dme-mir-4945- 12- and 20-way alignments

dme-mir-4945	chr3R:7267913-7268028 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 7267977-7267997
   star strand at position 7267937-7267958
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:7267898-7268043 -	TTGGTGtTGGTGtTGGTGtTGGTGgTGGTGGTGGTGCCTTCATT-------GTTTTTCTCTTCT----------------------------TTTTGTTGTTTGACTTTTACACTTTTG-A---------------------ACAAC--------------------------------AAGC----------------------------CGAAAGGAAA-AAGCATGAAGGAATGCAAAGTATTCGATAAAAAAT-TATGAAA
droSim1	chr3R:14102257-14102390 +	TTGGTGATGGTGCT------------GGTGGTGGTGCCTTCATT-------GTTTCCCTCTTCT----------------------------TTTTGTTGTTTGACTTTTACACTTTTG-A---------------------ACAAC--------------------------------AAGC----------------------------CGAAAGGAAA-AAGCATGAAGGAATGCAAAGTATTCGATAAAAAAT-TATGAAA
droSec1	super_0:14695532-14695664 +	TTGGTGATGGTGCT------------GGTGGTGGTGCCTTCATT-------GTTTCCCTCTTCT----------------------------TTTTGTTGTTTGACTTTTACACTTGTG-A---------------------AAAAC--------------------------------AAGC----------------------------CGAAAGGAAA-AAGCATGAAGGAATGCA-AGTATTCGATAAAAAAT-TATGAAA
droYak2	chr3R:11301709-11301828 -	TTGGTGG---------------------------TGCCTTCATT-------GTTTTCCTCTTCT----------------------------TTTTGTTGTTTGACTTTTACACTTTTG-A---------------------ACAAC--------------------------------AGGC----------------------------CGAAAGGAAAAAAGCATGAAGGAATGCAAAGCATTCGATAAAAAAT-TATGAAA
droEre2	scaffold_4770:14352366-14352483 +	TTGGTGG---------------------------TGCCTTCATT-------GTTTTCCTCATCT----------------------------TTTTGTTGTTTGACTTTTACACTTTTG-A---------------------ACAAC--------------------------------AAGC----------------------------CGAAAGGAAA--AGCATGAAGGAATGCAAAGCATTTGATAAAAAAT-TATGAAA
droAna3	Unknown	TCGGCAG---------------------------TGCCCCCATT-------GTTTTCTTCTCAT----T-----------------------TTTTCTTGTTTGACTTTTACACTTTTTTA---------------------ACAAC--------------------------------AA------------------------------CAAAAGCAAAGAGACAGGACGGAATGCAAAGTATTCGATATAAAAC-C-GAAAA
dp4	Unknown	TTGGCGGCGACGGC------------GACGGCG-TCTCTTCTCT-------GTCTCTCTCCCTCCCGTTCTCGTTCGCTCCCACAGGACGGCCTCTGTTGTTTGACTTTTGCACTTTTTTT-------------T-------TAAAC--------------------------------AGGCAGTGGGAGTGGGAGTGGGAGTGTGAGCG--AGAAGCAA--AACATAAA-GAATGCAAAGTATTCGATAAAACACACACAAAA
droPer1	super_0:8454463-8454536 -	CTGCTGC-------------------------GGCACCTTGAGC-------GGGCTCCAACTCT----------------------------TTCTGCTGCCTGACCCTAGCTCCACTG-C---------------------TCTGC--------------------------------TGCC----------------------------TGAAAAGCAA--AACATAAA-GAATGCAAAGTATTCGATAAAACACACACAAAA
droWil1	scaffold_181089:4216454-4216565 +	TTGGCAGCA--------------------------GCAGCCATT-------GTCTTAAG-----------------------------------CAGTTGTTTGACTTTTACACTTCTCCC----------------------GCAG--------------------------------CAAC----------------------------AACAAAGCAT--AAAAAGAAAACATGCAAAGTATTGGAAAAACACT-GAAAAAT
droVir3	scaffold_12855:9719553-9719632 -	TTGGTTC--GC-----------------------GCGCGCGCACGGCCATTGTCTTAAG-----------------------------------CAGTTGTTTGACTTTTGCACTTTTTTA---------------------ACAACAACAAAGAAAAGTC--------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6540:24748325-24748394 -	TTCGCGC---------------------------AG-GGCCATT-------GTCTTACG----------------------------------ACAGTTGTTTGACTTTTGCACTTTTTTA-------------A-------GAAAC--------------------------------AAAC----------------------------AAAAAACA----------------------------------------------
droGri2	scaffold_14830:2094020-2094205 -	TTTGGCGC----------------------------CCAGTATT-------GTTTTAAG-----------------------------------CAGTTGTTTGACTCTTGCACTTTTTTCTTCTTTTTTTTTAATAAGCAAACAACAACAAAGCCAAGTCAGCAACCTGTACACAGTC----TGAAGGGGGAAGGGCTGGAGTTTGCTTG--AAAAAGTA--TCTGC-AAAGAATGCAAAGTATTGTATACAAAGTGTGTAGAA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:7267898-7268043 -	NA	TTGGTG---ATGGTGATGGTGATGGTGCTGGTGGTGGTGCC------TTCATTGT-------------------------TTT---------TCTCTTCTT-TT------------TGTTGTTTGACTTTTACACTTTT---------------GAA-CA---------------------------ACA-----A---GCCGAAAGG--------------AAAA-----------------------------------------------AGCA----TGAAGGAATGCAAAGTATTCGATAAAAAAT---TATGAAA
droSim1	chr3R:14102257-14102390 +	2	TTGGTG---ATGG------------TGCTGGTGGTGGTGCC------TTCATTGT-------------------------TTC---------CCTCTTCTT-TT------------TGTTGTTTGACTTTTACACTTTT---------------GAA-CA---------------------------ACA-----A---GCCGAAAGG--------------AAAA-----------------------------------------------AGCA----TGAAGGAATGCAAAGTATTCGATAAAAAAT---TATGAAA
droSec1	super_0:14695532-14695664 +	1	TTGGTG---ATGG------------TGCTGGTGGTGGTGCC------TTCATTGT-------------------------TTC---------CCTCTTCTT-TT------------TGTTGTTTGACTTTTACACTTGT---------------GAA-AA---------------------------ACA-----A---GCCGAAAGG--------------AAAA-----------------------------------------------AGCA----TGAAGGAATGCA-AGTATTCGATAAAAAAT---TATGAAA
droYak2	chr3R:11301709-11301828 -	2	TTGGTG---G---------------------------TGCC------TTCATTGT-------------------------TTT---------CCTCTTCTT-TT------------TGTTGTTTGACTTTTACACTTTT---------------GAA-CA---------------------------ACA-----G---GCCGAAAGG-------------AAAAA-----------------------------------------------AGCA----TGAAGGAATGCAAAGCATTCGATAAAAAAT---TATGAAA
droEre2	scaffold_4770:14352366-14352483 +	1	TTGGTG---G---------------------------TGCC------TTCATTGT-------------------------TTT---------CCTCATCTT-TT------------TGTTGTTTGACTTTTACACTTTT---------------GAA-CA---------------------------ACA-----A---GCCGAAAGG---------------AAA-----------------------------------------------AGCA----TGAAGGAATGCAAAGCATTTGATAAAAAAT---TATGAAA
droEug1	scf7180000409797:893518-893638 -	3	TTGGTG---G---------------------------TGCC------TTCATTGT-------------------------TTT---------CCTCTTCTTTTT------------TGTTGTTTGACTTTTACACTTTT---------------CAA-CA---------------------------ACA-----A---ACCGAAAGA------------GAAAAA-----------------------------------------------AGCA----T-AAGAAATGCAAAGTATTTGAGAAAAAAT---TCTAAAA
droBia1	scf7180000302075:3486816-3486953 +	1	TTGCTG---G---------------------------TGCC------TTCATTGT-------------------------TTT---------TTGCATCTT-TTTTGCCCCCTTTCCCCTGTTTGACTTTTACACTTTT---------------TAA-CA---------------------------ACA-----GAAAGCAGAAAGCCGAGCA---------TAA-----------------------------------------------AGCA----A-AAGAAATGCAAAGTATTCGATAAAAAGT---AATGGAA
droTak1	scf7180000415763:161524-161645 +	1	TTGGTG---G---------------------------TGCC------TTCATTGT-------------------------TTT---------CCTCTTCTT-TC------------TCCTGTTTGACTTTTACACTTTT---------------TAA-CA---------------------------ACA-----A---GCGGAAAGAGA-------G---AAAAA-----------------------------------------------AGCG----A-GGGAAATGCAAAGTATTCGATAAGAAAT---TACAAAA
droEle1	scf7180000491080:2432030-2432155 +	1	TTGGTG---G---------------------------TGCC------TTCATTGT-------------------------TTT---------CCTCTTCCC-TT------------TGTTGTTTGACTTTTACACTTTTT--------------TAA-CA---------------------------ACA-----A---GCAGAAAGC-----ACAAGGC-AGAAA-----------------------------------------------AGCA----T-AAGAAACGCAAAGAAATCGATAAAAAAT---TA-AAAA
droRho1	scf7180000779097:49380-49510 +	1	TTGGTG---G---------------------------TGCC------TTTATTGT-------------------------TTT---------CCTCTTCTT-TT------------TGTTGTTTGACTTTTACACTTTTTT-----------T-TAA-CA---------------------------ACA-----A---ACGGAAAGAGAAGCATAAG---AAGCA-----------------------------------------------AGCG----T-GAGAAATGCAAAGAATTCGATAAAAAAT---TA-AAAT
droFic1	scf7180000453488:581987-582106 +	1	TCGGCG---G---------------------------TGCC------TTCATTGTT------------------------TTT---------CCTCATCCC-TT------------TGTTGTTTGACT-TTACACTTTTTT-------------GAA-CA---------------------------ACA-----G---GCGGAAAGA--------------GAAG-----------------------------------------------AGCA----G-AAGAAATGCAAAGTATTCGATAAAAAAT---TAAGAAA
droKik1	scf7180000302256:756786-756914 -	5	TTGGCG---G---------------------------CGCC------CTCATTGT-------------------------TTT---------CCTCCTCTT-TCT----------GCGTTGTTTGACTTTTACACTTTTT--------------TAA-CA---------------------------ACA-----A---CAAAAAAGCGAAGCA---AGAG---AC-----------------------------------------------AGGG----C-AAGAAATGCAAAGTATTCGATAAAAAAT---TAACAAG
droAna3	scaffold_13340:13702429-13702549 -	2	TCGGCA---G---------------------------TGCC------CCCATTGT-------------------------TTT---------CTTCTCATTTTT------------TCTTGTTTGACTTTTACACTTTTT--------------TAA-CA---------------------------ACA-----A---C--AAAAGC-------AAAGAG---AC-----------------------------------------------AATG----G-ACGGAATGCAAAGTATTCGATATAAAAC---CG-AAAA
droBip1	scf7180000396615:357623-357749 -	2	TTGGCA---G---------------------------TGCC------CCCATTGT-------------------------TTT---------CTTCTCATTTTT------------TCTTGTTTGACTTTTACACTTTTTT-------------CAA-CA---------------------------A-----------AAACAAAGC-----CCAAAGAG-ACAA-----------------------------------------------AGAA----T---GAAATGCAAAGTATTCGATAAAAAAAAGTGAATAAA
dp4	chr3:2000510-2000593 +	2	CTGGTG---GTGGTGGT------------GGTGGTGGT--C------TTGG----TGCTGCTGCTGCAATTCAATTTCGTTTC---------GCTTTTGTT-TCT----------TTTTTGTTTGCCTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	super_6:893248-893436 -	5	TTGGCG---GCGACGGC------------G-------TCTC------TTCTCTGTCTCTCTCCCTCCCGTTCTCGTTCGCTCCCACAGGACGG------CC-TC------------TGTTGTTTGACTTTTGCACTTCTTT---------TTTTAAA-CAGGGAGTGGGAGTGGGAGTGTGAGCGAGACA-----A---ACAGACAGC-------------AGCAA-----------------------------------------------AACA----T-AAAGAATGCAAAGTATTCGATAAAACACA--CACAAAA
droWil1	scaffold_181089:4216454-4216565 +	1	TTGGCA---GCA--------------------------GCA------GCCATTGT-------------------------CTT---------AAGC--------------------AGTTGTTTGACTTTTACACTTCTC--------------CCG-CA---------------------------GCA-----A---CAACAAAGC-----ATAAAA---AG-----------------------------------------------------------AAAACATGCAAAGTATTGGAAAAACACT---GAAAAAT
droVir3	scaffold_12855:9719552-9719632 -	2	TTGGTTCGCG---------------------------CGCGCGCACGGCCATTGT-------------------------CTT---------AA--------GC------------AGTTGTTTGACTTTTGCACTTTTT--------------TAA-CA---------------------------ACA-----A---CA---AAGAAAAG--------------------------------------------------------------------------------------------------T---C-----A
droMoj3	scaffold_6540:24748319-24748394 -	20	TTCGCG---C---------------------------AGG-------GCCATTGT-------------------------CTT---------AC------G-AC------------AGTTGTTTGACTTTTGCACTTTTT--------------TAAGAA---------------------------ACA-----A----------------------------------------------------------------------------------------------------------ACAAAAAAC---AATGAGC
droGri2	scaffold_14830:2094020-2094205 -	1	TTTG-----G---------------------------CGCC----C-AGTATTGT-------------------------TTT---------AAGC--------------------AGTTGTTTGACTCTTGCACTTTTTTCTTCTTTTTTTT-TAA-TA---------------------------AGCAAACAA---CAACAAAGCCAAGTC---A-----G-CAACCTGTACACAGTCTGAAGGGGGAAGGGCTGGAGTTTGCTTGAAAAAGTATCTGC-AAAGAATGCAAAGTATTGTATACAAAGTG--TGTAGAA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TTGGTGtTGGTGtTGGTGtTGGTGgTGGTGGTGGTGCCTTCATT-------GTTTTTCTCTTCT----------------------------TTTTGTTGTTTGACTTTTACACTTTTG-A---------------------ACAAC--------------------------------AAGC----------------------------CGAAAGGAAA-AAGCATGAAGGAATGCAAAGTATTCGATAAAAAAT-TATGAAA

Size

Hit Count

Total Norm

droSim1

TTGGTGATGGTGCT------------GGTGGTGGTGCCTTCATT-------GTTTCCCTCTTCT----------------------------TTTTGTTGTTTGACTTTTACACTTTTG-A---------------------ACAAC--------------------------------AAGC----------------------------CGAAAGGAAA-AAGCATGAAGGAATGCAAAGTATTCGATAAAAAAT-TATGAAA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................TCTTxT----------------------------TTTTGTTGTTTGGC...............................................................................................................................................................	19	1	2.00	0.00	0.00	2.00	0.00
.....................................................................................................................TG-A---------------------ACAAC--------------------------------AAAC----------------------------CGAAAT................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................TTCT----------------------------TTTTATTGTTTGGC...............................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................TTCT----------------------------TTTTGTTGTTGGGC...............................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

TTGGTGATGGTGCT------------GGTGGTGGTGCCTTCATT-------GTTTCCCTCTTCT----------------------------TTTTGTTGTTTGACTTTTACACTTGTG-A---------------------AAAAC--------------------------------AAGC----------------------------CGAAAGGAAA-AAGCATGAAGGAATGCA-AGTATTCGATAAAAAAT-TATGAAA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
TTGGTGGTGGTGGT------------GGTGGTGGTG.....................................................................................................................................................................................................................................	24	2	0.50	0.50	0.00	0.00
.....TATGTTGCT------------GGTGGTGGT......................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
..GGTGGTGGTGGT------------GGTGGTGGT......................................................................................................................................................................................................................................	21	6	0.17	0.00	0.00	0.17
........................................................................................................................A---------------------AAAAC--------------------------------AAGx----------------------------CGAAAGGAA.............................................	18	1	1.00	0.00	1.00	0.00
...GTGGTGGTTCT------------GGTGGTGG.......................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00
......................................................................................................................................................................................................................AAGGAAA-AAGGAGGAAGG................................	18	1	1.00	0.00	0.00	1.00
............................................................................................................................................................................................................................................GCA-CGTATTCGAAAAAAA..........	18	1	1.00	0.00	0.00	1.00
TTTGTGATGGTGGT------------GGTGG..........................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00
....TGTTGGTGAT------------GGTGGTGG.......................................................................................................................................................................................................................................	18	4	0.25	0.00	0.00	0.25
.TGGTGATGGTGGT------------GGTGGTGGG......................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
.......TGGTGCT------------GCTGGTGGAGCC...................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00

droYak2

TTGGTGG---------------------------TGCCTTCATT-------GTTTTCCTCTTCT----------------------------TTTTGTTGTTTGACTTTTACACTTTTG-A---------------------ACAAC--------------------------------AGGC----------------------------CGAAAGGAAAAAAGCATGAAGGAATGCAAAGCATTCGATAAAAAAT-TATGAAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................................................................................TTTG-A---------------------AGAAx--------------------------------AGGC----------------------------CGAAA.................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

TTGGTGG---------------------------TGCCTTCATT-------GTTTTCCTCATCT----------------------------TTTTGTTGTTTGACTTTTACACTTTTG-A---------------------ACAAC--------------------------------AAGC----------------------------CGAAAGGAAA--AGCATGAAGGAATGCAAAGCATTTGATAAAAAAT-TATGAAA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......G---------------------------TGCCTTCATC-------GTTTTCGT..............................................................................................................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00

droAna3

TCGGCAG---------------------------TGCCCCCATT-------GTTTTCTTCTCAT----T-----------------------TTTTCTTGTTTGACTTTTACACTTTTTTA---------------------ACAAC--------------------------------AA------------------------------CAAAAGCAAAGAGACAGGACGGAATGCAAAGTATTCGATATAAAAC-C-GAAAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................................................................................................................................................................AAGAGTCAGGATGGAATG............................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................AAAC--------------------------------AA------------------------------CAAAAGAAAAGA..........................................	18	2	0.50	0.00	0.00	0.00	0.50
..................................................................................................................................................................................................................................AGGACGGAATACAAAGAA.....................	18	1	1.00	0.00	0.00	1.00	0.00

dp4

TTGGCGGCGACGGC------------GACGGCG-TCTCTTCTCT-------GTCTCTCTCCCTCCCGTTCTCGTTCGCTCCCACAGGACGGCCTCTGTTGTTTGACTTTTGCACTTTTTTT-------------T-------TAAAC--------------------------------AGGCAGTGGGAGTGGGAGTGGGAGTGTGAGCG--AGAAGCAA--AACATAAA-GAATGCAAAGTATTCGATAAAACACACACAAAA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................................................................................................................................................................................GAGGGAGTGGGAGTGGGAGG.............................................................	20	1	2.00	2.00	0.00	0.00	0.00
.........................................................................................................................................................................................TGGGAGTGGGAGTGGGAGTGGG..........................................................	22	2	1.00	1.00	0.00	0.00	0.00
...................................................................................................................................................................................TGGGAGTGGGAGTGGGAGTGGG................................................................	22	2	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................TGGGAGTGGGAGTGGGAGTGGGT.........................................................	23	1	2.00	2.00	0.00	0.00	0.00
...........................................................................................................................................................................................GGAGTGGGAGTGGGAGTGGGCG........................................................	22	2	0.50	0.00	0.00	0.50	0.00
........................................................................................................................................................................................GTGGGAGTGGGAGTGGGCGTGGG..........................................................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................TGGGAGTGGGAGTGGGGGTGGGA.........................................................	23	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................................TCTTGCACTTCTTTT-------------T-------TA.........................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................CAGTGGCAGTGGCAGTGGGA...............................................................	20	1	1.00	1.00	0.00	0.00	0.00
..GACGGCGACGGC------------GACGGCG-A......................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................TGGAAGTGGGAGTGGGAGT.............................................................	19	2	0.50	0.50	0.00	0.00	0.00
...................................................................................................................................................................................TGGAAGTGGGAGTGGGAGT...................................................................	19	2	0.50	0.50	0.00	0.00	0.00
........................................................................................................................................................................................GTGGGAGTCGGAGTGGGAGTGGG..........................................................	23	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................................GTGGGAGTGGGAGTGGGAGTGG...........................................................	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................................GGAGTGGGAGTGGGAGTGGGAGTG............................................................	24	2	0.50	0.50	0.00	0.00	0.00
......................................................................................................................................................................................................GCGTGTGTGAGCG--AGAAGCA.............................................	20	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................GGAGTGGGAGTGGGAGTGGGAGTGG...........................................................	25	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................................GTGGGAGTGGGAGTGGGAGT.............................................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................TGGGAGTGGGAGTGGGAGGA............................................................	20	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................C--------------------------------AGGGAGTGGGAGTGGGAGTGGGAGTG............................................................	27	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................A--------------------------------AGGGAGTGGGAGTGGGAGTGGGA...............................................................	24	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................................GTGGGAGTGGGAGTGGGAGTGGT..........................................................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................TGGGAGTCGGAGTGGGAGTGGG..........................................................	22	1	1.00	1.00	0.00	0.00	0.00
.CGACGGCGACGGC------------GACGGC.........................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................GGAGTGGGAGTGGGAGTGGGAGT.............................................................	23	2	0.50	0.50	0.00	0.00	0.00
...........................................................................................................................................................................................GGAGTGGGAGTGGGAGTGGGAGT.......................................................	23	2	0.50	0.50	0.00	0.00	0.00
.....................................................................................................................................................................................GGAGTGGGAGTGGGAGTGGGCG..............................................................	22	2	0.50	0.00	0.00	0.50	0.00
.........................................................................................................................................................................................TGGGAGTGGGAGTGGCAGTGGG..........................................................	22	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................................................................................................................GGAGTGGGAGTGGGAGTGGGAGTG--....................................................	24	2	0.50	0.50	0.00	0.00	0.00

droPer1

CTGCTGC-------------------------GGCACCTTGAGC-------GGGCTCCAACTCT----------------------------TTCTGCTGCCTGACCCTAGCTCCACTG-C---------------------TCTGC--------------------------------TGCC----------------------------TGAAAAGCAA--AACATAAA-GAATGCAAAGTATTCGATAAAACACACACAAAA

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TTGGCAGCA--------------------------GCAGCCATT-------GTCTTAAG-----------------------------------CAGTTGTTTGACTTTTACACTTCTCCC----------------------GCAG--------------------------------CAAC----------------------------AACAAAGCAT--AAAAAGAAAACATGCAAAGTATTGGAAAAACACT-GAAAAAT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
............................................................................................................................................................................................................................................GCAAAGTATTGGAGAACC...........	18	1	4.00	0.00	0.00	0.00	4.00
.....................................................................................................................................................................................................................CAAAACAA--AAAAAGAAAA................................	18	16	0.13	0.00	0.13	0.00	0.00
...........................................................................................................................................................................................................................................TGCAAAGTATTGGAGAACC...........	19	1	2.00	0.00	0.00	0.00	2.00
....................................................................................................................................................................................AAC----------------------------AACAAAGTAA--AAAAA.....................................	18	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................AG--------------------------------CAAC----------------------------AACAAAGxAT--AAAAAT....................................	21	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................AA----------------------------AACAAAGCAA--AAAAAG....................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................................AAAGCAx--AAAAAGAAAGCA..............................	18	2	0.50	0.00	0.50	0.00	0.00
.................................................................................................................................................................................................................................................GTATTGGAAAAACAAT-CA.....	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

TTGGTTC--GC-----------------------GCGCGCGCACGGCCATTGTCTTAAG-----------------------------------CAGTTGTTTGACTTTTGCACTTTTTTA---------------------ACAACAACAAAGAAAAGTC--------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.......................................................TAAG-----------------------------------AAGTTGATTGACTT.............................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

TTCGCGC---------------------------AG-GGCCATT-------GTCTTACG----------------------------------ACAGTTGTTTGACTTTTGCACTTTTTTA-------------A-------GAAAC--------------------------------AAAC----------------------------AAAAAACA----------------------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TTTGGCGC----------------------------CCAGTATT-------GTTTTAAG-----------------------------------CAGTTGTTTGACTCTTGCACTTTTTTCTTCTTTTTTTTTAATAAGCAAACAACAACAAAGCCAAGTCAGCAACCTGTACACAGTC----TGAAGGGGGAAGGGCTGGAGTTTGCTTG--AAAAAGTA--TCTGC-AAAGAATGCAAAGTATTGTATACAAAGTGTGTAGAA

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