dme-mir-4961- 12- and 20-way alignments

dme-mir-4961	chrX:1267655-1267788 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 1267719-1267741
   star strand at position 1267685-1267706
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:1267640-1267803 +	AGAT-----------ATTACCCAGAAGCGATATC-CAATAGTAGCCAACTCTCTCGCT--CTCT----------ATGTGTATGTATGT----------------------------A--------------TC----TTGCTATCC--ATATATGTATATCCATATCAGAGAG----CCAGGATTGGTTGAGACCATACGA------TATA--------------------------ACCCGAAACCACACTGGCC-AGGAATAGCAAATCCA
droSim1	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec1	super_10:1091085-1091248 +	AGAT-----------ATTACCCAGAAGCAATATC-CAATAGTAGCCAACTCTCTCGCT--CTCT----------ATGTGAATGTATGT----------------------------A--------------TC----TTGCTATCC--ATTTATGTATATCCATATCAGAGAG----CCAGGATTGGTTGAGACCATACGA------TATA--------------------------ACCCGAAACCATACTGGCC-AGGAATAGCAAATCCA
droYak2	chrX:1175521-1175702 +	AGAT-----------ATAACCGAGAAGCAATACC-CAATAGTAGCCAACTCTCTCGCTCTCTCTGCGTCTCTCTATGTGTATGTATGT----------------------------A--------------TT----TCGCTATCC--ATATATGTATATCCATGTCAGAGAG----CCAGGATCGGTTGAGACCATACTATATCTATATA--------------------------ACCCGAAACCATACTGGCC-AGGAATAGCAAATCCA
droEre2	scaffold_4644:1251466-1251631 +	AGAT-----------ATAACCCAAAAGAAATACC-GAATAGTAGCCAACTCTCTCGCTCTCTCT----------ATGTGTATGTATGT----------------------------A--------------TT----TCGTTATCC--ATATATGTATATCCATGTCAGAGAG----CCAGGATCGGTTGAGACCATACTA------TATA--------------------------ACCCAAAACCATACTGGCC-AGGAATAGCAAGTCCA
droAna3	scaffold_13117:1856374-1856503 -	------------------------------------------------ctctctctct--ctct----------gtgt--------------ctctctAAATGCATGTATGTATGTG--------------TT----GTATTATCCGTATATATGTATATCCATGTTAGAGAG----CCAGGACGGGTTGAGATT------------------------------------------GCCCAAGA----ACTGGCCTAGGAATAGCAAAT-CA
dp4	Unknown	AAACTGAATCTAAATCATCCCCCT-CGTAATATCCCGGAAATAGCCCCCTCTATCTCTCTCTCT----------CTTTGACTCTGTGCGTCTCTCTCTACCTAGATGTATGTATGTGTTCGTACAGACAGACACACAGAAACACA--CA----------------------------------------------------AATGTATATATTCACACACACTGATTGATCGG-----------------------------TTGAAGATCGG
droPer1	Unknown	AAACTGAATCTAAATCATCCCCCT-CGTAATATCCCGGAAATAGCCCCCTCTATCTCTCTCTCT----------CTTTGACTCTGTGCGTCTCTCTCTACCTAGATGTATGTATGTGTTCGTACAGACAGACACACAGAAACACA--CA----------------------------------------------------AATGTATATATTCACACACACTGATTGATCGG-----------------------------TTGAAGATCGG
droWil1	scaffold_181150:418743-418839 +	CACC-----------AAAACCA-------ACACA-CAA-AATGAAGAACTCTCTATC-ataaat------------------------------------------atatatatatatatgtatcaatattct----gtattatat--atacatatatatatatatTAAAAAT----C-----------------------------------------------------------------------------------------------
droVir3	scaffold_13042:2614938-2615001 -	-------------------------------------------------------------TTt----------atatatatatatat----------------------------a--------------ta----tatatatat--attaatatatatTTTTAACAAGAAA----CTGAACTCGA--------------------------------------------------------------------------------------
droMoj3	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	-------------------------------------------------------------tat----------atgtatacatatat----------------------------a--------------ta----tatatatat--atatatatatatatatGTCAGCCCACCCACGAAATTTATTTGTGAGCCAAGCA------AAA-GAGACGCGGGCTGAATTTTCGGTTACACGCAA------------A-GAAAAACGAAAATCGA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:1267640-1267803 +	NA	AGATAT-TA----CCCAGA----AGCGA---------TATCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCT------------ATG----------------------------------------TGTATGTATGTAT--CTTGC----------------------------TATCCAT--ATATGTATATCCATA---TCAGAGAGCCAGGATT-----------------GGTTGAGACCATACGAT------A----T-AACCCGAAAC---C-------------------------------AC--A----CTGGCC-AGGA----A----TAGCAAATCCA
droSim1	chr3L:16407222-16407379 -	411	AGC----------------------------------------------------GA----------------------------A-ATTTTTCGACATTTCT----------ATTTAAAG---------------TACATATAGACATTACTATATACATACATATAT--ACTAT----------------------------ACCTTAT--------------------------ATACATGAAT-----------------ATTTATATACATATTT---------------------------AATATACGACGTTTACAAGCTAAGTTGGGTATTC--A----TTTTAT-ACGA----A----GCGTGAATCGA
droSec1	super_10:1091085-1091248 +	184	AGATAT-TA----CCCAGA----AGCAA---------TATCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCT------------ATG----------------------------------------TGAATGTATGTAT--CTTGC----------------------------TATCCAT--TTATGTATATCCATA---TCAGAGAGCCAGGATT-----------------GGTTGAGACCATACGAT------A----T-AACCCGAAAC---C-------------------------------AT--A----CTGGCC-AGGA----A----TAGCAAATCCA
droYak2	chrX:1175521-1175702 +	436	AGATAT-AA----CCGAGA----AGCAA---------TACCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCTCTGCGTCTCTCTATG----------------------------------------TGTATGTATGTAT--TTCGC----------------------------TATCCAT--ATATGTATATCCATG---TCAGAGAGCCAGGATC-----------------GGTTGAGACCATACTATATCTATA----T-AACCCGAAAC---C-------------------------------AT--A----CTGGCC-AGGA----A----TAGCAAATCCA
droEre2	scaffold_4644:1251466-1251631 +	6	AGATAT-AA----CCCAAA----AGAAA---------TACCGAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCTCT----------ATG----------------------------------------TGTATGTATGTAT--TTCGT----------------------------TATCCAT--ATATGTATATCCATG---TCAGAGAGCCAGGATC-----------------GGTTGAGACCATACTAT------A----T-AACCCAAAAC---C-------------------------------AT--A----CTGGCC-AGGA----A----TAGCAAGTCCA
droEug1	scf7180000409008:208095-208232 -	487	CT---------------------------------------------------------------------------------------CTCTC--TCTCT------------ATC-------TCTC---------TCTCTCTGTCTGTTCTTATATATATATATATAC--ATTCT-----------------------A-TATATACCAT---------------------------------ATT-----------------TAT--------------------ATATTT-AATT---------ACCAAAAACAAAATACAAAATC---CAAAA------ACAAATGCAAA-ATGA----A----AACAAAATCAA
droBia1	scf7180000302075:3548008-3548156 -	612	TATATAGATACAATGCA------------------------AAAG----TGTTGCCAATTACTTCATTAATGTATGAGGTAGAGAT-GT--------------------------------------------------------------------------------------------------------------------CTGCAT--ATGTGTGGGTGAGTA---TGTGTGAGC------T-----------------TATTAATAACATTTTACTCGTT-C----G-TATTCGTAAC---C-------------------------------GT--A----A--TCC-GTGA----T----ACGTAATTTAT
droTak1	scf7180000415289:447785-447964 +	138	AGATAT-AT----GCCAAAAAAAAGCTT----AAA--AATTGAAC----AATATCAA--------------------------TAT-ATCTCTCGCTCTCT------------ATG----------------------------------------TGAATGTATGTAT--GTTGTAAT-------------------------TGAATAT--ATATGTATATCCATC---TCAGAGAGCCAGGATCGAT---------CGATCGGTTGAGACTATACTAT------A----T-AAACTATA-----T-------------------------------TT--A----CTGGCC-AGGA----A----TAGCGAATC--
droEle1	scf7180000490996:88170-88351 +	231	AAATAG-TCCACATCCAG--------------------ATCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCTCT----------ATG----------------------------------------TGTATGTATGTAT--GTTGT----------------------------AACCCGT--ATATGTATATCCATG---TCAGAGACCCAGGATT-----------------GGTTAAGACCATACTATATATATA--TAT-AATCCAAAAC---T--------------------AAAATAAAAACAT--A----CTGGCC-AGGA----A----TAGCAAATCCA
droRho1	scf7180000778087:78186-78354 +	224	AGATAT-AA----TCCAA--------------------ATCCAAT----AACAGCCA----------------------------A-CTCTCTCGCTCTCTCTGCGTCTCTCTATG----------------------------------------TGTATGTATGTAT--GTTGT----------------------------AACCCGT--ATATGTATATCCATG---TCAGAGAGCCAGGAAA-----------------GGTTGAGTCCAAACTAT------A----A-AACCCAAAGC---T-------------------------------AC--A----CTGGCC-AGGA----A----CAGCAAATCCA
droFic1	scf7180000454072:1846816-1846999 -	1027	AGAAAA-AGCCGATCCAAA----ACTTA---------TATCCAAT----AGTACCCG----------------------------A-CTCTCTCGCTCTCTTT----------ATG----------------------------------------TGTATGTATGTAT--GTTGT----------------------------ACCCCGT--ATATGTATATTCATG---TTAGAGAGCCAGGATC-----------------GGTCGATACCATACTATTTCTGTT----TAAACCAAAAACCAAT-------------------------------ACTGA----CTGGCC-AGGA--ACA----TAGCAAATCCA
droKik1	scf7180000302621:326473-326630 -	797	AAATAC-AA----AAAAGA----AATCC----AAAAATAAATCGC----AGTCTTGA----------------------------AACTTTGTCTA-CTTTCC----------GTT----------------TCTTTTTTTTCTT--------CCATTTTTATTTGT----ATTTT-----------------------AT---TTTTGGTGG-AACGCA-----------TCCTAGTGCCA------------------------------------------------------AAAGCAAC---C-------------------------------GC--A----CAGAAT-CGGAAAACG----CAGCAAGGATA
droAna3	scaffold_13117:1856374-1856503 -	514	CT---------------------------------------------------------------------------------------CTCTC--TCTCTCTGTGTCTCTCTAAA----------------------------T--------GCATGTATGTATGT----GTTGT-----------------------AT---TATCCGTATATATGTATATCCATG---TTAGAGAGCCAGGACG-----------------GGTTGAGATT---------------------GCCCAAGA----------------------------------------A----CTGGCCTAGGA----A----TAGCAAATC-A
droBip1	scf7180000396425:207025-207154 +	176	CT---------------------------------------------------------------------------------------CTCTC--TCTCTCTGTGCCTCTCTAAG----------------------------------------TGCATGTATGTATGTGTTGT-----------------------AT---TATCCGTATATATGTATATCCATG---TTAGAGAGCCAGGACG-----------------GGTTGAGATT---------------------GCCCAAGA----------------------------------------A----CTGGCCTAGGA----A----TAGCAAATC-A
dp4	chr2:10126391-10126530 +	52	GAATAA-TC----CATA-A----ACAAA---------TATCTA------TGTAGTCA----------------------------C-ATCTATCTCTCTCTCT----------ATA----------------------------------------TATCTCTCTCTCT--CTTTC----------------------------TTTATTT--GTACATGTATTTATT---TCATGGGTTTAGTTTT-----------------GC---AAATGGTATAAA------A----C-ATCTCCAAAA---T-------------------------------AC--A----TT-----------------------------
droPer1	super_2:4840479-4840636 -	677	TAATAT-AT----TGGAGT----AGCAA---------TATCTATT----TGTATTCA----------------------------G-ATTTGTATTTATTT------------ATG------------------------------TGTTTGTGGTGATACAGATAT-------------------------------------ATAGTAT--ATATAGAAAT--ATA---TTTTAAAATCA---TA-----------------GGTACATACAGTATATT------G----T-ATCCCTATCC---A-------------------------------AT--G----C----A-TATG----T----GAACGTACTTA
droWil1	scaffold_180700:3267577-3267741 +	365	AAATAT-CA----TACCCA-----AAAA---------TATATACT----ACTACACA----------------------------ACCTCTCTCTCTCTCT------------CTA----------------------------------------TCTATCTATCTAT--CTTTGAACATAAAATGTACCTATACTAAAACAAAAACTCT--ATATCTAAATCGTTG---TGC-TTACCATTCATT-----------------TTCTACTACTATACTAT------A----T-AGGGCGAAAC---------------------------------------------------------------------------
droVir3	scaffold_12855:2148540-2148695 +	168	ATA-----A----CCCAAA----AGATA---------CCTCAATT----TGCATA-----------------------------------------TATATCTATGTCTATATAGA----------------------------------------TATATACATACAT--ATATA----------------------------TATACAT--ATATATATATAAATA---TATGTGTGCGTGCATT---------------------ATCGTCTTGTGAC------T----A-GGTCCAGAAC---T-------------------------------TT--A----CAGGTG-CGCA----G----TGTCGAAATCA
droMoj3	scaffold_6496:26031347-26031515 +	924	TGATGC-CA----CCCAG--------------------CCCCCAC----CGCCTCCT----------------------------G-CTCCCTCCCTCTCTAT--GTTTATATGTG----------------------------------------TATATGTGTGTG------------------------------------TGTCTGT--GTGTTTGTGTCCCTTCGATTGGCGTGCCTGAATGGCTGTGAAAACACAGCCAGTTGCAGCT-------------------------GTATC---C-------------------------------AC--A----A--TCA-TTAT----CACAAAAGCAAACTAC
droGri2	scaffold_14853:6570585-6570746 +	745	AAAAAC-AA----AAAACA----AACGAAGTAACA--GCCCAAGCCGACAATGGCTG----------------------------A-ATATATA--------------------TGTTATGTATTTGTATTATTGTCGTGTATA--------TATATCTATATATGTAT--ATTAC-----------------------ACTATATACTAT----ATGTAT------------------------------------------------------------------A----T-ATATATAGAC---A-------------------------------AT--G----TCTGAT-GGCT----A----TGCCAAAGCCA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

AGAT-----------ATTACCCAGAAGCGATATC-CAATAGTAGCCAACTCTCTCGCT--CTCT----------ATGTGTATGTATGT----------------------------A--------------TC----TTGCTATCC--ATATATGTATATCCATATCAGAGAG----CCAGGATTGGTTGAGACCATACGA------TATA--------------------------ACCCGAAACCACACTGGCC-AGGAATAGCAAATCCA

Size

Hit Count

Total Norm

droSim1

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

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

AGAT-----------ATTACCCAGAAGCAATATC-CAATAGTAGCCAACTCTCTCGCT--CTCT----------ATGTGAATGTATGT----------------------------A--------------TC----TTGCTATCC--ATTTATGTATATCCATATCAGAGAG----CCAGGATTGGTTGAGACCATACGA------TATA--------------------------ACCCGAAACCATACTGGCC-AGGAATAGCAAATCCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................................................................................TATGTATATCCATATCAGAGAG----C...............................................................................................	23	1	15.00	8.00	2.00	5.00
..................................................................................................................................................................ATATCAGAGAG----CCAGGATTG.......................................................................................	20	1	1.00	0.00	1.00	0.00
.......................................................................................................................................................TATGTATATCCATATCAGAGAG----................................................................................................	22	1	1.00	0.00	0.00	1.00
.........................................................T--CTCT----------ATGTGAATGTATGT----------------------------A--------------T.............................................................................................................................................	21	1	1.00	1.00	0.00	0.00
............................................................................................................................................................................G----CCAGGATTGGTTGAGACCATACGA------T.................................................................	26	1	1.00	0.00	1.00	0.00
........................................................................................................................................................................................................................................................TACTGGCC-AGGAATAGCA......	18	1	1.00	0.00	1.00	0.00
...................................................................................................................................................................TATCAGAGAG----CCAGGATTGGTTGA..................................................................................	24	1	1.00	1.00	0.00	0.00
..............................................................................................................................................................ATCCATATCAGAGAG----CCAGGAT.........................................................................................	22	1	1.00	0.00	1.00	0.00
.......................................................................................................................................................TATGTTTATCCATATCAGAGAG----C...............................................................................................	23	1	1.00	0.00	1.00	0.00
..........................................................................................................................................................................GAG----CCAGGATTGGTTGAGACCATA...........................................................................	24	1	1.00	1.00	0.00	0.00
..........................................................................................................................................................................GAT----CCAGGATTGGTTGAGACCATA...........................................................................	24	1	1.00	1.00	0.00	0.00
..................................................................................................................................................................ATATCAGAGAC----ACAGGATT........................................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

AGAT-----------ATAACCGAGAAGCAATACC-CAATAGTAGCCAACTCTCTCGCTCTCTCTGCGTCTCTCTATGTGTATGTATGT----------------------------A--------------TT----TCGCTATCC--ATATATGTATATCCATGTCAGAGAG----CCAGGATCGGTTGAGACCATACTATATCTATATA--------------------------ACCCGAAACCATACTGGCC-AGGAATAGCAAATCCA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................................................................................................................................................GAGAG----CCAGGATCGGTTGAGACCA.............................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
...............ATAACCGAGAAGCAATACC-CAATA.........................................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................GTCAGAGAG----CCAGGATCGGTTGA..................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AGAT-----------ATAACCCAAAAGAAATACC-GAATAGTAGCCAACTCTCTCGCTCTCTCT----------ATGTGTATGTATGT----------------------------A--------------TT----TCGTTATCC--ATATATGTATATCCATGTCAGAGAG----CCAGGATCGGTTGAGACCATACTA------TATA--------------------------ACCCAAAACCATACTGGCC-AGGAATAGCAAGTCCA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............ATAACACAAAAGAAATACC-GA............................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................G----CCAGGATCGGTTGAGACCAT............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
............................................................ATGT----------AxxTGTATGTATGT----------------------------A--------------T.............................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........................................................................ATGTGTATGTATGT----------------------------A--------------TG----G.......................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................................................GT----------GTGTGTATGTATGT----------------------------A--------------T.............................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................GAG----CCAGGATCGGTTGATACCAT............................................................................	23	1	1.00	0.00	0.00	0.00	1.00
............................................................CTCT----------ATGTGTACATATGT----------------------------.............................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droAna3

------------------------------------------------ctctctctct--ctct----------gtgt--------------ctctctAAATGCATGTATGTATGTG--------------TT----GTATTATCCGTATATATGTATATCCATGTTAGAGAG----CCAGGACGGGTTGAGATT------------------------------------------GCCCAAGA----ACTGGCCTAGGAATAGCAAAT-CA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................................................................................................................................................GAGAG----CCAGGACGGGTTGA..................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..................................................CTCTCTCT--CTGT----------GTGT--------------CGCTCT...............................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................................GATT------------------------------------------GCGCAATA----ACTGGCCT................	20	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................................................................................................................................................GA----ACTGGCCTAGGAATAGCAAAT-..	23	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................GCATGTATGTATGTG--------------TT----GT......................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................GAGAG----CCAGGACGGGTTGAGATT------------------------------------------G...................................	24	1	1.00	1.00	0.00	0.00	0.00
..................................................CTCTCTCT--CTGT----------GTGT--------------CGCT.................................................................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
....................................................CTCTCT--CTCT----------GTGT--------------GTCGCT...............................................................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
..............................................................................................................GTATGTG--------------TT----CTAxTATCCG..............................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................GATGTATGTATGTATGTG--------------T.............................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................TGTATATCCATGTTAGAGAG----C...............................................................................................	21	1	1.00	1.00	0.00	0.00	0.00

dp4

AAACTGAATCTAAATCATCCCCCT-CGTAATATCCCGGAAATAGCCCCCTCTATCTCTCTCTCT----------CTTTGACTCTGTGCGTCTCTCTCTACCTAGATGTATGTATGTGTTCGTACAGACAGACACACAGAAACACA--CA----------------------------------------------------AATGTATATATTCACACACACTGATTGATCGG-----------------------------TTGAAGATCGG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................................................TACCTACGTGTATGTATGT.............................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................................CTACCTxGATGTATGTATGT.............................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................CTCTCTCTCTCTCTCT----------CTC....................................................................................................................................................................................................	19	6	0.17	0.00	0.17	0.00	0.00
....................................................................................................................................ACACAGAAACACA--CA----------------------------------------------------AATGT...................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................CAGACAGACAGACAGACA....................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................GGACAGACAGACAGACAG.......................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................AGATGTATGTATGTGTGTGT.......................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................ATATGTATGTATGTGTGCGT.......................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
............................................CTCCCTCTATCTCTCTCTCG----------.......................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.................................................................................TCTGTGCGTCTCTCTCTACCTAGAT.......................................................................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
..............................................CTCTCTCTCTCTCTCTCT----------C......................................................................................................................................................................................................	19	6	0.17	0.00	0.17	0.00	0.00

droPer1

AAACTGAATCTAAATCATCCCCCT-CGTAATATCCCGGAAATAGCCCCCTCTATCTCTCTCTCT----------CTTTGACTCTGTGCGTCTCTCTCTACCTAGATGTATGTATGTGTTCGTACAGACAGACACACAGAAACACA--CA----------------------------------------------------AATGTATATATTCACACACACTGATTGATCGG-----------------------------TTGAAGATCGG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.....................................................................................................................................................................................................................CACACACACTGATTGATCGG-----------------------------T..........	21	1	3.00	0.00	0.00	0.00	0.00	3.00
........................................................CTCTCTCT----------CTTTGACTCTGTGCGTCT.....................................................................................................................................................................................	26	1	2.00	0.00	0.00	0.00	0.00	2.00
................................................................................................................................................................................................................ATATTCACACACACTGATTG.............................................	20	1	2.00	0.00	0.00	0.00	0.00	2.00
.....................................................TCTCTCTCTCT----------CTGTTAC................................................................................................................................................................................................	18	2	1.00	0.00	0.00	0.00	0.00	1.00
................................................CTCGTTCTCTCTCTCT----------CT.....................................................................................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.00	0.33
.........................................................................................................................GACAGACAGACAGACAGA......................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................ATATATTCACACACACTG.................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................................................................ACACACACAAACACA--CA----------------------------------------------------CAT.....................................................................	20	23	0.04	0.00	0.04	0.00	0.00	0.00
................................................................................................................................AGACACACAGAAACACT--C.............................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................CTCTCTCTCT----------CTCTGTCTCT.............................................................................................................................................................................................	20	6	0.17	0.00	0.17	0.00	0.00	0.00
.........................................................................................................................AACAGACAGACAGACAGAA.....................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................CTCTTTCTCTCTCTCT----------CT.....................................................................................................................................................................................................	18	8	0.13	0.00	0.00	0.13	0.00	0.00
....................................................ATCTCTATCTCT----------CTTTCACT...............................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................................TCTCTCTCTCT----------CxTGGACT...............................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
.........................................................................................................................GACAGACAGACATACAGA......................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
..........................................................................................................................ACAGACAGACAGACAGAC.....................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...................................................TCTCTCTCTCTCT----------CTTTGTC................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.33	0.00	0.00
.............................................................................................................................................................................................................................CTGATTGAGCGG-----------------------------CTGAAG.....	18	1	1.00	0.00	1.00	0.00	0.00	0.00
............................................................................................................................AGACAGACACAGAGACAC...................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................CACCCAGATGTATGTATGT.............................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
....................................................CTCTCTCTCTCT----------GTTTGACT...............................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

CACC-----------AAAACCA-------ACACA-CAA-AATGAAGAACTCTCTATC-ataaat------------------------------------------atatatatatatatgtatcaatattct----gtattatat--atacatatatatatatatTAAAAAT----C-----------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................................................................ATATATATATGTAGGTAT.....................................................................................................................................................	18	3	0.67	0.00	0.67	0.00	0.00
...........................................................................................................................TCAATATTCT----GTATGAGA................................................................................................................................	18	1	2.00	0.00	0.00	2.00	0.00
..........................................................ATAAAT------------------------------------------AGATATATATATGT.........................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
..........................................................................................................ATATATATATATGTGTGT.....................................................................................................................................................	18	8	0.25	0.00	0.25	0.00	0.00
..............................................................AT------------------------------------------ATATATATATGTGTGT.......................................................................................................................................................	18	8	0.25	0.00	0.25	0.00	0.00
............................................................AAAT------------------------------------------AGATATATATATGT.........................................................................................................................................................	18	3	0.67	0.00	0.67	0.00	0.00
..............................................................AA------------------------------------------ATAGATATATATATGT.......................................................................................................................................................	18	3	0.67	0.00	0.67	0.00	0.00
..........................................................ATAAAT------------------------------------------ATATATATATGTGT.........................................................................................................................................................	20	2	1.00	0.00	1.00	0.00	0.00
..............................................................AT------------------------------------------AAATATATATATATGTGT.....................................................................................................................................................	20	2	1.00	0.00	1.00	0.00	0.00
..............................................................AT------------------------------------------ATAGATATAGATATGT.......................................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
..............................................................AT------------------------------------------ATGTATATATATATGTGT.....................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
..........................................................ATTAAT------------------------------------------ATATATATATATATATA......................................................................................................................................................	23	3	0.33	0.00	0.33	0.00	0.00
................................................................................................................................................CT--ATACATATAAATATATAT...........................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..............................................................AT------------------------------------------ATATACATACATATGTA......................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................ATAATAT--ATACATACATATA................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................................TAT------------------------------------------ATATATATATATGTGT.......................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
........................................................C-ATAAAT------------------------------------------ATATGGATATA............................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................ATATATATATATGTGTATA....................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
..........................................................ATAAAT------------------------------------------ATATATGTAGAT...........................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...............................................................T------------------------------------------ATATATATTTATATGAAT.....................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
............................................................ATAT------------------------------------------AAATATATATxTATGT.......................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................ATAT--ATACATATATGTGT...............................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
....................................................................................................................................T----GAGTTATAT--ATACATATATA..................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................ATAT--ATACATATAGATATGT.............................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................ATATATACATATATGTGT.....................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
..............................................................................................................................................ATAC--ACAxATATATATATATA............................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.............................................................................................................................................TATxT--TTACATATATATATATAT...........................................................................................................	22	3	0.33	0.00	0.33	0.00	0.00
....................................................................................................................................................ATACATAAATTTATATATT..........................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................TAT--ATAGATATATATATATAT...........................................................................................................	21	4	0.25	0.00	0.00	0.25	0.00
..........................................................................................................ATATATATATATTTGTGT.....................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
..........................................................ATACAT------------------------------------------ATATATATATAT...........................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
..............................................................AT------------------------------------------ATATATATATTTGTGT.......................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
...............................................................T------------------------------------------GTATATATATATGTGTA......................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.............................................................................................................................................TATAC--ATACATATATACATATATT..........................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................TATATATATATATTCAATAT----................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..........................................................ATACAT------------------------------------------ATATATATATATAT.........................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.............................................................................................................................................TATAT--AGATATATATATATAT.............................................................................................................	21	4	0.25	0.00	0.00	0.25	0.00
....................................................................................................................................................ATACATCTATATTTATAT...........................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
..........................................................................................................................................GATTATAT--ATGCATATATA..................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.....................A-------ACACA-CAA-AATGAAGAACTCTCT...........................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................ATAC--ATACATATATATATA..............................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
...........................................................................................................................................................TATATATATATGAGAAAT----C-----------------------------------------------------------------------------------------------	19	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................TATAT--ACATATATATATATATA............................................................................................................	22	5	0.20	0.00	0.20	0.00	0.00
.............................................................................................................................................TATAG--ATACATATACATAT...............................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
..............................................................AT------------------------------------------ATATAxGTATCTATGTA......................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.............................................................................................................................................TATAT--ACAxATATATATATG..............................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
..............................................................................................................................................ATAT--AAACATAGATATATAT.............................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..........................................................ATAAAT------------------------------------------ATATATATATATAT.........................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
................................................................................................................................................AT--ACACATATATATAGATAT...........................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
..............................................................................................................................................ATAC--AxACATATATATATATAT...........................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
..........................................................ATAAAT------------------------------------------AGATATATATATG..........................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................................A-ATTAAT------------------------------------------ATATATATATAT...........................................................................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
...............................................................................................................................................TAT--ATACAxATATATATATG............................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
..............................................................................................................................................ATAT--ATACATACATATGTA..............................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
..........................................................................................................ATATATATGTATGTGTAT.....................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
................................................................................................................................................AT--ATACATCTATATTTATAT...........................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................ATACAT--ATxCATATATATATAT.............................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00
...............................................................T------------------------------------------ATATATATATATATGTGT.....................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
..........................................................ATACAT------------------------------------------ACATATATATATA..........................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
...........................................................TACAT------------------------------------------ATATATATATATA..........................................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
.......................................................TT-ATACAT------------------------------------------ATATATATATATAT.........................................................................................................................................................	22	3	0.33	0.00	0.00	0.33	0.00
................................................................................................................ATATATATGTGTCGATAT...............................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................TACATATATATATATATA..........................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
..............................................................................................................................................ATTT--AxGCATATATATATATA............................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................ATACATATATATATATAT...........................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
..........................................................................................................................................TATAATAT--ATACATACATATAT...............................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................AT------------------------------------------ATATATATATAAAAGTAT.....................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
..........................................................AGATAT------------------------------------------ATATATATATATATGT.......................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................AT------------------------------------------ATATACATATATGTGT.......................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
...........................................................TTGAT------------------------------------------ATATATATATATATGT.......................................................................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
...............................................................................................................................................AAT--ATACATATATACATAT.............................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................TTATAC--ATATATATATATATAT.............................................................................................................	22	3	0.33	0.00	0.00	0.33	0.00
..............................................................AT------------------------------------------ATGTATATATGTATGTA......................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
...............................................................................................................................................TAT--ATACATATATATATATATA..........................................................................................................	22	5	0.20	0.00	0.20	0.00	0.00
....................................................................................................................................................ATACATACATATATATATA..........................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
..........................................................................................................ATATATATATGTGTGTAT.....................................................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00

droVir3

-------------------------------------------------------------TTt----------atatatatatatat----------------------------a--------------ta----tatatatat--attaatatatatTTTTAACAAGAAA----CTGAACTCGA--------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..................................................................................ATATAC----------------------------A--------------CA----TATATATAT--A............................................................................................................................	19	12	0.08	0.00	0.00	0.00	0.00	0.08
..........................................................................ATATACACATATAT----------------------------A--------------TA----TA......................................................................................................................................	19	12	0.08	0.00	0.00	0.00	0.00	0.08
......................................................................................AT----------------------------A--------------TC----GATATATAT--ATTA.........................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
............................................................................ATATACACATAT----------------------------A--------------TA----TATA....................................................................................................................................	19	12	0.08	0.00	0.00	0.00	0.00	0.08
....................................................................................................................A--------------TG----GATATATAT--ATTAATA......................................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................ATATACACAT----------------------------A--------------TA----TATATA..................................................................................................................................	19	12	0.08	0.00	0.00	0.00	0.00	0.08
................................................................................ATATACAC----------------------------A--------------TA----TATATATA................................................................................................................................	19	12	0.08	0.00	0.00	0.00	0.00	0.08

droMoj3

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

-------------------------------------------------------------tat----------atgtatacatatat----------------------------a--------------ta----tatatatat--atatatatatatatatGTCAGCCCACCCACGAAATTTATTTGTGAGCCAAGCA------AAA-GAGACGCGGGCTGAATTTTCGGTTACACGCAA------------A-GAAAAACGAAAATCGA

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									None
UNAFold Image		None									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