dme-mir-4984- 12- and 20-way alignments

dme-mir-4984	chr2L:8141539-8141662 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 8141568-8141589
   star strand at position 8141608-8141632
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:8141524-8141677 -	TTAAAATAGT-----------------------CTCAA--CTTCGCTCGAGGTGTGAAAACC--TTT--------------TGGCCA--GCGAA-------TACGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTCGCCATGTTTT-------------------------------------GC----------------------GGCC----AAGTGCTTTCATT
droSim1	chr2L:7922185-7922338 -	TTAAAATAGT-----------------------CTCCA--CTCCGCTCGAGGTGTGAAAACC--TTT--------------TGGCCA--GCGAA-------TGCGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTCGCCATGTTTT-------------------------------------GC----------------------GGCC----AAGTGCTTTCATT
droSec1	super_3:3638638-3638791 -	TTAAAATAGT-----------------------CTCCA--CTCCGCTCGAGGTGTGAAAACC--TTT--------------TGGCCA--GCGAA-------TACGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTCGCCATGTTTT-------------------------------------GC----------------------GGCC----AAGTGCTTTCATT
droYak2	chr2L:10772572-10772720 -	TTAAAATAGT-----------------------CTCGA--G-----ACGAGGTGTGAAAACC--TTT--------------TGGCCG--GCAAA-------TACGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTTGCCATGTTTT-------------------------------------GC----------------------GGCC----ATGTGCTTTCATT
droEre2	scaffold_4929:17047208-17047355 -	TTAAAATAGT-----------------------CTCTA--C-----TCGAGGTGTGAAAACC--TT---------------TGGCCA--GCAAA-------TACGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTTGCCATGTTTT-------------------------------------GC----------------------TGCC----ATGTGCTTTCATT
droAna3	scaffold_12916:9486383-9486598 -	TTTAAATAGT-----------------------CTCTCGAGGGTCTTCGGGGTGTGAAAACC--TTT----------CGGTTAGCCA--GCCA---GCGA-GACACTTAACTCAC--TTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GGCGAAtTGGgtgGTgTGtgtTGGttTGGgtTGGgtTGtGtTGGGgtTGGTtTGGTTGGTTGGTGC----------------------GACTAAA-TAATGGTTTCATT
dp4	Unknown	TTAAAATAGTTGCAGCGCCGCCGCCGGCGCAT--TGGA--C---ATTGGAGGTGTGAAAACC--AAT--------------------------A-------TTCGC-----------TTC---AGGT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----TGGCAAATGACACGTTTTGGA---------------------------------------------CCTGCAATTTC-----------CAGC----ATTTACTTTCATT
droPer1	super_1:4362183-4362198 +	TTAAAATAGT-----------------------TGCAG--C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180703:2787401-2787579 -	TCTCTCC---------------ACCAACATAATATGGA---------CAAGGTGTTAAGGTCTCTTT--------------TGGATG--GTAGTCAG---TTGCTA-----------GTT---AACT-CAAATCACGTTTCAAGATCGAGGTGAATTCTTTGA-ATACTGTCA-----AGCGAAATGACACGTTT----TGTCTT-------------------------------------AACCCGCACCGGCCGGCCCCCAC-T--TACATAGATATTTTTAGT
droVir3	scaffold_12963:13862249-13862408 +	TTAAAGCGGC-----------------------TTCAA---------CAAGGTGTTAAAATC--GCA-------------AAGGCCGTCACAGC-------CACA---------GTCCAC---AGTC-CGAATCACGTTTTAAGATCGAGGTGAATTCTT-AACACCGCCGCTTGCCCAGCCAAATGGCACGTTTTCAATGGGCT-------------------------------------G--------------G----CAGCAGCC----CCAAGCCCTCAGC
droMoj3	scaffold_6500:5788115-5788289 -	TTACAGCGGC-----------------------TACAA---------CAAGGTGTTAAAAAC--AGAAAAAAGCGAACCAAAGGCCG--GCACACAG---CCACA--CA-----GTCCAC---AGTT-CGAATCACGTTTTAAGATCGAGGTGAATTCTTA-CTACCGACGCTCAGCCAGCCAAATGGCACGTTTGCCATGGCAT--------------------------------------C-------------G--CTCAACAGCT----TTAAG----CCCT
droGri2	scaffold_15126:6028231-6028402 -	TTACACCGACTTCAG--------------------CA---------ACTAGGTGTTAAAGCC--ACC------------AAAGGCCT-TGCAGA-------CACA---------GTTCAC---AGTC-CGAATCACGTTTTATGATCGAGGTGAATTCTTTGGTAGAGCCGCTTACCCAGCCAAATGGCACGTTTGCTAAGCATG-------------------------------------GA----------CAGATCCCCAAGAGCC----CCAAGCTCTAAGC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:8141524-8141677 -	NA	TTAAAATAGTCTC--AA------------------------------------CTTCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT
droSim1	chr2L:7922185-7922338 -	1	TTAAAATAGTCTC--CA------------------------------------CTCCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------G--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT
droSec1	super_3:3638638-3638791 -	2	TTAAAATAGTCTC--CA------------------------------------CTCCGC-----------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTCGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AAGTGCTTTC----------ATT
droYak2	chr2L:10772572-10772720 -	1	TTAAAATAGTCTC--GA------------------------------------G----------------------ACGAGGTGTGAAAACC--------------TTTTGGCCG-GCAAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------ATGTGCTTTC----------ATT
droEre2	scaffold_4929:17047208-17047355 -	1	TTAAAATAGTCTC--TA------------------------------------C----------------------TCGAGGTGTGAAAACC--------------TT-TGGCCA-GCAAAT----------------------------------------------A--C---GCCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCT--------------------------------------------------------------------------------GC-C------------ATGTGCTTTC----------ATT
droEug1	scf7180000409461:136449-136599 -	1	TTAAAATAGTCTC--AA------------------------------------G----------------------TCGGGGTGTGAAAACC--------------TTTCGGCCA-GCAAAT----------------------------------------------A--CTC-GCCTCGT---TG-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----AG-CCAAATGACACGTTTGCCATGTTTT----GCC--------------------------------------------------------------------------------GG-C------------AAATGCTTTC----------ATT
droBia1	scf7180000302408:3185378-3185528 -	1	TTAAAACAGTCCC--AA------------------------------------G----------------------TGGAGGTGTGAAAACC--------------TTTTGGCCA-GCGAAT----------------------------------------------A--GCC-CGTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGCATTTGCT-----GG-CCAAACGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GG-C------------AAATGCTTTC----------ATT
droTak1	scf7180000415287:134548-134699 +	2	TTAAAATAGTCGC--AA------------------------------------G----------------------TCGAGGTGTGAAAACC--------------TTTTGGCCA-GCAAAT----------------------------------------------A--CTC-ACTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCC-----GGTCCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AATAGCTTTC----------ATT
droEle1	scf7180000491338:774218-774368 +	2	TTAAAATAGTCTC--AG------------------------------------G----------------------TCGAGGTGTGAAAACC--------------TTTCGGCCA-GCAAAT----------------------------------------------A--CCC-GCTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GG-CCAGATGACACGTTTGCCATGTTTT----ACG--------------------------------------------------------------------------------GC-C------------AATTGCTTTC----------ATT
droRho1	scf7180000770662:26011-26160 -	1	TTAAAATAGTCTC--AA------------------------------------G----------------------TTGAGGTGTGAAAACC--------------TTTCGGCCA-GCA-AT----------------------------------------------A--CTC-GCTTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----GG-CCAAATGACACGTTTGCCATGTTTT----GCG--------------------------------------------------------------------------------GC-C------------AATTGCTTTC----------ATT
droFic1	scf7180000453925:826752-826904 -	1	TTAAAATAGTCTC--AA----------------------------------TAG----------------------TCGAGGTGTGAAAACC--------------ATTTGGCCA-GCA-GT----------------------------------------------A--CTC-ACTTCGG---GT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGGATTTGCT-----GG-ACAAACGACACGTTTGCCATGTTTT----GCC--------------------------------------------------------------------------------TCTC------------AATTGCTTTC----------GTT
droKik1	scf7180000302468:119229-119407 -	2	TTAAAATAGTCGC--GG------------------------------------T----------------------TAGAGGTGTGAAAACC--------------TTTCGGCCG-GCAAAAAAGAACAAGAAATAAGTCCAAGCTCAAAGAACTCAAGCTGCAGCTCA-GCAG-CTCTCGG---AT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTTGCT-----GG-GCAAACGGCACGTTTGCCATGCTTT------------------------------------------------------------------------------------------------------------------------------
droAna3	scaffold_12916:9486383-9486598 -	2	TTTAAATAGTCTCTCGA------------------------------------GGGTCT-----------------TCGGGGTGTGAAAACC--------------TTTCGGTTA-GCCAGCCAGCGAGACACTT--------------------------------AA--CTC-ACTTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GG-CGAAATGGCACGTCTGACATGGAAT----GGCATGGCATGAGATGGGCATGGTATGGT-TGGTTGGTGCG------------------------------------------AC-T--------AAAT-AATGGTTTC----------ATT
droBip1	scf7180000396580:1551536-1551742 +	1	TTTAAATAGTCTC--GG------------------------------------GGGTCT-----------------TCGGGGTGTGAAAACC--------------TTTCGGCCA-GCCGAG-------ACACTT--------------------------------TA--CTC-ACTTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GG-CGAAATGGCACGTTTGGCATGTCAT----CCCACCGCATGGCAC-GGCATGGCATGGCATGGTTGGTGCG------------------------------------------GC-A--------AAAT-AATGCTTTC----------ATT
dp4	chr4_group3:2877715-2877892 +	2	TTAAAATAGTTGC--AGCCCACAAGTCACATGCCGCCGCCGGCGCATTGGACAT----------------------TGGAGGTGTGAAAACC--------------A-------------AT----------------------------------------------A--TTC-GCTTCAG---GT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----TG-GCAAATGACACGTTTTGGACCT--------GC-------------------------------------------------------------------------AATTTCCAG-C------------ATTTACTTTC----------ATT
droPer1	super_1:4362183-4362198 +	2	TTAAAATAGTTGC--AG------------------------------------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180703:2787401-2787579 -	2	TCTC------------------------------TCCACCAACATAATA--TGG----------------------ACAAGGTGTTAAGGTC------------TCTTTTGGATG-GTAGTC----------------------------------------------A-GTTGCTAGTTAA---CT-CAAATCACGTTTCAAGATCGAGGTGAATTCTTTGA-ATACTGTCA-----AG-CGAAATGACACGTTT----TGTCTTAACCCGCACCGG-------------------------------------------------------------------------CCGG-CCCCCACTTACATAGATATTTTT----------AGT
droVir3	scaffold_12963:13862249-13862454 +	3	TTAAAGCGGCTTC--AA------------------------------------------------------------CAAGGTGTTAAAATC------------G-CAAAGGCCG-TCACAG----------------------------------------------CCACAG-TCCACAG---TC-CGAATCACGTTTTAAGATCGAGGTGAATTCTT-AACACCGCCGCTTGCCCAG-CCAAATGGCACGTTTTCAATGGGCT----GGCA----------------------------------------GCAGCCCCAAGCCCTCAGCCAGCTTCATCTGCAATTGCGAC-G------------ACTTTCTTTCTGGCCCAACGAAC
droMoj3	scaffold_6500:5788118-5788309 -	3	TTGGAATACTTGA---A----------------------------------CA--CTGGTTACAGCGGCTAC---AACAAGGTGTTAAAAACAGAAAAAAGCGAACCAAAGGCCG-GCACAC-----------------------------------------AGC-CACACAG-TCCACAG---TT-CGAATCACGTTTTAAGATCGAGGTGAATTCTTA-CTACCGACGCTCAGCCAG-CCAAATGGCACGTTTGCCATGGCAT-----CG--------------------------------------------------------------------------------CT-C------------AACAGCTTTA----------AGC
droGri2	scaffold_15126:6028218-6028422 -	1	TTTGAATACTTGA---A----------------------------------CA--CTGGTTACACCGACTTCAGCAACTAGGTGTTAAAGCC------------ACCAAAGGCCTTGCAGAC----------------------------------------------A--CAG-TTCACAG---TC-CGAATCACGTTTTATGATCGAGGTGAATTCTTTGGTAGAGCCGCTTACCCAG-CCAAATGGCACGTTTGCTAAGCATG----GAC--------------------------------AGATCCCCAAGAGCCCCAAGCTCTAA----------------------GC-C-------------AGTTCCATC----------ATC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TTAAAATAGT-----------------------CTCAA--CTTCGCTCGAGGTGTGAAAACC--TTT--------------TGGCCA--GCGAA-------TACGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTCGCCATGTTTT-------------------------------------GC----------------------GGCC----AAGTGCTTTCATT

Size

Hit Count

Total Norm

droSim1

TTAAAATAGT-----------------------CTCCA--CTCCGCTCGAGGTGTGAAAACC--TTT--------------TGGCCA--GCGAA-------TGCGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTCGCCATGTTTT-------------------------------------GC----------------------GGCC----AAGTGCTTTCATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.........................................................................................................................................................AATTCTTTGACGTATTCGCT-----G............................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................................................................AATTCTTTGACGTATTCGCT-----GGC..........................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00

droSec1

TTAAAATAGT-----------------------CTCCA--CTCCGCTCGAGGTGTGAAAACC--TTT--------------TGGCCA--GCGAA-------TACGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTCGCCATGTTTT-------------------------------------GC----------------------GGCC----AAGTGCTTTCATT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................................................................................................................AATTCTTTGACGTATTCGCT-----GG...........................................................................................................	22	1	37.00	19.00	9.00	9.00
.........................................................................................................................................................AATTCTTTGACGTATTCGCT-----GGT..........................................................................................................	23	1	5.00	2.00	0.00	3.00
.........................................................................................................................................................AATTCTTTGACGTATTCGCT-----GT...........................................................................................................	22	1	2.00	1.00	0.00	1.00
...................................................................................................................................................GAGGTGAATTCTTGGACC..........................................................................................................................	18	1	1.00	0.00	1.00	0.00
.........................................................................................................................................................AATTCTTTGACGTATTCGCT-----GGAA.........................................................................................................	24	1	1.00	1.00	0.00	0.00

droYak2

TTAAAATAGT-----------------------CTCGA--G-----ACGAGGTGTGAAAACC--TTT--------------TGGCCG--GCAAA-------TACGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTTGCCATGTTTT-------------------------------------GC----------------------GGCC----ATGTGCTTTCATT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................................................................................................TTCAAGTTCGAGGTGAATCCT................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TTAAAATAGT-----------------------CTCTA--C-----TCGAGGTGTGAAAACC--TT---------------TGGCCA--GCAAA-------TACGC-----------CTC---GGAT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTTGCCATGTTTT-------------------------------------GC----------------------TGCC----ATGTGCTTTCATT

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

TTTAAATAGT-----------------------CTCTCGAGGGTCTTCGGGGTGTGAAAACC--TTT----------CGGTTAGCCA--GCCA---GCGA-GACACTTAACTCAC--TTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GGCGAAtTGGgtgGTgTGtgtTGGttTGGgtTGGgtTGtGtTGGGgtTGGTtTGGTTGGTTGGTGC----------------------GACTAAA-TAATGGTTTCATT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.........................................................................................................................................................................................TGGGTGGTGTGTGGTGGGT...................................................................................	19	1	27.00	0.00	27.00	0.00	0.00
.........................................................................................................................................................................................TGGGTGGTGTGTGGTGGG....................................................................................	18	1	26.00	1.00	25.00	0.00	0.00
............................................................................................................................................................................................................................TGGGTGGGTTTGGTTGGT.................................................	18	1	6.00	0.00	6.00	0.00	0.00
............................................................................................................................................................................................................................TGGGTTGGTTTGGTGGGT.................................................	18	1	4.00	0.00	4.00	0.00	0.00
......................................................................................................................................................................................................TTGGGTTGGGTTGGGTTGGG.....................................................................	20	2	2.00	0.00	2.00	0.00	0.00
........................................................................................................................................................................................GTGGGTGGTGTGTGGTGGT....................................................................................	19	1	4.00	0.00	4.00	0.00	0.00
...........................................................................................................................................................................................................TTGGGTTGGGTTGGGTTGGG................................................................	20	2	2.00	0.00	2.00	0.00	0.00
............................................................................................................................................................................................................TGGGTTGGGTTGGGTTGGG................................................................	19	3	0.67	0.00	0.67	0.00	0.00
........................................................................................................................................................................................TTGGGTGGTGGGTGGTGG.....................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
.....................................................................................................................................................................................................................................TTGGTTGGTTGGTGG----------------------GTC..................	18	7	0.29	0.00	0.29	0.00	0.00
....................................................................................................................................................................................................................................TTTGGTTGGTTGGTGG----------------------GT...................	18	7	0.29	0.00	0.29	0.00	0.00
...........................................................................................................................................................................................................TTGGGTTGGGTTGGGTTGGGT...............................................................	21	2	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................................TGGGTTGGGTTGGGTTGGG.....................................................................	19	3	0.67	0.00	0.67	0.00	0.00
......................................................................................................................................................................................................TTGGGTTGGGTTGGGTTGGGT....................................................................	21	2	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................TTTGGTTGGTTGGTGG----------------------GTC..................	19	1	2.00	0.00	2.00	0.00	0.00
...........................................................................................................................................................................CT-----GGCGxATCGGGTGGTGT............................................................................................	18	1	2.00	1.00	1.00	0.00	0.00
...........................................................................................................................................................................CT-----GGxGGATTGGGTGGTGT............................................................................................	18	1	2.00	1.00	1.00	0.00	0.00
..................................................................................................................................................................................................TGGGTTGGGTTGGGTTGGG..........................................................................	19	3	0.67	0.00	0.67	0.00	0.00
.........................................................................................................................................................................................TGGGTGGTGGGTGGTGGT....................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
...........................................................................................................................................................................................................TTGGGTTGGGTTGTGTTGTGGC..............................................................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................TTGGGTTCTGTTGGGATT.............................................................	18	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................................................................................................CT-----AGCGxATTGGGTGGTGT............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................GTGGGTGGTGGGTGTTGGT....................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.....................................................GTGAAAACC--TTT----------CGGTTAGCCA--GCCA---GCG............................................................................................................................................................................................	29	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................................................................................................................GGGGTTGGGTTGGGTTGG.................................................................	18	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................................TTGGGTTCTGTGTGTTG......................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................................TTGGATTGGGTTGGGTTGGG.....................................................................	20	2	0.50	0.00	0.50	0.00	0.00
........................................................................................................................................................................................TTGGGTGGTGxGTGTTGGGT...................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................TGTTGGTTTGGGTTGGGTTCA......................................................................	21	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................................................GGTTTGGGTTGGGTTGGGTTG..................................................................	21	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................TTGGGTTCTGTTGGGGC..............................................................	17	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................................TTGGGTGGTGTGTGGTGGG....................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................TGGGTTGGGTTGGGTCGGG................................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................TTGGGTTGTGTGGGGA...............................................................	16	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................................................GTxTGGTGGxTTGGGTTGGGTT........................................................................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................TTGGGTTCTGxTGGGGTTG............................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................TGGGGGTTGGxTTGGTTGGT.................................................	19	3	0.33	0.00	0.33	0.00	0.00
..............................................................................................................................................................................................TGTGTGxGTTGGGTTGGGT..............................................................................	18	2	0.50	0.00	0.50	0.00	0.00
................................................................................................................................................................................................................TTGGGTTGGGTTTGGGTT.............................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................GTGGGTGGTGTGTGGTGGTT...................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................GTGGGTGGTGTGTGTGGG.....................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................TTGGATTGGGTTGGGTTGGG................................................................	20	2	0.50	0.00	0.50	0.00	0.00
...................................................................................................................................................................................................................................GGTTGGTTGGTTGGTGC----------------------T....................	18	3	0.33	0.00	0.33	0.00	0.00
..............................................................................................................................................................................................................................AGTTGGTTTGGTTCGTTGGT.............................................	20	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................................................................................................................TGTGGTGTGTGTTGGTTGGGGT..............................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................................................GTTGGGCTTGGGTTGGTT....................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................................GTGGGTGTTGGTGTGGGT..............................................................................	18	5	0.20	0.20	0.00	0.00	0.00
.................................................................................................................................................................................................................TGGGTTGGGTTGGGGGTG............................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................TTGGGTTCTGTTGGGAT..............................................................	17	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................................................................TTGGGTTGTGTTGGGAGT.............................................................	18	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................TTTGGTTGGxTGGTTC----------------------GA...................	17	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................................................................GTGGGTTTTGTTGGTTGG..............................................	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................TATCxAGATCGAGGTAAAT...................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................................................GTTGGGTTATxTTGGGGTT.............................................................	18	1	1.00	0.00	0.00	1.00	0.00
............................................................................................................................................................................T-----AGCGxATTGGGTGGTGT............................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................TGGGTGGTGGGTGTTGGGT...................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

dp4

TTAAAATAGTTGCAGCGCCGCCGCCGGCGCAT--TGGA--C---ATTGGAGGTGTGAAAACC--AAT--------------------------A-------TTCGC-----------TTC---AGGT-CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----TGGCAAATGACACGTTTTGGA---------------------------------------------CCTGCAATTTC-----------CAGC----ATTTACTTTCATT

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TTAAAATAGT-----------------------TGCAG--C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TCTCTCC---------------ACCAACATAATATGGA---------CAAGGTGTTAAGGTCTCTTT--------------TGGATG--GTAGTCAG---TTGCTA-----------GTT---AACT-CAAATCACGTTTCAAGATCGAGGTGAATTCTTTGA-ATACTGTCA-----AGCGAAATGACACGTTT----TGTCTT-------------------------------------AACCCGCACCGGCCGGCCCCCAC-T--TACATAGATATTTTTAGT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...................................................GTGTTAAGGTCGCTTT--------------GG............................................................................................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
..................................................GGTGTTAAGGTCGCTTT--------------GG............................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................TCAAGATCAAGCTGAATT..................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................ATACTGTCC-----AGxGAAATGA...................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................CAACATAATCTGGA---------CGAGG...........................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................AGTCAG---TTGCTx-----------GTT---AAAT-CA.............................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00

droVir3

TTAAAGCGGC-----------------------TTCAA---------CAAGGTGTTAAAATC--GCA-------------AAGGCCGTCACAGC-------CACA---------GTCCAC---AGTC-CGAATCACGTTTTAAGATCGAGGTGAATTCTT-AACACCGCCGCTTGCCCAGCCAAATGGCACGTTTTCAATGGGCT-------------------------------------G--------------G----CAGCAGCC----CCAAGCCCTCAGC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...............................................................................................................................................................................................GTATTCGATGGGCT-------------------------------------G--------------G----CA.......................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................................GGCACGTTGTCACTGGGC...................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................CGAATCACGTTTTAAGATCGAG.........................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

TTACAGCGGC-----------------------TACAA---------CAAGGTGTTAAAAAC--AGAAAAAAGCGAACCAAAGGCCG--GCACACAG---CCACA--CA-----GTCCAC---AGTT-CGAATCACGTTTTAAGATCGAGGTGAATTCTTA-CTACCGACGCTCAGCCAGCCAAATGGCACGTTTGCCATGGCAT--------------------------------------C-------------G--CTCAACAGCT----TTAAG----CCCT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......................................................TGAAAAC--AGAAAACAGCGAA..................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droGri2

TTACACCGACTTCAG--------------------CA---------ACTAGGTGTTAAAGCC--ACC------------AAAGGCCT-TGCAGA-------CACA---------GTTCAC---AGTC-CGAATCACGTTTTATGATCGAGGTGAATTCTTTGGTAGAGCCGCTTACCCAGCCAAATGGCACGTTTGCTAAGCATG-------------------------------------GA----------CAGATCCCCAAGAGCC----CCAAGCTCTAAGC

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																None
UNAFold Image																None