------------------------GGCC-------------------------T--TCTTCTT
droWil1	Unknown	GG----------------------T-AAAAG--TGTAGCATACTTACTGGCAGGCAAAAGCAG---------T--G-----CAGAAGA-AGCTGCCACATTTTTTAGATTGGTTTTTTTTG-----------------TG--TCCTTGC-----T---TGTTATT---GTTTGACTGAATGGTTTA-------------------------------TTTTGTATCCCGTTTTGAAAGGGTTCTTTTTTTTTTGGCTCTCGTCGCCCCCGTGTTTGC
droVir3	scaffold_12963:17362491-17362582 +	CTG--C---------TGCTGT-CGCAGAAAG--TGTAGCATACTTTTTGGCAGTCG----TTGCCAAAGCAGCAGGCGGCGGCAAGCA-GAAGC-----AACCTTTGATTGGTTTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:22410645-22410809 +	tgctcctgccgctgctgctgT-CGCAGAAAG--TGTAGCATACTTTTTGGCAGTCG----TCGCAAAAGCAGCAGGCGG---CAAGGCAGCAGC-----AACCTTTGATTGGTTTTTGGGT-----------------TT--TGTATGCAGTGCTTGTTGTTATTTTCAG------------------------------------TTTG------------GG-CAA--GGGCTA-AGGGC-------------------------T-CCATTGAA
droGri2	scaffold_15252:14795101-14795287 +	TGTTTC-----------TCTG-CTC-CTTGT--CCTTAGATACTTTTTGGCAGAGTTGCGTCGCCA--------GG-----CAAAAGCAAAAGC-----AACCTTTGATTGGTTTTTGGGG-----------------TT--tctgtct-----g------tctctctgtccgactgtccgactgtct--CCTCTGGTGTGGCTCTGTCTGCAATTGTGTTGTTTCATGTCGTTTAAGGGCT-------------------------TCAAACTGAA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:12284754-12284892 +	NA	AAA----------AGTTCCTTGCGC-CAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGATTGGTTTTCTT-TTTGAT-------------T---------TTCGTTCGCCATAG--GTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTCTA
droSim1	chr2L:12084763-12084872 +	1	AAA----------AGTTCCTTGCGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGAT----------------------------------------------------AG--ATATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTGTA
droSec1	super_16:474625-474734 +	1	AAA----------AGTTCCTTGCGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTGTGAT----------------------------------------------------AG--ATATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TGGA------------------------------CT-GCGGTGTA
droYak2	chr2L:8714891-8715022 +	1	AAA----------AGTTCTTTTCGC-AAAAGTG--TTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCAGATTGGTTTACTT-TTC----------------T-----CCTTTG------CCATAG--GTTTTGTTATTCTC---------GATTCT-------------------------------------------------------------------------TCGA------------------------------CT-GCCTTGTA
droEre2	scaffold_4929:13133063-13133194 -	1	AAC----------AGTTCTTTTCGC-AAAAGTG--TTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGAACAA-------CCCTCAGATTGGTTTTCTT-TTG----------------C-----CCCTTG------CCATAG--GTATAGTTATTCTC---------GATTCC-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTGTA
droEug1	scf7180000409122:667028-667164 +	1	AAA----------GTTTTCTTTTGC-GAAAGTG--TTGCATACTTTTCGGCTGGCGGAAA------------------TCGCTA-AAGAGAACAA--C----CCCTCTGATTGGTTTTCTT-TCT----------------T-TGTTCTTTTG------CCATTG--CTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TAGA------------------------------CT-GGTTTTTT
droBia1	scf7180000302422:707901-708031 -	1	AAA----------AGTTG--TTCGC-AAAAGTG--TTGCATACTTT-TGGGAGGCGGAAA------------------TCGCTA-AAGAGAACAA-------CCCTCTGATTGGTTTTCTT-TTC----------------CCT---ACTTTT------CTACTG--CTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TAGA------------------------------CT-GGGCTGTA
droTak1	scf7180000415865:331344-331479 -	1	CAA----------AGTTTTTTCCAC-AAAAGTG--TTGCATACTTTTTGGGAGGCGGAAA------------------TCGCTA-AAGAGGACAG--CAA--CCCCCTGATTGGTTTCCCTTTTC----------------T-----CTTTTC------CTATTG--CTATTGTTATTTTT---------GATTCT-------------------------------------------------------------------------TCAA------------------------------CT-GGGCTGTA
droEle1	scf7180000491028:2849763-2849871 -	1	AAA----------AGTTTC-ATTGC-AAAAGAG--TGGCAT---TTTAGGCAGGCGGATA------------------TCGCTA-GAGAGGAAAA-------A------ATTGTTTTTCTT-TT-------------------------TTTG------CTATAA--CTATTGTTTTTCTT---------GATTCT-------------------------------------------------------------------------TATA------------------------------T----------
droRho1	scf7180000780043:108180-108289 +	1	AAA----------AGTTGT-TTCGC-AAAAGTG--TTGCATATTTTTTGGCAGGCGGATA------------------TCGATA-AAGAGGACAA-------CCTTCTT---------C---TTC----------------T-----CTTTTG------CTATTG--CTAATGATATTCT--------------------------------------------------------------------------------------------A------------------------------CT-GTAATTTA
droFic1	scf7180000454015:137236-137368 +	3	AAA----------GTTTTCCTTCGC-AAAAGTG--TTGCATACTT-TTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGATTGGTTTTCTT-TTT----------------C-----TTTTTG------CTGTTCCTCTATTCTTATTTTC---------GATTCG-------------------------------------------------------------------------TCGT------------------------------CT-GTGGTGTA
droKik1	scf7180000301476:370791-370905 +	1	CGT----------TTTACCACCCAC-CAAAGTG--TTGCATACTTTTTGG-------------------------------CTA-AGAAGGACAA-------ACCTCTGATTGGTTTTCTT-TGG----------------CCT---CGT------------TCG--ACATTGTTATTCCT---------GATTCT-------------------------------------------------------------------------TCGA------------------------------CT-GGGGTGTA
droAna3	scaffold_12916:13110146-13110270 -	1	ACC----------CGTTTG-CCTGC-AAAAGTG--TTGCATACTTTTTGGCAGGCTAAC-------------------G--------GGGGACAG--ACCTCCCCTGCGATTGGTTTTCTT-CTC----------------T---------TT------CATCCG--CCATTGTTATTCCT---------GATTCG-------------------------------------------------------------------------GAGA------------------------------GTCGCATTCGA
droBip1	scf7180000396580:411008-411118 +	2	ACC----------CGTTTT-CCGGC-AAAAGTG--TTGCATACTTTTTGGCAGGC---------------------------TA-ACG-GGACAG-------ACCTCCGATTGGTTTTCTT-TTC----------------T---------TT------CATCCG--CCATTGTTATTCCT---------GATTCG-------------------------------------------------------------------------GGGA------------------------------AT-------CA
dp4	chr4_group3:5836352-5836516 -	2	GAG----------TGT------CGC-AAAAGTG--TTGCATACTTTTTGGCAGGCAGCAA------------------T-GCTA-AAGAGGGCAG--A----GCCTTTGATTGGTTTTTCT-TTGGGCTCGGGGCTCCCAC---GT-TCTGTG------GCATTG--CTATTGTTATTCCTGGCAGACCG------AGAGAGAG--AGAG--AGC-------------------------------------------------AGGCTTGGC------------------------------CT--TCTTCTT
droPer1	super_1:7324752-7324918 -	2	GAG----------TGT------CGC-AAAAGTG--TTGCATACTTTTTGGCAGGCAGCAA------------------T-GCTA-AAGAGGACAG--A----GCCTTTGATTGGTTTTTCC-TTGGGCTCGGGGCTCCCAC---GT-TCTTTG------GCATTG--CTATTGTTATTCCTGGCAGACCG------AGAGAGAG--AGAGACAGC-------------------------------------------------AGGCATGGC------------------------------CT--TCTTCTT
droWil1	scaffold_180708:9979069-9979243 +	3	A---------------------------AAGTG--TAGCATACTTACTGGCAGGCAAAAG---------CA-------GTGCAG-AAGAAGCTGCCACAT--TTTTTAGATTGGTTTTACG-AGT----------------TT----TGTG--------TCCTTG--C--TTGTTATTGTT---TGACTG------AAT-------------------------------------------GGTTTATTTTGTATCCCGTTTT-----GAAAGGGTTCTTTTTTTTTTGGCTCTCGTCGCCCCC-GTGTTTGC
droVir3	scaffold_12963:17362502-17362582 +	3	CAG------------------------AAAGTG--TAGCATACTTTTTGGCAGTCG----TTGCCAAAGCAGCAGGCGGCGGCA-AGCAGAAGCA-------ACCTTTGATTGGTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:22410643-22410826 +	1	CTGCTCCTGCCGCTGCTGCTGTCGCAGAAAGTG--TAGCATACTTTTTGGCAGTCG----TCGCAAAAGCAGCAGGC---GGCAAGGCAGCAGCA-------ACCTTTGATTGGTTTTTGG-GTT----------------T-----TGTATG------CAGTGC--TTGTTGTTATTTTC---------AGTTTGGGCAAGGGCTAAGG--------------------------------GCTCCATT-----GAAG-----A-GCTTTG-------------------------------CA--GTTTCAA
droGri2	scaffold_15252:14795099-14795283 +	2	ACT----------GTTTCTCTGCTC-CTTGTCC--TTAGATACTTTTTGGCAGAGTTGCGTCGCC--------A----G-GCAA-AAGCAAAAGC--A----ACCTTTGATTGGTTTTTGG-GGT----------------T-----TCT-GT------CTGTCT--------CTCTGTCC---------GACTGT-CCGACTG--TCTC--CTCTGGTGTGGCTCTGTCTGCAATTGTGTTGTTTCATGTCGTTTAAGGGCTT-----CAAA------------------------------C----------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

AAAAGT---------TCCTTG-CGC-CAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GGACA-----ACCCTCTGATTGGTTTTCTTTTTGATT------------TT--CGTTCGCCATAGGTATTGTTATTCTTGA------------------------------------TTCT---------------------------TTGAC-------------------------T-GCGTTCTA

Size

Hit Count

Total Norm

droSim1

AAAAGT---------TCCTTG-CGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GGACA-----ACCCTCTGAT-------------------------------------------AGATATTGTTATTCTTGA------------------------------------TTCT---------------------------TTGAC-------------------------T-GCGTTGTA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

AAAAGT---------TCCTTG-CGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GGACA-----ACCCTGTGAT-------------------------------------------AGATATTGTTATTCTTGA------------------------------------TTCT---------------------------TGGAC-------------------------T-GCGGTGTA

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

AAAAGT---------TCTTTT-CGC-AAAAG--TGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GGACA-----ACCCTCAGATTGGTTTACTTTT-----------------CT--CCTTTGCCATAGGTTTTGTTATTCTCGA------------------------------------TTCT---------------------------TCGAC-------------------------T-GCCTTGTA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................TTGCATACTTTTTGGCGCGC..............................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

AACAGT---------TCTTTT-CGC-AAAAG--TGTTGCATACTTTTTGGCAGGCGGAAATCG------------------CTAAAGA-GAACA-----ACCCTCAGATTGGTTTTCTTTT-----------------GC--CCCTTGCCATAGGTATAGTTATTCTCGA------------------------------------TTCC---------------------------TTGAC-------------------------T-GCGTTGTA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.............................................TTTGGCAGGCGGAACTGG------------------C...................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droAna3

ACCCGT---------T--TGCCTGC-AAAAG--TGTTGCATACTTTTTGGCAGGCTAACG---------------------GG------GGACAGACCTCCCCTGCGATTGGTTTTCTTCT-----------------CTTTCATC------CGCCATTGTTATTCCTGA------------------------------------TTCG---------------------------GAGAG-------------------------TCGCATTCGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................................................G------GTACAGACCTCCCCGGC...........................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

dp4

TGGAGT-------------GT-CGC-AAAAG--TGTTGCATACTTTTTGGCAGGCAGCAAT-G------------------CTAAAGA-GGGCAG----AGCCTTTGATTGGTTTTTCTTTGGGCTCGGGGCTCCCACGT--TCTGTGGCATTGCTATTGTTATTCCTGGCAGACCGAGAGAGAGAGAG--AGCAGGCTT--------------------------------------GGCC-------------------------T--TCTTCTT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
............................................................................................................................................................................GAGAGAGAGAGAGAGAG--A.....................................................................................	18	8	0.88	0.25	0.63	0.00	0.00
...........................................................................................................................................................................AGAGAGAGAGAGAGAGAG--A.....................................................................................	19	6	0.67	0.33	0.33	0.00	0.00
.............................................................................................................................................................................AGAGAGAGAGAGAGAG--AG....................................................................................	18	9	0.22	0.22	0.00	0.00	0.00
...........................................................................................................................................................................AGAGGGAGAGAGAGAGAG--A.....................................................................................	19	2	1.00	0.50	0.50	0.00	0.00
...........................................................................................................................................................................AGAGAGAGAGAGAGAGAG--......................................................................................	18	9	0.22	0.22	0.00	0.00	0.00
............................................................................................................................................................................GAGCGAGAGCGAGAGAG--A.....................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................AGGGCTCCCACxT--TCTGTGGC...............................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................GAGAGAGAGAGAT--AGCAGGCC..............................................................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................................................................GAGAGAGAGAGAT--AGCAGG................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
.................................................................................................................................................................................AGAGAGAGAGAG--AGTAGA................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................GACAGAGAGAGAGAGAG--AGA...................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................AGCGAGAGAGAG--GGCAGGC...............................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................ACGAGAGAGAGTGAG--AGC...................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................CAGAGAGAGAGAGAGAGA.........................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
...........................................................................................................................................................................AGAGCGAGAGCGAGAGAG--A.....................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................AGAGAGAGAGAG--AGCGAG................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
................................................................................................................................................................................GAGAGAGAGAGAT--AGCCGGC...............................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................................................................GT--TCTGCGGCATTGCTGTTG.....................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................ACAGAGAGAGAGAGAG--AG....................................................................................	18	3	0.33	0.33	0.00	0.00	0.00
...........................................................................................................................................................................AGAGCGAGAGAGAGAGAG--T.....................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................AGACAGCGAGAGAGAGAG--......................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................................AGAGAGAGAGAGAG--AGAA..................................................................................	18	4	0.25	0.25	0.00	0.00	0.00
.................................................................................................................................................................................AGAGAGAGAGAG--AGGATGC...............................................................................	19	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................................GAGTGAGAGAGAG--AGCAGG................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................................................................................................AGACAGTGAGAGAGAGAG--A.....................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................AGACAGAGAGAGAGATAG--AG....................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
.........................................................................................................................................................................GCAGAAAGAGAGAGAGAGAG--A.....................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................GATAGAGAGAGAGAGAG--A.....................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................................................AGAGCGAGAGAGxGAGAG--A.....................................................................................	18	2	0.50	0.50	0.00	0.00	0.00
..............................................................................................................................................................................CAGAGAGAGAGAGAG--AGA...................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
.............................................................................................................................................................................ATAGAGAGAGAGAGAG--AG....................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
...........................................................................................................................................................................AGACGGAGAGAGAGAGAG--A.....................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................................................................GAGAGAGAGAGAT--AGCAGGC...............................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

TGGAGT-------------GT-CGC-AAAAG--TGTTGCATACTTTTTGGCAGGCAGCAAT-G------------------CTAAAGA-GGACAG----AGCCTTTGATTGGTTTTTCCTTGGGCTCGGGGCTCCCACGT--TCTTTGGCATTGCTATTGTTATTCCTGGCAGACCGAGAGAGAGAGAGACAGCAGGCAT--------------------------------------GGCC-------------------------T--TCTTCTT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........................................................................................................................................................................AGAAAGAGAGAGAGAGAGA.......................................................................................	19	7	0.57	0.14	0.43	0.00	0.00	0.00
...............................................................................................................GTTTTTATTTGGGCTCGG....................................................................................................................................................	18	1	4.00	0.00	0.00	0.00	0.00	4.00
................................................................................................................................................................................GAGAGAGAGAGAGAGAGG...................................................................................	18	14	0.21	0.21	0.00	0.00	0.00	0.00
............................................................................................................................................................................GACAGAGAGAGAGAGAGA.......................................................................................	18	10	0.20	0.20	0.00	0.00	0.00	0.00
................................................................................................................................................................................CAGAGAGAGAGAGAGAGC...................................................................................	18	5	0.40	0.00	0.20	0.00	0.00	0.20
...........................................................................................................................................................................AGAGCGAGAGAGAGAGAGA.......................................................................................	19	4	0.50	0.50	0.00	0.00	0.00	0.00
...............................................................................................................................................................................AGAGAGAGAGAGAxATAGC...................................................................................	18	3	0.67	0.00	0.67	0.00	0.00	0.00
............................................................................................................................................................................GACAGAGAGAGAGAGAGAGA.....................................................................................	20	7	0.29	0.00	0.29	0.00	0.00	0.00
............................................................................................................................................................................GACAGACAGAGAGAGAGA.......................................................................................	18	6	0.33	0.00	0.17	0.00	0.00	0.17
........................................................................................................................................................................GACAGACAGAGAGAGAGA...........................................................................................	18	6	0.33	0.00	0.17	0.00	0.00	0.17
...........................................................................................................................................................................AGACAGAGAGAGAGAGAGAGA.....................................................................................	21	6	0.33	0.33	0.00	0.00	0.00	0.00
..........................................................................................................................................................................CAxAACGAGAGAGAGAGAGA.......................................................................................	19	2	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................................................................................................GAGGGAGAGAGAGAGAGA.......................................................................................	18	11	0.18	0.18	0.00	0.00	0.00	0.00
...........................................................................................................................................................................AGACGGAGAGAGAGAGAGA.......................................................................................	19	4	0.50	0.00	0.00	0.00	0.00	0.50
.............................................................................................................................................................................ACCGAGAGAGAGAGAGAGAGA...................................................................................	21	3	0.33	0.33	0.00	0.00	0.00	0.00
.........................................................................................................................................................................AGAGACCGAGAGAGAGAGA.........................................................................................	19	4	0.25	0.25	0.00	0.00	0.00	0.00
.........................................................................................................................................................................GTAGAGCGAGAGAGAGAG..........................................................................................	18	2	0.50	0.50	0.00	0.00	0.00	0.00
..........................................................................................................................................................................GAGACAGAGAGAGAGAGA.........................................................................................	18	10	0.10	0.10	0.00	0.00	0.00	0.00
.............................................................................................................................................................................AAAGAGAGAGAGAGAGAC......................................................................................	18	7	0.14	0.00	0.00	0.00	0.00	0.14
..........................................................................................................................................................................GAGACAGAGAGAGAGAGAG........................................................................................	19	8	0.13	0.00	0.00	0.00	0.00	0.13
........................................................................................................................................................................TGCAGxCCGAGAGAGAGAGAG........................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
............................................................................................................................................................................GACAGAGAGCGAGAGAGA.......................................................................................	18	4	0.25	0.00	0.25	0.00	0.00	0.00
................................................................................................................................................................................GAGAGAGAGAGAGATAGCA..................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................................................................................................GACGGAGATAGAGAGAGA.......................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................................................................................................GACGGAGAGAGAGAGAGG.......................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................................................................................................................TGACAGAGAGAGAGAGAGA.......................................................................................	19	4	0.25	0.25	0.00	0.00	0.00	0.00
..........................................................................................................................................................................GAGACAGAGAGAGAGAGAGA.......................................................................................	20	8	0.13	0.13	0.00	0.00	0.00	0.00
.............................................................................................................TTGTTTTTCTTTGGGCTC......................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................................................................................AGCGAGAGAGAGAGAGAC......................................................................................	18	6	0.17	0.00	0.00	0.00	0.00	0.17
...............................................................................................................................................................................CGAGAGAGAGAGAGAGAGT...................................................................................	19	5	0.20	0.20	0.00	0.00	0.00	0.00
................................................................................................................................................................................GAGAGAGAGAGAGATAGCAGGCC..............................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................................................................................................................AGAACGAGAGAGAGAGAGA.......................................................................................	19	4	0.25	0.00	0.25	0.00	0.00	0.00
............................................................................................................................................................................GACAGAGAGAGACAGAGA.......................................................................................	18	4	0.25	0.25	0.00	0.00	0.00	0.00
..............................................................................................................................................................................TCGAGAGAGAGAGAGAGAG....................................................................................	19	7	0.14	0.00	0.00	0.00	0.00	0.14
...........................................................................................................................................................................AGAGGGAGAGAGAGAGAG........................................................................................	18	11	0.09	0.09	0.00	0.00	0.00	0.00
...........................................................................................................................................................................AGAGTGAGAGAGAGAGAGA.......................................................................................	19	8	0.13	0.13	0.00	0.00	0.00	0.00
............................................................................................................................................................................GAGCGAGAGAGCGAGAGA.......................................................................................	18	6	0.17	0.00	0.17	0.00	0.00	0.00
............................................................................................................................................................................GATAGAGAGAGAGAGAGA.......................................................................................	18	10	0.10	0.10	0.00	0.00	0.00	0.00
...........................................................................................................................................................................AGCCAGAGAGAGAGAGAGA.......................................................................................	19	5	0.20	0.00	0.20	0.00	0.00	0.00
........................................................................................................................................................................GGGAGACAGAGAGAGAGAG..........................................................................................	19	5	0.20	0.20	0.00	0.00	0.00	0.00
...........................................................................................................................................................................ACACAGAGAGAGAGAGAGA.......................................................................................	19	3	0.33	0.00	0.33	0.00	0.00	0.00
...............................................................................................................................................................................CGAGAGAGAGAGAGAGAGC...................................................................................	19	6	0.17	0.00	0.00	0.00	0.00	0.17
.........................................................................................................................................................................GGAGACAGAGAGAGAGAGAG........................................................................................	20	3	0.33	0.33	0.00	0.00	0.00	0.00
...........................................................................................................................................................................AGAAAGAGAGAGAGAGAG........................................................................................	18	8	0.13	0.13	0.00	0.00	0.00	0.00
................................................................................................................................................................................GAGAGAGAGAGAGATAGG...................................................................................	18	8	0.13	0.13	0.00	0.00	0.00	0.00
........................................................................................................................................................................TGCAGACAGAGAGAGAGAGA.........................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................................GAGAACGAGAGAGAGAGAGA.......................................................................................	20	4	0.25	0.00	0.25	0.00	0.00	0.00
..........................................................................................................................................................................CAAAGCGAGAGAGAGAGA.........................................................................................	18	5	0.20	0.20	0.00	0.00	0.00	0.00
..........................................................................................................................................................................CAAAGCGAGAGAGAGAGAGA.......................................................................................	20	4	0.25	0.25	0.00	0.00	0.00	0.00

droWil1

GG----------------------T-AAAAG--TGTAGCATACTTACTGGCAGGCAAAAGCAG---------T--G-----CAGAAGA-AGCTGCCACATTTTTTAGATTGGTTTTTTTTG-----------------TG--TCCTTGC-----T---TGTTATT---GTTTGACTGAATGGTTTA-------------------------------TTTTGTATCCCGTTTTGAAAGGGTTCTTTTTTTTTTGGCTCTCGTCGCCCCCGTGTTTGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................................................................................................................................TTATT---ATTTGACTGAATA................................................................................................	18	1	4.00	0.00	0.00	0.00	4.00
..........................................................................................................................................................................................................................................................TTTGGCTGTCGTCGCCGC.........	18	1	2.00	0.00	0.00	0.00	2.00
..........................................................................................................................................................................................................................................AGAxGATTCTTTTTTTTTT........................	18	1	2.00	0.00	2.00	0.00	0.00
..................................................................................AGAAGA-TGCGGCCACATT................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................TTTTTTAGATTTGTTTGT................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
............................................................................................................................................................................................................................................AGCGTTCATTTTTTTTTG.......................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................GGTTGACTGAGTGGTTTA-------------------------------............................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................GAAGCxG---------T--G-----CAGAAGA-AGCT........................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................................T---GGTTGACTGAGTGGTTTA-------------------------------............................................................	19	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................TTTG-----------------TG--ATCTTGC-----T---TGTTATT---GT...........................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................................................................................TCTTTGGCTGTCGTCGCC...........	18	1	1.00	0.00	0.00	0.00	1.00

droVir3

CTG--C---------TGCTGT-CGCAGAAAG--TGTAGCATACTTTTTGGCAGTCG----TTGCCAAAGCAGCAGGCGGCGGCAAGCA-GAAGC-----AACCTTTGATTGGTTTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.............................GG--TGTAGCATACTTTTCGG...................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..G--C---------TGCTGT-xGCAGAAAC--TGT.................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................G----TTGGCAAAGCAGCAGCC........................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

tgctcctgccgctgctgctgT-CGCAGAAAG--TGTAGCATACTTTTTGGCAGTCG----TCGCAAAAGCAGCAGGCGG---CAAGGCAGCAGC-----AACCTTTGATTGGTTTTTGGGT-----------------TT--TGTATGCAGTGCTTGTTGTTATTTTCAG------------------------------------TTTG------------GG-CAA--GGGCTA-AGGGC-------------------------T-CCATTGAA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.GCTGCTGCCGCTGCTGCTGT-C..............................................................................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.50	0.00
...................................................................................................................TTGGGT-----------------TT--TGxATGCAGG.............................................................................................................................	17	1	1.00	0.00	1.00	0.00	0.00

droGri2

TGTTTC-----------TCTG-CTC-CTTGT--CCTTAGATACTTTTTGGCAGAGTTGCGTCGCCA--------GG-----CAAAAGCAAAAGC-----AACCTTTGATTGGTTTTTGGGG-----------------TT--tctgtct-----g------tctctctgtccgactgtccgactgtct--CCTCTGGTGTGGCTCTGTCTGCAATTGTGTTGTTTCATGTCGTTTAAGGGCT-------------------------TCAAACTGAA

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image