sblock177975- 12- and 20-way alignments

sblock177975	chrX:5963712-5963792 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 5963727-5963746
   star strand at position 5963761-5963786
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:5963697-5963807 -	CGGAGAC------------------AA--GTCGAAACAAAATTGAACTGGC--AG-----------------CAA-------------AATGACAAATTCGCACTGGGCACAGTGTGAACATGTCATATTGCTGCCGGTG--AAACAATCACATA------------TTTAGTTAGC
droSim1	chrX:4687883-4687994 -	CGAAGAC------------------AAGAGTCGA-ACAAAATTGAACTGGC--AG-----------------CAA-------------GATGACAGATTCGCACTGGGCGCAGTGTGAACATGGCATAATGCTGCCGGTG--TAACAATCACATA------------TTTAGTTAGC
droSec1	super_4:802740-802849 +	CGAAGAC------------------AA--GTCGA-ACAAAATTGAACTGGC--AG-----------------CAA-------------GATGGCAGATTCGCACTGGACGCAGTGTGAACATGGCATAATGCTGCCGGTG--AAACAATCACATA------------TTTAGTTAGC
droYak2	chrX:1971149-1971223 -	CGAAGAC------------------AT--ATCGA-ACAAAATTGAACTGGC--AG-----------------CAA-------------GT---------------------------------------TGCTACCGGTGTTAAACAATCACATATA----------TGTAGTTAGC
droEre2	scaffold_4690:14942392-14942483 -	CGAAGAC------------------AT--ATCGA-ACAAAATTAAACTGGC--AG-----------------CCA-------------GATGAC----------------CAGTGTGAACGTGGCATAAGGCTGCCG--G--TAACAATCACATA------------TTTAGTTAGC
droAna3	Unknown	CGAAAAA------AAAGAAAACAA----------AACAAAACATATCGAAC--AA-----------------CAAAATTGTTTGGAGG--------CTTT-C-TTGGGCACAATGTGAACACA---------CTCACAAA--AAATACAGTGTTG------------TTTAGGTAGC
dp4	chrXL_group1e:5411649-5411745 +	AGAAAAG------------------CGTATTCGA----------------------AGT----------------------TCATTAG--------GTTT-C-ATTAG------AAGGACGTGGCGTAGATCCTCGACAG--AAACACTCACACATATCGAAACCGGTTTAGTTAGT
droPer1	super_21:323762-323858 +	AGAAAAC------------------CGTATTCGA----------------------AGT----------------------TCATTAG--------GTTT-C-GTCAG------AAGTACGTGGCGTAGATCCTCGACAG--AAACACTCACACATATCGAAACCGGTTTAGTTAGT
droWil1	scaffold_181150:1838781-1838880 +	AGAAAAAAGAAAAAA------AAACAT--ATCTA-AAAA-------ACATATACGAAAACTTAGGTCAGCTTCAA-------------A-------------ACCGAACGGAAGCTGAACA-----------------------AAGGCTAAACT------------ATTAGTTAGT
droVir3	Unknown	CGAGGCGAAAAAGCA------AGCTGA--GCC----CAAAGCTGAGTTCAC--ACAAGT----------------------TTAGTAT--------TTTT-----------------TCTGTTGCTTGTCTCTTTTCCAG--CAGTATTTAATCT------------ATTAGTTAGC
droMoj3	scaffold_6328:1569306-1569319 +	TC-------------------------------------------------------------------------------------------------------------------------------------------------------CA------------ACTAGCTTTC
droGri2	Unknown	AAAGAAGGAAAAACAAGAAAACAA----------CATATTATATATCT--------------------------------------------------------------------------------------------------ATTTATGCA------------GTTAGTTAGT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:5963697-5963807 -	NA	CGGAGACAAG--TCG-------A--------------AAC----AAAA----TTGAACTGGCAGCAAAAT-----G-----ACAAA------TTCGCACTGGGCA------------------------CAGTGTGA---ACATGTCATATTGCTGCCGGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----
droSim1	chrX:4687883-4687994 -	1	CGAAGACAAGAGTC----------------------GAAC----AAAA----TTGAACTGGCAGCAAGAT-----G-----ACAGA------TTCGCACTGGGCG------------------------CAGTGTGA---ACATGGCATAATGCTGCCGGTG--TAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----
droSec1	super_4:802740-802849 +	1	CGAAGACAAG--TC----------------------GAAC----AAAA----TTGAACTGGCAGCAAGAT-----G-----GCAGA------TTCGCACTGGACG------------------------CAGTGTGA---ACATGGCATAATGCTGCCGGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----
droYak2	chrX:1971149-1971223 -	1	CGAAGACATA--TC----------------------GAAC----AAAA----TTGAACTGGCAGCAAG----------------------------------------------------------------------------------TTGCTACCGGTGTTAAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----TAT----------ATGTAGTTAGC-----
droEre2	scaffold_4690:14942392-14942483 -	1	CGAAGACATA--TC----------------------GAAC----AAAA----TTAAACTGGCAGCCAGAT-----G-----AC----------------------------------------------CAGTGTGA---ACGTGGCATAAGGCTGCCGGT----AACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----
droEug1	scf7180000409033:286585-286701 -	1	CGAAGACATA--TC----------------------GAAC----AAAA----TTTAAG--GCGTTAAGAC-----C-----A---A---------TCACTATATG------------------------GAGTGTGAAAAGAATGGGTTAATGCTCCCAGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAA----------A----TATTTGCAAAGTTATTTAGTTAGC-----
droBia1	scf7180000302421:723293-723411 -	2	CGAAGACATA--TC----------------------GAAC----AAAA----TTCAGGGG--ACTGGGAT-----G-----ACACG------TTCGCACTGAAGG------------------------CAGTGTGG---ACAGGGCTC-ATGTCCCCAGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------G----TATTTACAAAGACGTTTAGTTAGC-----
droTak1	scf7180000415769:469591-469710 +	2	CGAAGACATA--TC----------------------GAAC----AAAA----TTTAGAGGG--CTAAGAT-----G-----GTGTG------TTCGCACTGAAGG------------------------CAGTGCGA---ACAGGGCATTAAGCTCCAAGTG--ACCAA--------------------------------------------------------------------------------------------------------ATCAC----------A----CATTTACCAAGATGATTAGTTAGC-----
droEle1	scf7180000490141:671400-671527 -	2	CGAAGACATA--TC----------------------GAAC----AAAA----TTTAAG-GGCGCTAGGAT-----G-----ACGTG------TCCACATCAACGG------------------------CAGTGTGA---ACAGGGCATAATGTTCCCAGTG--TT-----------------------------------------------------------------------------------------CCCA------------CAATCAC----------ATACATATATACAGAGATGTTTAGTTAGC-----
droRho1	scf7180000778072:152382-152502 -	2	CGAAGACATA--TC----------------------GAAC----AAAA----TTTAAG-GGCGCTAAAAT-----G-----TCGTG------TTTACATTAAAGA------------------------CAGTGTGA---ACAGGGCATAATGTACCCAATG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----GATATACAGAGATGTTTAGTTAGC-----
droFic1	scf7180000454072:1399768-1399881 +	1	CGAAAACATA--TC----------------------GAAC----AAAT----CTAAAG-GG---CTAGAC-----G-----ATGTG------TTCGCACTGTGGG------------------------CAGTGTGA---ACGGGACATACGGCTCCCAGTA--AAACA--------------------------------------------------------------------------------------------------------AACGC----------A----C----ACAGAGATGTTAAGTTAAC-----
droKik1	scf7180000302610:1501511-1501678 +	1	CAAAAACATA--AC----------------------GAAA----AAGAAAAATTCAAT--G---CGAACA-----G-----GTCAA------CTTACACTGAAAGACAGTGAGAAGAGGACATTATGCTCAGTGTAA---ACGCCGCATAATGCTTTCCGTT--AA---------------------------------T-----GTTA---TTCAGTGTGCAGAGGGCATTTTT-------------------------------------GTTCTCAAA-AAATATG----------------TATTTAGTTAGC-----
droAna3	scaffold_13417:548659-548772 -	1	CGAAAAAAAA--GA---AAACAAAACAAAACATATCGAAC----A------------------ACAAAATTGTTTGGAGGCT-------------------------------------------------------------------------------------------------------------------------TTCTT------------------------------GGGCAATCTCCAATGTGAACA------------CACTCACAAA-------------AAATACAGTGTTGTTTAGGTAGC-----
droBip1	scf7180000396362:585451-585558 +	1	CGAAAAAAAA--A---------AAACAAAACATATCGAAC----A------------------ACAAAATTGTTTGGAGGCT-------------------------------------------------------------------------------------------------------------------------TTCTT------------------------------GGGCAATCTCCAGTGTGAACA------------CACTCACAAA-------------AAATACAGTGTTGTTTAGGTAGC-----
dp4	chrXL_group1e:5411646-5411745 +	1	GGAGAAAAGC--GT----------------------ATTC----GAAG----TTCATTAG--------------------------------G----------TT------------------------TCATTAGAAGGACGTGGCGTAGATCCTCGACAG--AAACA--------------------------------------------------------------------------------------------------------CTCAC----------A----CATATCGAAACCGGTTTAGTTAGT-----
droPer1	super_21:323762-323858 +	1	AGAAAACCGT--------------------------ATTCGAAGTTCA----TTAGG----------------------------------------------TT------------------------TCGTCAGAAGTACGTGGCGTAGATCCTCGACAG--AAACA--------------------------------------------------------------------------------------------------------CTCAC----------A----CATATCGAAACCGGTTTAGTTAGT-----
droWil1	scaffold_181150:1838778-1838880 +	1	AGGAGAAAAA--AGA-------AAAAAAAACATATCTAAA---AAACA----TATA-------------C-----GAAAACTTAGGTCAGCTTCAAAACCGAACG------------------------GAAGCTGA---ACAAAGGCT-------------------------------------------------------------------------------------------------------------------------------AA----------A----------------CTATTAGTTAGT-----
droVir3	scaffold_12928:603918-604086 +	3	AAATGCTAAG--GC----------------------GAAA----AAAT----ATCTGA-AG---CGAGGC-----GAAAAAGCAAG----------------------------------------------------------------CTGAGCCCAAAG--CTGAGTTCACACAAGTTTAGTATTTTTTCTGTTGCTTGTCTCTTTTCCAGCAGTATTTAGT-GGTATTTTTTTTGTGAAGTCAGCTTTGCGAG------------CCT-CTAAT---------------------------CTATTAGTTAGC-----
droMoj3	scaffold_6328:1569195-1569320 +	2	TGATGCATCA--TCCAAA-------------------AGC----CCAG----CTGAGCTCGCCGTTCGTC-----T-----A---A------TTAG----------------------------------------------------------------------------------------------------TATTTCTCTCTT------------------------------ATTCAGTATTCACTGTAAGCGACGGTGCGTGCTT-CAGCT-CTATTCACTG----T------------ATCCAACTAGCTTTCT
droGri2	scaffold_14853:7866730-7866831 -	2	CAAATAATAC--TC----------------------GTAA----CATA----TCTGAAAG----AAAGAA-----GGAAAAACAAG------AAAACA-----TT------------------------TATCAAGAAGCCCAA-----AAAGCTG-----------AATTCACAA-------------------------------------------------------------------------------------------------CGCCT----------G----------------TTTTTAGTATTT-----

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CGGAGAC------------------AA--GTCGAAACAAAATTGAACTGGC--AG-----------------CAA-------------AATGACAAATTCGCACTGGGCACAGTGTGAACATGTCATATTGCTGCCGGTG--AAACAATCACATA------------TTTAGTTAGC

Size

Hit Count

Total Norm

droSim1

CGAAGAC------------------AAGAGTCGA-ACAAAATTGAACTGGC--AG-----------------CAA-------------GATGACAGATTCGCACTGGGCGCAGTGTGAACATGGCATAATGCTGCCGGTG--TAACAATCACATA------------TTTAGTTAGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.................................................................................................................TGTGAACATGGCATAATGCTG...........................................	21	1	2.00	0.00	2.00	0.00	0.00
...................................................................................................................TGAACATGGCATAATGCTGCCT........................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................AATGCTGCCGATG--TAACT..............................	18	1	1.00	0.00	0.00	1.00	0.00
................................GA-ACAAAATTGAAATGCC--............................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droSec1

CGAAGAC------------------AA--GTCGA-ACAAAATTGAACTGGC--AG-----------------CAA-------------GATGGCAGATTCGCACTGGACGCAGTGTGAACATGGCATAATGCTGCCGGTG--AAACAATCACATA------------TTTAGTTAGC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................................................G-----------------CTA-------------GATGGCCGATTCGC...........................................................................	18	1	1.00	0.00	1.00	0.00
.........................................TTGAAxAGGC--AG-----------------CAA-------------GATG.....................................................................................	18	1	1.00	0.00	1.00	0.00
...........................................................................................GGCAGAGTCGCACTGGAAGC..................................................................	20	1	1.00	0.00	0.00	1.00
....................................CAAAATTGATCTGGG--AG-----------------C........................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

CGAAGAC------------------AT--ATCGA-ACAAAATTGAACTGGC--AG-----------------CAA-------------GT---------------------------------------TGCTACCGGTGTTAAACAATCACATATA----------TGTAGTTAGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..............................TCGA-ACAAAATTGAACTGGC--A...........................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00

droEre2

CGAAGAC------------------AT--ATCGA-ACAAAATTAAACTGGC--AG-----------------CCA-------------GATGAC----------------CAGTGTGAACGTGGCATAAGGCTGCCG--G--TAACAATCACATA------------TTTAGTTAGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.................................................................................................................TGTGAACGTGCAATAAGGC.............................................	19	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................TAAGGCTGCCG--G--TAACAATC...........................	20	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................TGAACGTGGCATAAGGCTGCC.........................................	21	1	1.00	0.00	1.00	0.00	0.00
.................................................GC--AG-----------------CCA-------------GACGAG----------------CAGTGT.............................................................	19	1	1.00	0.00	0.00	0.00	1.00

droAna3

CGAAAAA------AAAGAAAACAA----------AACAAAACATATCGAAC--AA-----------------CAAAATTGTTTGGAGG--------CTTT-C-TTGGGCACAATGTGAACACA---------CTCACAAA--AAATACAGTGTTG------------TTTAGGTAGC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.........................................................................................................GGGCACAATGTGTACAAA---------.............................................	18	1	4.00	0.00	3.00	0.00	1.00
..AAAAA------AAAGAAAAAAA----------AA.............................................................................................................................................	18	42	0.05	0.00	0.00	0.00	0.05
.............AAAGAAAACAA----------AAAAAAA........................................................................................................................................	18	46	0.04	0.00	0.00	0.00	0.04
....AAA------AAAAAAAACAA----------AACAAA.........................................................................................................................................	20	41	0.02	0.00	0.00	0.00	0.02
.GAAAAA------AAAGAACACCA----------A..............................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..AAAAA------AAAGACCACAA----------AACAA..........................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....AAA------AGAGxAAACAA----------AAGAAAA........................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..AAAAA------AGAAAAAACAA----------AA.............................................................................................................................................	18	49	0.02	0.00	0.00	0.00	0.02
......A------AAAGAAAACAA----------AACCAAA........................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
......A------AAAGAAAGCAA----------ACCAAAA........................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.............AGAGAAAACAG----------AACAAAA........................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...AAAA------AGAGAACAxAA----------AACA...........................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
......A------AAAAAAAACAG----------AACAAAA........................................................................................................................................	19	7	0.14	0.00	0.00	0.00	0.14
..AAAAA------AAAGAAAAAAA----------GACA...........................................................................................................................................	20	5	0.20	0.00	0.00	0.00	0.20
.GAAAAA------ACAGAAGACAA----------A..............................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.............AAAGAAAACxA----------ACCAAAACA......................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..AAAAA------GAGGAAAACAA----------AA.............................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..AAAAA------ACAGAACACAA----------AA.............................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
.GAAAAA------AAACAAAACAA----------AC.............................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
.................AAGACAA----------AACAAAACAGA....................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.............AGAxAAAACAC----------AACAAAACA......................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.GAAAAA------AAAGAAAAAAA----------GA.............................................................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25
................................................................................................................ATGTCAACACA---------TTCACAAA--AAA................................	22	1	1.00	0.00	0.00	0.00	1.00
..AAAAA------AAAGAAAAGAA----------AAAAA..........................................................................................................................................	21	26	0.04	0.00	0.00	0.00	0.04
.....AA------AAAGAAAAGAA----------AAAAAAA........................................................................................................................................	20	31	0.03	0.00	0.00	0.00	0.03
...............AGAAAACAG----------AACAAAAGA......................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....AAA------AAAGAAAGAAA----------AACAA..........................................................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25
..AAAAA------AAAGAAAGAAA----------AA.............................................................................................................................................	18	44	0.02	0.00	0.00	0.00	0.02
....AAA------GAAGAAAACAA----------AACT...........................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...AAAA------AAAGACAACAA----------AACA...........................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
.....AA------AAAGACAACAA----------AAAAAA.........................................................................................................................................	19	8	0.13	0.00	0.00	0.00	0.13
...AAAA------CAAGAAAAGAA----------AACA...........................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
...AAAA------ACAGAAAAGAA----------AACA...........................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.....AA------AAAGAAAAGAA----------AAGAAA.........................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..AAAAA------GGAxAAAACAA----------AACAAAA........................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...AAAA------AAAGAAAAGAA----------AAGA...........................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
..AAAAA------AAAAGAAACAA----------AACA...........................................................................................................................................	20	8	0.13	0.00	0.00	0.00	0.13
...AAAA------AAAGAAAAGAA----------AACCAA.........................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
..AAAAA------AAAGAAAAAAA----------AAGAAA.........................................................................................................................................	22	21	0.05	0.00	0.00	0.00	0.05
..AAAAA------AAGGAAAACAT----------AA.............................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
..AAAAA------AAAGAGAAGAA----------AA.............................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
....AAA------AAAGAAAACAC----------AAAAAAA........................................................................................................................................	21	6	0.17	0.00	0.00	0.00	0.17
......A------AAACAAAACAG----------AACAAAA........................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
....AAA------AAAAAAACCAA----------AACA...........................................................................................................................................	18	14	0.07	0.00	0.00	0.00	0.07
.....AA------AAAGAAAAAAC----------AACAAAA........................................................................................................................................	20	7	0.14	0.00	0.00	0.00	0.14
.CGAAAA------AAAGAAAACAA----------A..............................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
....AAA------AAAGAAAAGAA----------AAAA...........................................................................................................................................	18	46	0.02	0.00	0.00	0.00	0.02
.....AA------AAAGAAAACGA----------GACAAA.........................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.....AA------AAAGAAAACAA----------ACAAA..........................................................................................................................................	18	8	0.13	0.00	0.00	0.00	0.13
.....AA------AAAGAAAACAA----------AACCCA.........................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.GAAAAA------AAAGAAAAAAA----------AAA............................................................................................................................................	20	38	0.03	0.00	0.03	0.00	0.00
......A------AAAGAAAACAG----------AAxAAAACA......................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
.GAAAAA------CAAGGAAACAA----------A..............................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
......A------AAAGAAAACAA----------AACGCAAC.......................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
AGGAAAA------AAAGAAAACAA----------A..............................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.....AA------AAAGAAAAGCA----------AACAAAA........................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.............AAAGAAAACAA----------AACAAAGGA......................................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
..AAAAA------AAAGAAAAGAA----------AAAA...........................................................................................................................................	20	31	0.03	0.00	0.00	0.00	0.03
..AAAAA------AAAGAGAAAAA----------AA.............................................................................................................................................	18	45	0.02	0.00	0.02	0.00	0.00
....AAA------CAAGAAAACAA----------AACAGA.........................................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
..AAAAA------AGAAAAAACAA----------AACA...........................................................................................................................................	20	8	0.13	0.00	0.00	0.00	0.13
......A------AAAGAAAACAA----------GAAAAA.........................................................................................................................................	18	5	0.20	0.00	0.00	0.00	0.20
.....AA------AAAGAGAACAA----------AAAAAA.........................................................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25

dp4

AGAAAAG------------------CGTATTCGA----------------------AGT----------------------TCATTAG--------GTTT-C-ATTAG------AAGGACGTGGCGTAGATCCTCGACAG--AAACACTCACACATATCGAAACCGGTTTAGTTAGT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.........................................................................................................TAG------AAGGACGTGGCGAAGATCCTCTAC.......................................	27	1	1.00	0.00	0.00	1.00	0.00

droPer1

AGAAAAC------------------CGTATTCGA----------------------AGT----------------------TCATTAG--------GTTT-C-GTCAG------AAGTACGTGGCGTAGATCCTCGACAG--AAACACTCACACATATCGAAACCGGTTTAGTTAGT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................................................................................GTCAG------AAGTACGGGGTGT..................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

AGAAAAAAGAAAAAA------AAACAT--ATCTA-AAAA-------ACATATACGAAAACTTAGGTCAGCTTCAA-------------A-------------ACCGAACGGAAGCTGAACA-----------------------AAGGCTAAACT------------ATTAGTTAGT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................................TCAA-------------A-------------ACCGAACGGAAGCTGAAC.........................................................	23	1	5.00	0.00	0.00	0.00	5.00
..........................................................ACTTAGGTCAGCTTCAA-------------A-------------AC.........................................................................	20	1	4.00	0.00	0.00	0.00	4.00
...........................................................................................................ACGGAAGCTGAACA-----------------------AAGGCTAAAC.......................	24	1	3.00	0.00	0.00	0.00	3.00
.........................................................................................................GAACGGAAGCTGAACA-----------------------AAGGCTAAAC.......................	26	1	2.00	0.00	0.00	0.00	2.00
........................................................................CAA-------------A-------------ACCGAACGGAAGCTGAACA-----------------------.................................	23	1	2.00	0.00	0.00	0.00	2.00
......................................................................TTCAA-------------A-------------ACCGAACGGAAGCTGAAC.........................................................	24	1	2.00	0.00	0.00	0.00	2.00
AGTAAAAGGAAAAAA------AAAC........................................................................................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
.........................................................................................................GAACGGAAGCTGAACA-----------------------AAG..............................	19	1	2.00	0.00	0.00	0.00	2.00
..AAAAAAGAAAAAA------AAAAA.......................................................................................................................................................	18	37	0.05	0.00	0.05	0.00	0.00
..AAAAGAGAAAAAA------AAAGA.......................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..AAAAAGGAAAAAA------AAAAA.......................................................................................................................................................	18	49	0.02	0.00	0.02	0.00	0.00
.AAAAAAAGAAAAAA------AAAGA.......................................................................................................................................................	19	39	0.03	0.00	0.03	0.00	0.00
..AAAAAGGAAAAAA------AAACC.......................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
..AAAAAAGAAGAAA------AAAGA.......................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.GAAAAAAGAAAAAG------AAAAA.......................................................................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
AAAAAAAGGAAAAAA------AAA.........................................................................................................................................................	18	45	0.02	0.00	0.02	0.00	0.00
AGGAAAAAGAAAAAA------GAA.........................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................................ACGGAAGCTGAACA-----------------------AAGGCT...........................	20	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................AACGGAAGCTGAACA-----------------------AAGGCTAAAC.......................	25	1	1.00	0.00	0.00	0.00	1.00
...AAAAACAAAAAA------AAACAC--A...................................................................................................................................................	19	10	0.10	0.00	0.10	0.00	0.00
.........................................................................................................GAACGGAAGCTGAACA-----------------------AAGGCT...........................	22	1	1.00	0.00	0.00	1.00	0.00
..AAAAAAGAACAAA------AAACAA--....................................................................................................................................................	19	11	0.09	0.00	0.09	0.00	0.00
.AAAAAAAGAAAAAA------AAACA.......................................................................................................................................................	19	42	0.02	0.00	0.02	0.00	0.00
AxAAGAGAGAAAAAA------AAACA.......................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
..AAAAAGGAAAAAC------AAACA.......................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
......................................................................................................ACCGAACGGAAGCTGAAA.........................................................	18	1	1.00	0.00	0.00	0.00	1.00
AGAAAAGAGAAAAAA------AGA.........................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
...AAAAAGAAAAAA------AAAGAG--A...................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..AAAAAAGAAAAAA------AAAGAA--A...................................................................................................................................................	20	27	0.04	0.00	0.04	0.00	0.00
AAAAAAAAGAAAGAA------AAA.........................................................................................................................................................	18	45	0.02	0.00	0.02	0.00	0.00
....AAAAGAAAAAA------AAAAAG--A...................................................................................................................................................	18	47	0.02	0.00	0.02	0.00	0.00
...................................................TACGAAAACTTAGGTCAGCTTC........................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..AAGAAAGAAAGAA------AAACA.......................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
AAAGAAAAGAAAAAA------AAA.........................................................................................................................................................	18	44	0.02	0.00	0.02	0.00	0.00
AGAAAAAATAAAAAA------AAAG........................................................................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
AGAAAAAAGGAAAAA------AGA.........................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..AAAAAAGGAAAAA------AAAAA.......................................................................................................................................................	18	45	0.02	0.00	0.02	0.00	0.00
AGGAAAAACAAAAAA------AAA.........................................................................................................................................................	18	11	0.09	0.00	0.09	0.00	0.00
......................................................GGAAACTTAGGTCAGCTTCAA-------------A-------------ACC........................................................................	25	1	1.00	0.00	0.00	1.00	0.00
...AAAAAGAAAAAA------GAACAA--A...................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
..AAAACAGAAAAAA------AAAAA.......................................................................................................................................................	18	48	0.02	0.00	0.02	0.00	0.00
...........................................................CTTAGGTCAGCTTCAA-------------A-------------ACC........................................................................	20	1	1.00	0.00	0.00	0.00	1.00
......AAAAAAAAA------AAACAG--ATC.................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
....AAGAGAAAAAA------AAACAA--AT..................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
AAAAAAAAGAAAAAA------AAAGA.......................................................................................................................................................	20	34	0.03	0.00	0.03	0.00	0.00
.GAAAAAAGAATAGA------AAAC........................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................A-------------ACCGAACGGAAGCTGAACA-----------------------.................................	20	1	1.00	0.00	0.00	0.00	1.00
...AAAAAGAAAAAA------AAAGAA--....................................................................................................................................................	18	46	0.02	0.00	0.02	0.00	0.00
..AAAAAAGAGAAAA------AAAGA.......................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.......................................................................TCAA-------------A-------------ACCGAACGGAAGCTGAA..........................................................	22	1	1.00	0.00	0.00	1.00	0.00
..AAAAAAAAAAAAA------AAACA.......................................................................................................................................................	18	39	0.03	0.00	0.03	0.00	0.00
.GAAAAAAGAAAACA------AAAT........................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
..AAAAAAGAAAAAA------AAACAA--A...................................................................................................................................................	20	31	0.03	0.00	0.03	0.00	0.00
..AAAAAAGAAAAAA------AAGAA.......................................................................................................................................................	18	43	0.02	0.00	0.02	0.00	0.00
......................................................................TTCxx-------------A-------------ACCGAACGGAAGCTGAAC.........................................................	22	1	1.00	0.00	0.00	0.00	1.00
........................................................................CAA-------------A-------------ACCGAACGGAAGCTGAAC.........................................................	22	1	1.00	0.00	0.00	0.00	1.00
AxAAAAGAGAAAGAA------AAACA.......................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00
...AAAAAGAAAAAA------ACAAAT--A...................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
..AAAACAGAAAAGA------AAACA.......................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
AAAAAAAAGCAAAAA------AAA.........................................................................................................................................................	18	51	0.02	0.00	0.02	0.00	0.00
.AAAAAAAGAAAAAC------AAACA.......................................................................................................................................................	19	6	0.17	0.00	0.17	0.00	0.00
..AAAAAACAAAAAA------AAAGA.......................................................................................................................................................	18	49	0.02	0.00	0.02	0.00	0.00
AAAAAAAAGAAAAGA------AAA.........................................................................................................................................................	18	41	0.02	0.00	0.02	0.00	0.00
AGAAAAAAGAAAAAA------AAA.........................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00

droVir3

CGAGGCGAAAAAGCA------AGCTGA--GCC----CAAAGCTGAGTTCAC--ACAAGT----------------------TTAGTAT--------TTTT-----------------TCTGTTGCTTGTCTCTTTTCCAG--CAGTATTTAATCT------------ATTAGTTAGC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TC-------------------------------------------------------------------------------------------------------------------------------------------------------CA------------ACTAGCTTTC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

AAAGAAGGAAAAACAAGAAAACAA----------CATATTATATATCT--------------------------------------------------------------------------------------------------ATTTATGCA------------GTTAGTTAGT

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

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