dme-mir-4943- 12- and 20-way alignments

dme-mir-4943	chr2L:16528374-16528491 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 16528403-16528425
   star strand at position 16528441-16528462
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:16528359-16528506 -	ATTTTAAACAACTATTT---CGGATCGTTTGAATGACCAATTTTGTCTTTTATTTTCTCTGTG-------TT------TTCAGTTAATG-AAAGATAG-TGAACACAG--------------------------------TGCTAAATGAAAGATAATGAGACCCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG
droSim1	chr2L_random:601476-601603 -	ATTT-------------------ATT-TTTGAATGACCAATTTTGGCTTT---CTTCTCTGTC-------GT------TTCAGTTAATG-AAAAGTAG-TAAACACAG--------------------------------TGCTAAATGAAAGAGAATGAGACCCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG
droSec1	super_7:174891-175018 -	ATTT-------------------ATT-TTTGAATGACCAATTTTGTCTTT---CTTCTCTTTC-------TT------TTCAGTTAATG-AAAAGTAG-TAAACACAG--------------------------------TGCTAAATGAAAGAGAATGAGACCCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG
droYak2	chr2R:4574442-4574584 +	ATTTTATAAAACTATGG---GGGATA-CTTAGATAATTAATTTTGTCATT---GTTCTTTGTC--------T------TTCAGTTAATG-AAAAGTAG-TAAACACAG--------------------------------TGCTAAATGAAAGAGAATGAGACGCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG
droEre2	scaffold_4845:19592406-19592554 -	ATTTTATGCAACTATTGTGT-GTATC-TTTAAATGACTAATTTTGTCATT---CTTCTCTGTTTTT----TT------TTCAGTTAATG-AATAGTAG-CAAACACAG--------------------------------TGCTAAATGAAAGAGAATGAGACGCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG
droAna3	scaffold_12916:16031637-16031788 +	tTGTTTt--------ttT---GtTTttttttTTtTGTTgttgTttTTtTT---ttTTTtTtTTTTtTTGTCTTCCCATTACAGTTAATGAAAAAGTAATTTAAAAAAT--------------------------------CGCTAAATGAAAGAGAATGAGACCCAGTCGACA-TTTCCCAAGAAGACCATGTTGATTG
dp4	chr4_group3:8251613-8251714 -	TTGTT---------------------------------------------------CCTTTT-----------CTCTTTACAGTTATTTGCCAAGCAG--AAGAAAAG--------------------------------TGCTAAATGAAAGAGAATGAGACACAGTCGACA-GACGAACAGAAGACGATGTTGATTG
droPer1	super_1:9700572-9700673 -	TTGTT---------------------------------------------------CCTTTT-----------CTCTTCACAGTTATTTGCCAAGCAG--AAGAAAAG--------------------------------TGCTAAATGAAAGAGAATGAGACACAGTCGACA-GACGAACAGAAGACGATGTTGATTG
droWil1	scaffold_180772:4810613-4810735 -	GTTGG----------TATTT-CCATT-TTAAAATTGCTAACATTTACCTT---AATTTCTCTTCTTTTCTTT--------------TTC-AATTCCAG-CTTACGTTG--------------------------------CTATAAATGAGAAAGGATCAA-------------GATCAAACGAAAAGGATGTTGATTG
droVir3	scaffold_12963:12964466-12964493 +	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAAAGCCAGGTGATAAAATGTTGATTG
droMoj3	scaffold_6500:7110768-7110869 -	AATTAAC-----TAATA---C-AATT--------------------------------------------------------------------------AAATGAATTACTAAATTGAAGCTATTTCCTTCGATTCCAGTG--------------TTGCGAGCTTATCAACAAAGATCAGTTAATAAAATGTTGATTG
droGri2	Unknown	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:16528359-16528506 -	NA	ATTTTAA------ACAACTAT-----------------------------T-T--------------------CGGATCGTTTGAATG-AC------------------------------------------------------------------CAATTTTGTC---------------------------------------------------------------TTTT-A--TTTTCTC---------------------------------------T-----GTGTTT-------------TCAGTTAA-TG-AAAGAT-AG-TGAACACAGTGCTAAATGAAAGATAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droSim1	chr2L_random:601476-601603 -	6	ATTTAT------------------------TT-------------------------------------------------TTGAATG-AC------------------------------------------------------------------CAATTTTGGC--------------------------------------------------------------------T-TTCTTCTC---------------------------------------T-----GTCGTT-------------TCAGTTAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droSec1	super_7:174891-175018 -	6	ATTTAT------------------------TT-------------------------------------------------TTGAATG-AC------------------------------------------------------------------CAATTTTGTC--------------------------------------------------------------------T-TTCTTCTC---------------------------------------T-----TTCTTT-------------TCAGTTAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droYak2	chr2R:4574442-4574584 +	1	ATTTTAT------AAAACTAT-----------------------------G-G--------------------GGGATAC-TTAGATA-AT------------------------------------------------------------------TAATTTTGTC--------------------------------------------------------------------A-TTGTTCTT---------------------------------------T-----GTC-TT-------------TCAGTTAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droEre2	scaffold_4845:19592406-19592554 -	3	ATTTTAT------GCAACTATTGTGTGTATCT-------------------------------------------------TTAAATG-AC------------------------------------------------------------------TAATTTTGTC--------------------------------------------------------------------A-TTCTTCTC---------------------------------------T--GTTTTTTTT-------------TCAGTTAA-TG-AATAGT-AG-CAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droEug1	scf7180000408961:97346-97507 -	4	ATATCTA------AAAA---------------------------------------------------------------------TG-ACTAA--GATT------------CTCT----TC----AAC--------------------------------------------------------------------AACATGAC----------AAATT--AACTTATA-----A--TCTTCTC--T-------------------------TTGCTTG-TT-T-----TTCTTT-------------TTAGTAAA-TG-AAAAAT-AG-TAAACAAAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droBia1	scf7180000301468:656432-656584 -	3	TGTGAAA------GTAGTTAG-----------------------------------------------------------------------------TTATAGTTTAAAATATGG----AG---------------------------------------------------------------------------------------------ATATTAAATGAAATCCCTT----ACTTTCT---------------------------------------T-----ATCGTT-------------TCAGTTGA-TG-AAAAGT-AG-TGAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droTak1	scf7180000415914:214815-214954 -	4	ACTCTAC------CTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAAAGTGTC----------AAATT--GACTAATCGTCTTG-TTCTTTCT---------------------------------------T-----ATCATT-------------TTAGTAAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droEle1	scf7180000490579:831701-831934 +	1	ATGTTGCTTCTATAAAACTAT-----------------------------TAA--------------------AAAATAA-TTA------------------------AAATCTG-AAGTTCCCGAAAA---GTGTTTATTAACACTTTTATATTAATTA-GTTAAA------TACAAACTAAGTTTAT-TTCATGAAAGGTG------------ACAATTTTTCAAATCTCCAT-----TTTCC---------------------------------------T-----TTCTTT-------------TTAGTAAA-TG-AAAAGT-AA-TAGACAAAGAGCTAAATGATAGAGAATGAGACCCAGTCAACAGGACC---------CAAAAAGACAATGTTGATTG
droRho1	scf7180000780143:38260-38494 -	2	ATTTTCC------AAAACAAA-GTTCGT--TTTTAAATCTTAAAAATTATTATAAGATATCTTTTAAAATTTTCAAATCAAATAAACG-A---------------------TCTG-ATGGCTC---------------------------------------------------------------------CATAAAAGGTGCAAAATTGAAAAATATTTTTTCTAATCCCCTGT-TTTCTGTT---------------------------------------T-----TTCTTT-------------TTAGTAAA-TG-AAAAGT-AA-TTCACCAAGTGCTAAATGATAGAGAATGAGACCCAGTCGACAGGACC---------CAAAAAGACAATGTTGATTG
droFic1	scf7180000454078:456928-457118 -	5	AATATAA------TAAA-----------------------------------T--------------------GTGACCATTAAAAAGTAC------------------------------------------------------------------CACTTATGTCTTTAAATT-----GATA-----T---------------------------------------T----AAA----TA-TTTTTGACAAAACTATAACTACAATATACTATCTCGTTTAT-----CTCTTT-------------TTAGTAAA-TG-AAAAGT-AA-TATACAAAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------TAAGAAGACGATGTTGATTG
droKik1	scf7180000302382:320881-321046 -	7	CTTCTTG------ATAATTGC-----------------------------TGG--------------------GAAATTT-TTA------------------------AATTTTGT----TT----AAC----------------------------TAAATTTAT------------------------T------------------------A--------CTTATTCCTT-----------------------------------------AATTT-TT-TTCTTATTTTTT-------------ACAGTAAA-TG-AAAAGT-AG-TACACGCAGTGCTCAATGAATGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droAna3	scaffold_12916:16031637-16031788 +	2	ATGTTTA------AA-----------------------------------------------------------------------TG-ATTAAAAAATT------------ATGT----TC----AACTAATTAT---------------------TA----------------------------------------------------------------------------AT----TT-ATAT-------------------------TTTATTG-TC-T----TCCCATT-------------ACAGTTAA-TGAAAAAGT-AATTTAAAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCC---------CAAGAAGACCATGTTGATTG
droBip1	scf7180000396717:268070-268207 +	3	ATTTTAA------AATA------------------------------------------------------------------------------------------------TTT----TT----AAT--------------------------------------------TT-----AAAA-----T---------------------------------------T----AAT----TA-TTTT-------------------------TTTATCA-TT-T----TCTCATT-------------ACAGTTGA-TG-AAAAGT-AG-TTATAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCC---------CAAGAAGACCATGTTGATTG
dp4	chr4_group3:8251613-8251715 -	3	TTTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------CC-TT-T----TCTCTTT-------------ACAGTTATTTG-CCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGA---------ACAGAAGACGATGTTGATTG
droPer1	super_1:9700572-9700674 -	1	TTTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------CC-TT-T----TCTCTTC-------------ACAGTTATTTG-CCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGA---------ACAGAAGACGATGTTGATTG
droWil1	scaffold_180772:4810613-4810759 -	7	AAGTTTA------CCAATTAA-----------------------------TAG--------------------CAAATTG-TTG------------------------GTATTT------CC-------------------------------------ATTTTAAA-----ATT-----GCT-------A------------------------ACATTTA--------CCTTAAT----TT-CTCT-------------------------TCTT-------T-----TC---------------------TTTT-TC-AATTCC-AG-CTTACGTTGCTATAAATGAGAAAGGATCAAGAT------------CA---------AACGAAAAGGATGTTGATTG
droVir3	scaffold_13052:1601321-1601473 -	20	ATATTGC------GCAACCAT-----------------------------T-C--------------------TGG----------------------TC-------------CG-AATTTCATTGAGT-------------------------CAGTCATTTTGGG------TAACTCTTGAGT--------------------------------------------------------TT-ATTT-------------------------CTTA-------A--TT-GTC-TTTCGCTGAAATTGTGCAATAAA-TA-----AC-AA-TT---------------------TTACCATCAGCATTAGCCAGCACA---------CACACGCACGCTATCGGTTT
droMoj3	scaffold_6500:21042727-21042874 -	20	AATTATA------ATT---G---AACACTTG-------------------A-T--------------------GCGATT----------GC------------------------------------------------------------------CAAATTTTTG--------------------------------------------------------------------A-TTTTTGGT---------------------------------------T--C-TATTTTT-------------AGAGTTAC-AG-CTAA----A-TGAAAACTATACCAATTATAAAATCAAAAGGGCTACACAAGAACATTTATGATTTCAAAGAAAAGTGTTTCATTTG
droGri2	scaffold_14822:853797-853916 -	12	GCATGAT------GA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTGTGGTCTCT-ATTCTATA---------------------------------------T-----GCTGGT-------------TGAGTTTG-TG-AATGGTCAG-TTGCCGTGGCGAAAGATAAAAGACAA--GGAACAGGTTGGATTGACC---------AAAGAGAAATATGATCATAG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ATTTTAAACAACTATTT---CGGATCGTTTGAATGACCAATTTTGTCTTTTATTTTCTCTGTG-------TT------TTCAGTTAATG-AAAGATAG-TGAACACAG--------------------------------TGCTAAATGAAAGATAATGAGACCCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG

Size

Hit Count

Total Norm

droSim1

ATTT-------------------ATT-TTTGAATGACCAATTTTGGCTTT---CTTCTCTGTC-------GT------TTCAGTTAATG-AAAAGTAG-TAAACACAG--------------------------------TGCTAAATGAAAGAGAATGAGACCCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................................................................................................................................AAATGAAAGATAATGAGACC...................................	20	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................GAGACCCAGTCGACA-GGACCCAAG................	24	1	1.00	0.00	0.00	0.00	1.00
ATTT-------------------ATT-TTTTATTGACCA................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................TGAGACCCAGTCGACA-GGACCC...................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................GAGACCCAGTCGACA-GGACC....................	20	1	1.00	0.00	0.00	0.00	1.00

droSec1

ATTT-------------------ATT-TTTGAATGACCAATTTTGTCTTT---CTTCTCTTTC-------TT------TTCAGTTAATG-AAAAGTAG-TAAACACAG--------------------------------TGCTAAATGAAAGAGAATGAGACCCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................................................................................................................................GACA-GGACCCAAGAAGACGATGTTGA...	26	1	1.00	1.00	0.00	0.00
....................................................................................................................................................................................ACGAAGACGATGTTGATGG	19	1	1.00	0.00	1.00	0.00
...............................................................................................................................................................................GAxCTAAGAAGACGATGTT.....	18	1	1.00	0.00	1.00	0.00
.............................................................................................AGTAG-TAAACACAG--------------------------------TGCTAAATGAAAG..............................................	27	1	1.00	0.00	0.00	1.00
.................................................................................CGTTAATG-AAAAGTAG-TAAACACAG--------------------------------T..........................................................	26	1	1.00	1.00	0.00	0.00
.............................................................................................................................................................TGAGACCCAGTCGACA-GGA......................	19	1	1.00	0.00	1.00	0.00

droYak2

ATTTTATAAAACTATGG---GGGATA-CTTAGATAATTAATTTTGTCATT---GTTCTTTGTC--------T------TTCAGTTAATG-AAAAGTAG-TAAACACAG--------------------------------TGCTAAATGAAAGAGAATGAGACGCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................................................................................................................ACCCAAGAAGACGATGTTG....	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................TA--------T------TTGAGTTAATG-AAAAG........................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................GGACCCAAGAAGACGATGT......	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................GACA-GGACCCAAGAAGACGATGTTGA...	26	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................CGACA-GGACCCAAGAAGACGATGTTG....	26	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................GAGACGCAGTCGACA-GGACC....................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................TGAGACGCAGTCGACA-GGACCC...................	22	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

ATTTTATGCAACTATTGTGT-GTATC-TTTAAATGACTAATTTTGTCATT---CTTCTCTGTTTTT----TT------TTCAGTTAATG-AATAGTAG-CAAACACAG--------------------------------TGCTAAATGAAAGAGAATGAGACGCAGTCGACA-GGACCCAAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...........................................................................................ATAGTAG-CAAACACAG--------------------------------TGCT.......................................................	20	1	1.00	1.00	0.00	0.00	0.00
...........................TTTAAATGACxAACTTTGT.........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................GAxCTAAGAAGACGATGTT.....	18	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................................ACCCAAGAAGACGATGTTT....	19	1	1.00	1.00	0.00	0.00	0.00

droAna3

tTGTTTt--------ttT---GtTTttttttTTtTGTTgttgTttTTtTT---ttTTTtTtTTTTtTTGTCTTCCCATTACAGTTAATGAAAAAGTAATTTAAAAAAT--------------------------------CGCTAAATGAAAGAGAATGAGACCCAGTCGACA-TTTCCCAAGAAGACCATGTTGATTG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..........................................TTTTTTTT---TTTTTTTTTTT.......................................................................................................................................	19	32	0.13	0.00	0.13	0.00	0.00
..............................................TTTT---TTTTTTTTTTTTTTT...................................................................................................................................	19	32	0.13	0.00	0.13	0.00	0.00
...........................................TTTTTTT---TTTTTTTTTTTT......................................................................................................................................	19	32	0.13	0.00	0.13	0.00	0.00
.............................................TTTTT---TTTTTTTTTTTTTT....................................................................................................................................	19	32	0.13	0.00	0.13	0.00	0.00
............................................TTTTTT---TTTTTTTTTTTTT.....................................................................................................................................	19	32	0.13	0.00	0.13	0.00	0.00
.........................................ATTTTTTTT---TTTTTTTTT.........................................................................................................................................	18	47	0.04	0.00	0.04	0.00	0.00
..........................................ATTTTTTT---TTTTTTTTTT........................................................................................................................................	18	47	0.04	0.00	0.04	0.00	0.00
..............................................ATTT---TTTTTTTTTTTTTT....................................................................................................................................	18	47	0.04	0.00	0.04	0.00	0.00
...........................................ATTTTTT---TTTTTTTTTTT.......................................................................................................................................	18	47	0.04	0.00	0.04	0.00	0.00
...............................................ATT---TTTTTTTTTTTTTTT...................................................................................................................................	18	47	0.04	0.00	0.04	0.00	0.00
............................................ATTTTT---TTTTTTTTTTTT......................................................................................................................................	18	47	0.04	0.00	0.04	0.00	0.00
.............................................ATTTT---TTTTTTTTTTTTT.....................................................................................................................................	18	47	0.04	0.00	0.04	0.00	0.00
.........................................................................................................................................................AGAATGAGACCCAGTCGACA-TT.......................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................GTTATTTTT---CTTTTTTTT.........................................................................................................................................	18	5	0.20	0.00	0.00	0.20	0.00
...TTCT--------TTT---GTTTTTTTTTTTTT....................................................................................................................................................................	21	33	0.03	0.00	0.00	0.00	0.03
...........................................ATTTTTT---TTTTTTTTTTTT......................................................................................................................................	19	40	0.03	0.00	0.03	0.00	0.00
.......................................TTTTTTCTTTT---TTTTTTTTTTTT......................................................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
..........................................TTCTTTTG---TTTTTTTTTTTTT.....................................................................................................................................	21	33	0.03	0.00	0.00	0.00	0.03
.........................................GATTTTTTT---TTTTTTTTTTG.......................................................................................................................................	20	10	0.10	0.00	0.00	0.10	0.00
............................................TTCTTT---TGTTTTTTTTTTTTT...................................................................................................................................	21	33	0.03	0.00	0.00	0.00	0.03
............................................TTTTTT---TATTTCTTTTTTTTT...................................................................................................................................	21	25	0.04	0.00	0.00	0.00	0.04
..........................................CTTTTTTT---TTTTTTTTTT........................................................................................................................................	18	45	0.02	0.00	0.00	0.02	0.00
.......................................................................................................AAAAT--------------------------------xGCTAAAAGAAAGA.............................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................TTTATGTTATTGTTTTTT.......................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
............................................CTTTTT---TTTTTTTTTTTT......................................................................................................................................	18	45	0.02	0.00	0.00	0.02	0.00
............................................TTTTTT---TTTTTTTCTTTTT.....................................................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
........................................................................................................................................................GAGAATGAGACCCAGTCGAC...........................	20	1	1.00	1.00	0.00	0.00	0.00
......................................GTTATTTTTCTT---TTTTTT............................................................................................................................................	18	5	0.20	0.00	0.00	0.20	0.00
..............................TTCTTGTTGTTGTTGTTTTT---TT................................................................................................................................................	22	2	0.50	0.00	0.00	0.50	0.00
............................TTTGTGTGTTGTTGTTTT.........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................TTTTGxTGTAGTTTTTTTT---..................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
..........................................TTTTTTTT---TTTTTCTTTTT.......................................................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
..........................................TTTTTTTA---TTTCTTTTTTTTT.....................................................................................................................................	21	25	0.04	0.00	0.00	0.00	0.04
..............................................CTTT---TTTTTTTTTTTTTT....................................................................................................................................	18	45	0.02	0.00	0.00	0.02	0.00
............................................ATTTTT---TTTTTTTTTTTTT.....................................................................................................................................	19	40	0.03	0.00	0.03	0.00	0.00
..........................................ATTTTTTG---TTTTTTTTTTTTTTT...................................................................................................................................	23	22	0.05	0.00	0.00	0.00	0.05
..............................................GATT---TTTTTTTTTTTTTTTG..................................................................................................................................	20	10	0.10	0.00	0.00	0.10	0.00
...............................................................................................................................................TAAAAGAAAGAGAAAGAGA.....................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................................ATTTTTTT---TTTTTTTTTTT.......................................................................................................................................	19	40	0.03	0.00	0.03	0.00	0.00
.............................................ATTTT---TTTTTTTTTTTTTT....................................................................................................................................	19	40	0.03	0.00	0.03	0.00	0.00
...............................................CTT---TTTTTTTTTTTTTTT...................................................................................................................................	18	45	0.02	0.00	0.00	0.02	0.00
............................................TTTGTG---TTTTTTTTTTTTTTTG..................................................................................................................................	22	8	0.13	0.13	0.00	0.00	0.00
..............................................ATTT---TTTTTTTTTTTTTTT...................................................................................................................................	19	40	0.03	0.00	0.03	0.00	0.00
...........................................CTTTTTT---TTTTTTTTTTT.......................................................................................................................................	18	45	0.02	0.00	0.00	0.02	0.00
...........................................TTTTTTC---TTTTTTTTTTTTTTTT..................................................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
...........................TTCTTGTTGTTGTTGTTTTTTT......................................................................................................................................................	22	2	0.50	0.00	0.00	0.50	0.00
.........................................TTTTTTCTT---TTTTTTTTTTTTTT....................................................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
......................TTTTTTTTTTTTTGGGGT...............................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................TTTTTT---CTTTTTTTTTTTTTTTT.................................................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
...TTTT--------TTT---ATTTCTTTTTTTTT....................................................................................................................................................................	21	25	0.04	0.00	0.00	0.00	0.04
..........................................TTTTTTCT---TTTTTTTTTTTTTTT...................................................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
...............TTT---GGTTTTGTTTTTTTG...................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
...ATTT--------TTT---GTTTTTTTTTTTTTTT..................................................................................................................................................................	23	22	0.05	0.00	0.00	0.00	0.05
.............................................CTTTT---TTTTTTTTTTTTT.....................................................................................................................................	18	45	0.02	0.00	0.00	0.02	0.00
......................................GTTGTTGTTGTT---TTTTTTTTTTT.......................................................................................................................................	23	3	0.33	0.00	0.00	0.00	0.33
....TTT--------TTT---CTTTTTTTTTTTTTTTT.................................................................................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
.......................................TTCTTTTGTTT---TTTTTTTTTT........................................................................................................................................	21	33	0.03	0.00	0.00	0.00	0.03
...........................................TTCTTTT---GTTTTTTTTTTTTT....................................................................................................................................	21	33	0.03	0.00	0.00	0.00	0.03
.........................................................................................................................................................................GACA-TTTCCCAAGAAGACC..........	19	1	1.00	0.00	0.00	0.00	1.00
...........................................TTTTTTT---TTTTTTCTTTTT......................................................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
........................................TTTTTTCTTT---TTTTTTTTTTTTT.....................................................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
ATGTATT--------TTT---GTTTTTTTTT........................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
..............................................TTTT---TTTTTTTTTCTTTTT...................................................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
..................................................................................................................................................ATGCAAGAGAATGTGAC....................................	17	1	1.00	0.00	0.00	1.00	0.00
.........................................ATTTTTTGT---TTTTTTTTTTTTTT....................................................................................................................................	23	22	0.05	0.00	0.00	0.00	0.05
.........................................CTTTTTTTT---TTTTTTTTT.........................................................................................................................................	18	45	0.02	0.00	0.00	0.02	0.00
...........................................TTTTTTT---TGTTTTTTTTTTTTTTTCT...............................................................................................................................	26	8	0.13	0.00	0.00	0.00	0.13
...........................................TTTTTTT---ATTTCTTTTTTTTT....................................................................................................................................	21	25	0.04	0.00	0.00	0.00	0.04
.............................................TTTTT---TTTTTTTTCTTTTT....................................................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
.........................................ATTTTTTTT---TTTTTTTTTT........................................................................................................................................	19	40	0.03	0.00	0.03	0.00	0.00
...............................GTTTGTTGCTGTTTTTTTT---TTT...............................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
................................GTTGTTGTTGTTTTTTTT---TTTTT.............................................................................................................................................	23	3	0.33	0.00	0.00	0.00	0.33
...................................GTTGTTGTTGTTTTT---TTTTTTTT..........................................................................................................................................	23	3	0.33	0.00	0.00	0.00	0.33
.................................TTCTTGTGGTTTTTTTT---TTTTTTT...........................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...........................................TTTTTTT---TTTTTTTTTTTTTTT...................................................................................................................................	22	56	0.02	0.00	0.02	0.00	0.00

dp4

TTGTT---------------------------------------------------CCTTTT-----------CTCTTTACAGTTATTTGCCAAGCAG--AAGAAAAG--------------------------------TGCTAAATGAAAGAGAATGAGACACAGTCGACA-GACGAACAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..............................................................................................................................................................GAGACACAGTCGACA-GAC......................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................GACGACx-GACGAACAGAAGA............	19	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................CGACA-GACGAACAGAAGACGAT........	22	1	1.00	1.00	0.00	0.00	0.00

droPer1

TTGTT---------------------------------------------------CCTTTT-----------CTCTTCACAGTTATTTGCCAAGCAG--AAGAAAAG--------------------------------TGCTAAATGAAAGAGAATGAGACACAGTCGACA-GACGAACAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................................................................................................................................GAGACACAGTCGACA-GACGA....................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
...................................................................................................................................................................................ACAGAAGATGATGTTGAGT.	19	1	2.00	2.00	0.00	0.00	0.00	0.00
........................................................................................................AAAG--------------------------------TGCTAAATGAAAGAGAAT.........................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................................................................................................................................CAGATGGCGATGTTGATT.	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

GTTGG----------TATTT-CCATT-TTAAAATTGCTAACATTTACCTT---AATTTCTCTTCTTTTCTTT--------------TTC-AATTCCAG-CTTACGTTG--------------------------------CTATAAATGAGAAAGGATCAA-------------GATCAAACGAAAAGGATGTTGATTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
......................CTTT-TTAAAATTGCAAAC..............................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
............................................................................................................................................ATTTAAATGAGAAAGGAT.........................................	18	1	2.00	0.00	2.00	0.00	0.00
........................TT-TTAAAATTGCAAACAAT...........................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................AAACGAAAAGGATGTTGATTG	21	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................GGTTCAA-------------GATCAAAAGAAA.............	19	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................GTTG--------------------------------CTATAAATGAGAAAGGATCAA-------------GAT......................	28	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................AATGAGAAAGGATCAA-------------GAT......................	19	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................TCAA-------------GxTCAAACGAAAAGA..........	18	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................ATAAATGAGAAAGGATCAA-------------.........................	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAAAGCCAGGTGATAAAATGTTGATTG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

AATTAAC-----TAATA---C-AATT--------------------------------------------------------------------------AAATGAATTACTAAATTGAAGCTATTTCCTTCGATTCCAGTG--------------TTGCGAGCTTATCAACAAAGATCAGTTAATAAAATGTTGATTG

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

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

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

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