dme-mir-4917- 12- and 20-way alignments

dme-mir-4917	chrX:14093578-14093654 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 14093578-14093602
   star strand at position 14093632-14093653
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:14093563-14093669 +	GAGAGCCCCAGCAGAGTGAGTAG------------------------------------------------CGATG---------------------GGGGT-CAGAT----GGCCGTGGAAGATATGTGACGATTG-------------------------CCCCCTTAC-TAC--T------A-----------------TCGTCTG---CTCAACAGGAAAGCAAACTACAT
droSim1	chrX_random:3764305-3764407 +	GAGAGCCCC---AGAGTGAGTAG------------------------------------------------CGATG---------------------GGGGT-CAGATGGATGGCCGTGGATGATATGTGACGATTG-------------------------C--CCTTAC-TAC----------------------------GCTCTG---CCCAACAGGAAAGCAAGCTACAT
droSec1	super_20:697977-698075 +	GAGAGCCCC---AGAGTGAGTAG------------------------------------------------CGATG---------------------GGGGT-CAGAT----GGCCGTGGATGATATGTGACGATTG-------------------------C--CCTTAC-TAC----------------------------GCTCTG---CCCAACAGGAAAGCAAGCTACAT
droYak2	chrX:8347469-8347564 +	GAGAGCCCC---AGAGTAAGTAG------------------------------------------------CCAGG---------------------GGGAT-CAGGA----GGCCGCGGAAGGTATGTGATGATTC-------------------------C--C-------AT--T------A-----------------CCCTCCG---ATCCACAGGAAAGCAACCTACAT
droEre2	scaffold_4690:12836867-12836962 -	GAGAGCCCC---AGAGTGAGTAC------------------------------------------------GCAGT---------------------CGGGT-CAGAA----GGCCGCGGAAGATATGTGATGATTC-------------------------C--C-------AT--T------C-----------------CCCTCCG---ATCAACAGGAAAGCAACCTACAC
droAna3	scaffold_13047:1616598-1616749 +	GATACCCCG---AGAGTGAGTTAAATAGGTAGACTGGGTTTTACGGGTTTTGGGGATTAGGGTTAAGGGGTTT--AAGGATCAGGGACTTGGCTAGAAGGAC-CA-----------AAGGACT-------------------------------TAAGAACTAACA-------AA--A------A-----------------TTCACCA---TTCCACAGGCAAGCACGGTACAC
dp4	chrXL_group1e:6144259-6144391 -	GAAAACTCC---AGAGTGAGTTGAGTGAG-----------------------------------------GTT--G---------------------AGAGCCGGGGT----GC--TCGGAAGA----------CCATCCTCACTGATCCTATTCTAATCTTCCCCTCTTTCGTCTATATCTC--TCT--------------CTCTCTC---GTCCGCAGGCAAGCGAACTATAC
droPer1	super_21:1109353-1109492 -	GAAAACTCC---AGAGTGAGTGG------------------------------------------------TT--G---------------------AGAGCCGGGGT----GCTCGCA--AGA----------CCTTCCTCACTGATCCTATTCTAATCTTCCCCTCTTTCGTCTATAtctc--tctctctctctctctctcgctctc---GTCCGCAGGCAAGCGAACTATAC
droWil1	scaffold_180702:2428501-2428590 +	GAGAACACA---AGGGTGAGTGG------------------------------------------------GAGGA---------------------GAGAT-GAGAG----GAGAATGGACT-------------------------------------------TTAACCGCCATTATTTC--------------------T--TTC---TTCCACAGGGAAGTGAACTACAA
droVir3	Unknown	GAAAACACA---CGAGTAAGTGG------------------------------------------------AA--------------------------------------------------------------------------------------------C-------AT----------------------------TTTCTATCCAACAGCAGTCAAGCGAAATACAG
droMoj3	scaffold_6359:2739408-2739517 -	GAAAACACA---AGAGTGAGTGA------------------------------------------------CAAGA---------------------TTTAT-ATATA----TTTATAGGAAT-------------------------------ATAATACTAATTCTTATCTACGTTATTCCCGTCT--------------CACTCAA---TCAATTAGTCGAGCCGAATACAT
droGri2	Unknown	GAAAACAGA---GGAGTAAGTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACAGTCGAGCGAAATACAG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:14093563-14093669 +	NA	GAGAGCCCCAGCAGAGTGAGTAGCGATGGGGGTCAGATG----GCCGTGGAAGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC--CC-----CCTTACTACTAT-----------------------------------------------CGTCTG--C-T----CAACAGGAAAGCA----A----------ACTACAT
droSim1	chrX_random:3764305-3764407 +	1	GAGAGCCCCA---GAGTGAGTAGCGATGGGGGTCAGATGGATGGCCGTGGATGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC---------CCTTACT---AC-----------------------------------------------GCTCTG--C-C----CAACAGGAAAGCA----A----------GCTACAT
droSec1	super_20:697977-698075 +	1	GAGAGCCCCA---GAGTGAGTAGCGATGGGGGTCAGATG----GCCGTGGATGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC---------CCTTACT---AC-----------------------------------------------GCTCTG--C-C----CAACAGGAAAGCA----A----------GCTACAT
droYak2	chrX:8347469-8347564 +	1	GAGAGCCCCA---GAGTAAGTAGCCAGGGGGATCAGGAG----GCCGCGGAAGG---------------------------------------------------------------------TATGT-----------------GATGATT---------------------CC---------CATT------AC-----------------------------------------------CCTCCG--A-T----CCACAGGAAAGCA----A----------CCTACAT
droEre2	scaffold_4690:12836867-12836962 -	1	GAGAGCCCCA---GAGTGAGTACGCAGTCGGGTCAGAAG----GCCGCGGAAGA---------------------------------------------------------------------TATGT-----------------GATGATT---------------------CC---------CATT------CC-----------------------------------------------CCTCCG--A-T----CAACAGGAAAGCA----A----------CCTACAC
droEug1	scf7180000409008:504391-504474 +	1	GAAAGCCCCA---GAGTGAGTAGAAGTGGGGGCGAGAAA----TCTACGGAAGA---------------------------------------------------------------------GATATGATCC--------A---TATGATT------------------------------------------------------------------------------------------------------------ACAGGAAAGCA----A----------CCTACAC
droBia1	scf7180000302041:1138735-1138821 +	1	GAAAGTCCTA---GGGTGAGTAGCGCCGC----CAT------------------------------------------------------------------------------------------ATGATCCATGACGCAC---GATGATT---------------------AC---------CCTA-------------------------------------------------------CCTCCG--A-T----CAGCAGGAAAGCA----A----------CCTACAC
droTak1	scf7180000415667:540030-540111 -	3	GAGAGCCCCA---GAGTGAGTAGTTTATA--TTT--------------------------------------------------------------------------------------------AAGATTC--------AAGAGATGATT---------------------TT---------TATA-------------------------------------------------------AATTTG--G-T----TAGCAGGAAAGCA----A----------CCTACAC
droEle1	scf7180000491011:415435-415552 -	3	GAGAGCCCCA---GAGTGAGTGAATGCATGGA----------------GAAAGC---------------------------------------------------------------------TACACGATCC--------C---AATGATA---------------------AC---------CATC--------CATCCAAC-----TATCCA--------TCCAACCAACCATCCG----GCGCCG--C-A----CAACAGGAGAGCA----G----------CCTACAG
droRho1	scf7180000776513:33442-33533 +	1	GAGAGCCCCA---GAGTGAGTAGTAGTGGTAGTAGA--G----ATCACCAATGA---------------------------------------------------------------------TTACC-----------------AATGATA---------------------AC---------CTTA-------------------------------------------------------CCTCCG--C-C----CAACAGGAAAACA----G----------CCTACAC
droFic1	scf7180000454073:905651-905737 -	1	GAGAGCCCCA---GAGTGAGTAGCGGGGA----------------------GAA---------------------------------------------------------------------TATGTGATCC--------A---ATTGATT---------------------GC---------CCTA-------------------------------------------------------ACTCCGTAC-C----AAGCAGGAAAGCAGCC-A----------CCTACAC
droKik1	scf7180000302517:390473-390554 -	4	GAAAGCCCCA---GAGTAAGTTTTAATTT-------------------------------------------------------------------------------------------------------------------------------------------------C---------TC-----------TCTAAAAAGCAATTTTTAAAG-------------------------CTTTTT--C-T----TTACAGGCAAGCAGCA-A----------CCTACAG
droAna3	scaffold_13047:1616598-1616749 +	1	GATACCCCGA---GAGTGAGTTAAATAGGTAGACT----------------------GGGTTTTACGGGTTTTGG-GGATTAGGGTTAAGGGGTTTAAGGATCAGGGACTTGGCTAGAAGGACCAAAGGACTT--------A---AGAACTA---------------------AC---------AAAA------AT-----------------------------------------------TCACCA--T-T----CCACAGGCAAGCA----C----------GGTACAC
droBip1	scf7180000396740:414605-414756 +	2	GATACCCCGA---GAGTGAGTTAAATAGGTAGAATT--T----ATCGTAA--CCTATGGGGTTTACGGGTTTTTGGG--------GCAAAGGGCTTAAGGGTTA----------------------AAGATTA--------AA--ATCAAAA---------------------AC---------TTTA-------------------------------------------------------ATAACTTAA-C----GGGTTAAAAGTCAGACAATCGAACGGATGGATCTT
dp4	chrXL_group1e:6144259-6144391 -	3	GAAAACTCCA---GAGTGAGTTGAGTGAG--GTT--------------------------------------------------------------------------------------------GAGAGCCGGGGTGCTC-G-GAAGACCATCCTCACTGATCCTATTCTAAT---------CTTC--------CCCTCTTT-----CGTCTATATCTCTCTC------------------TCTCTC--G-T----CCGCAGGCAAGCG----A----------ACTATAC
droPer1	super_21:1109353-1109492 -	3	GAAAACTCCA---GAGTGAGTGGTTGAGA--GCCGGG---------------------------------------------------------------------------------------------------GTGCTC-GCAA-GACCTTCCTCACTGATCCTATTCTAAT---------CTTC--------CCCTCTTT-----CGTCTATATCTCTCTCTCTCTCTCTCTCTC----GCTCTC--G-T----CCGCAGGCAAGCG----A----------ACTATAC
droWil1	scaffold_180702:2428501-2428590 +	1	GAGAACACAA---GGGTGAGTGGGAGGAGAGATGAGAGG----AGAATGGAC---------------------------------------------------------------------------------------------TTTAACC---------------------GC---------CATTATT----------------------------------------------------TCTTTC--T-T----CCACAGGGAAGTG----A----------ACTACAA
droVir3	scaffold_12932:1910954-1911056 +	1	AGGAACGGCA---GCAGCAGCGGCAGCGGCGGCGGCGCC----ACC---GTCAG---------------------------------------------------------------------TTGGT-----------------GCTGCGC---------------------CC---------GCTG-------------------------CACAG------------------CC-----GCCGCC--CTCGGCAGGCGAAGCAGCCG----C----------TAAATCC
droMoj3	scaffold_6359:2739408-2739517 -	3	GAAAACACAA---GAGTGAGTGACAAGATTTATATATAT----TTA-------------------------------------------------------------------------------TAGGAATA--------T---AATACTA---------------------ATTCTTATCTACGT--------------------------TATTC------------------CCGTCTCACTCAA--T-C----AATTAGTCGAGCC----G----------AATACAT
droGri2	scaffold_15081:1312788-1312809 -	3	T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAACAGTCGAGCG----A----------AATACAG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GAGAGCCCCAGCAGAGTGAGTAG------------------------------------------------CGATG---------------------GGGGT-CAGAT----GGCCGTGGAAGATATGTGACGATTG-------------------------CCCCCTTAC-TAC--T------A-----------------TCGTCTG---CTCAACAGGAAAGCAAACTACAT

Size

Hit Count

Total Norm

droSim1

GAGAGCCCC---AGAGTGAGTAG------------------------------------------------CGATG---------------------GGGGT-CAGATGGATGGCCGTGGATGATATGTGACGATTG-------------------------C--CCTTAC-TAC----------------------------GCTCTG---CCCAACAGGAAAGCAAGCTACAT

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

GAGAGCCCC---AGAGTGAGTAG------------------------------------------------CGATG---------------------GGGGT-CAGAT----GGCCGTGGATGATATGTGACGATTG-------------------------C--CCTTAC-TAC----------------------------GCTCTG---CCCAACAGGAAAGCAAGCTACAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
............AGAGTGAGTAG------------------------------------------------CCATG---------------------GAG.......................................................................................................................................	19	1	1.00	1.00	0.00	0.00
..................AGTAG------------------------------------------------CGATG---------------------CTGGT-CAG.................................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

GAGAGCCCC---AGAGTAAGTAG------------------------------------------------CCAGG---------------------GGGAT-CAGGA----GGCCGCGGAAGGTATGTGATGATTC-------------------------C--C-------AT--T------A-----------------CCCTCCG---ATCCACAGGAAAGCAACCTACAT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

GAGAGCCCC---AGAGTGAGTAC------------------------------------------------GCAGT---------------------CGGGT-CAGAA----GGCCGCGGAAGATATGTGATGATTC-------------------------C--C-------AT--T------C-----------------CCCTCCG---ATCAACAGGAAAGCAACCTACAC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................................................................................................................................................................T--T------C-----------------CCGTCCG---ATCAACTG...............	18	1	1.00	0.00	0.00	1.00	0.00

droAna3

GATACCCCG---AGAGTGAGTTAAATAGGTAGACTGGGTTTTACGGGTTTTGGGGATTAGGGTTAAGGGGTTT--AAGGATCAGGGACTTGGCTAGAAGGAC-CA-----------AAGGACT-------------------------------TAAGAACTAACA-------AA--A------A-----------------TTCACCA---TTCCACAGGCAAGCACGGTACAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..............................AGCCTGGGTTTTACGCG............................................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................AACA-------AA--A------A-----------------TTCGTCA---TTCC...................	19	1	1.00	0.00	0.00	0.00	1.00
..................................TGGGTTTTGCGGATTTTG.......................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
........................................TTACGGGTTATGGGGATG.................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

dp4

GAAAACTCC---AGAGTGAGTTGAGTGAG-----------------------------------------GTT--G---------------------AGAGCCGGGGT----GC--TCGGAAGA----------CCATCCTCACTGATCCTATTCTAATCTTCCCCTCTTTCGTCTATATCTC--TCT--------------CTCTCTC---GTCCGCAGGCAAGCGAACTATAC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..............................................................................................................................................................................CTCTCTCTC--TCT--------------CTCTCTC---.......................	19	6	0.17	0.00	0.17	0.00	0.00

droPer1

GAAAACTCC---AGAGTGAGTGG------------------------------------------------TT--G---------------------AGAGCCGGGGT----GCTCGCA--AGA----------CCTTCCTCACTGATCCTATTCTAATCTTCCCCTCTTTCGTCTATAtctc--tctctctctctctctctcgctctc---GTCCGCAGGCAAGCGAACTATAC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...................................................................................................................................................................................TCTC--TCTxGCGCTCTCTCTCT.................................	20	2	1.50	0.00	0.00	0.00	0.00	1.50
....................................................................................................................................................................................CTG--TCTCTGTCTCTCTCT...................................	18	3	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................................C--TGTCTCTGTCTCTCTCT.................................	18	3	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................................CTCTCTCTCTCTGTCGCGC..............................	19	2	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................................C--TCGCTCTCTCTCTCTCTCTCTCT...........................	24	2	1.00	0.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................CTC--GCTCTCTCTCTCTCTCTCTCT.............................	24	2	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................CTCTCTCTCTCTGTCGCGC............................	19	2	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................................CTCTCTCTCTCTCTGTCTCT.............................	20	6	0.17	0.00	0.17	0.00	0.00	0.00
......................................................................................................................................................................................C--TCTCTCTCTCTGTCCCT.................................	18	4	0.25	0.00	0.00	0.00	0.00	0.25
.............................................................................................................................................................................CATATxTCTC--TCTCTCTCTCTCT.....................................	22	2	0.50	0.00	0.50	0.00	0.00	0.00
.....................................................................................................................................................................................TC--TCTCCCTCTCTCTTTCTC................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00
.................................................................................................................................................................................TCTCTC--TCTTTCTCTCTCT.....................................	19	7	0.14	0.00	0.00	0.00	0.14	0.00
.............................................................................................................................................................................................TCTCTCTCTTTCTCTCTCT...........................	19	7	0.14	0.00	0.00	0.00	0.14	0.00
............................................................................................................................................................................................CTCTTTCTCTCTCTCTCT.............................	18	8	0.13	0.00	0.00	0.13	0.00	0.00
....................................................................................................................................................................................CTC--TCTCTCTCTCTGTCTCT.................................	20	6	0.17	0.00	0.17	0.00	0.00	0.00
.........................................................................................................................................................................................TCTCTCTCTCTCTCGCTG................................	18	5	0.20	0.00	0.00	0.00	0.00	0.20
.........................................................................................................................................................................................TCTCTCTCTTTCTCTCTCT...............................	19	7	0.14	0.00	0.00	0.00	0.14	0.00
..................................................................................................................................................................................CTCTC--TCTCTCTCTCTCTCT...................................	20	5	0.20	0.00	0.00	0.00	0.00	0.20
....................................................................................................................................................................................CTC--TCGCTCGCTCTCTCTC..................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
..................................................................................................................................................................................CTCTC--TCTCTCTCTGTCTCT...................................	20	6	0.17	0.00	0.17	0.00	0.00	0.00
....................................................................................................................................................................................CTC--TCTCTCTCTGTCCCT...................................	18	4	0.25	0.00	0.00	0.00	0.00	0.25
....................................................................................................................................................................................CTC--TCTCTCTCTCTCTCTCT.................................	20	5	0.20	0.00	0.00	0.00	0.00	0.20
.............................................................................................................................................................................................TCTCTCTCTCTCTCGCTG............................	18	5	0.20	0.00	0.00	0.00	0.00	0.20
......................................................................................................................................................................................C--GCTCTGTCTCTCTCTCTCGCT.............................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................................TC--TCTCTCTCTCTCTGTCTCTCT.............................	23	4	0.25	0.00	0.00	0.00	0.00	0.25
......................................................................................................................................................................................C--TCTCTCTCTGTCACTCTC................................	19	4	0.25	0.00	0.00	0.00	0.00	0.25
....................................................................................................................................................................................CTC--TCTCTCTGTCACTCTC..................................	19	4	0.25	0.00	0.00	0.00	0.00	0.25
...........................................................................................................................................................................................TCTCTCTCTCTCTCTCGCTG............................	20	3	0.33	0.00	0.00	0.00	0.00	0.33
..............................................................................................................................................................................CTCTTTCTC--TCTCTCTCT.........................................	18	8	0.13	0.00	0.00	0.13	0.00	0.00
......................................................................................................................................................................................C--TCTCTCTCTCTCTGTCTCT...............................	20	6	0.17	0.00	0.17	0.00	0.00	0.00
.....................................................................................................................................................................................TC--TCTCTCTCTCTCGCTG..................................	18	5	0.20	0.00	0.00	0.00	0.00	0.20
...................................................................................................................................................................................TCTC--TCTCTCTCTCGCTG....................................	18	5	0.20	0.00	0.00	0.00	0.00	0.20
......................................................................................................................................................................................C--TCTCTxGCGCTCTCTCTC................................	18	4	0.25	0.00	0.00	0.00	0.25	0.00
..............................................................................................................................................................................................CTCTCTCTCTCGCGCACT...........................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................CTC--TCTxGCGCTCTCTCTC..................................	18	4	0.25	0.00	0.00	0.00	0.25	0.00
...................................................................................................................................................................................TCTC--TCCCTCTCTCTTTCTC..................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00
............................................................................................................................................................................................CTCTCTCTCTCTGTCCCT.............................	18	4	0.25	0.00	0.00	0.00	0.00	0.25
......................................................................................................................................................................................C--TCTTTCTCTCTCTCTCT.................................	18	8	0.13	0.00	0.00	0.13	0.00	0.00
.....................................................................................................................................................................................TC--TCTCTCTTTCTCTCTCT.................................	19	7	0.14	0.00	0.00	0.00	0.14	0.00
..........................................................................................................................................................................................CTCTTTCTCTCTCTCTCT...............................	18	8	0.13	0.00	0.00	0.13	0.00	0.00
................................................................................................................................................................................ATAGCTC--TCTCTCTCTCCCTCT...................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................................TC--TCTCTCTCTCTCTCGCTG................................	20	3	0.33	0.00	0.00	0.00	0.00	0.33
......................................................................................................................................................................................C--TCTCGCTCGCTCTCTCTC................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
...................................................................................................................................................................................TCTC--TCTCTCTCTCTTTGTC..................................	20	3	0.33	0.00	0.00	0.33	0.00	0.00
.........................................................................................................................................................................................TCTCTCTCTCTCTCTGTCTCTCT...........................	23	4	0.25	0.00	0.00	0.00	0.00	0.25
..............................................................................................................................................................................................CTCTTTCTCTCTCTCTCT...........................	18	8	0.13	0.00	0.00	0.13	0.00	0.00
..........................................................................................................................................................................................CTCTCTCTCTCTCTCTCTCT.............................	20	5	0.20	0.00	0.00	0.00	0.00	0.20
...........................................................................................................................................................................................TCTCTCTCTTTCTCTCTCT.............................	19	7	0.14	0.00	0.00	0.00	0.14	0.00
...................................................................................................................................................................................TCTC--TCCCTCTCTCTTTCTCT.................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
...................................................................................................................................................................................TCTC--TCTCTCTCTCTGTCTCTCT...............................	23	4	0.25	0.00	0.00	0.00	0.00	0.25
..................................................................................................................................................................................CTCTT--TCTCTCTCTCTCT.....................................	18	8	0.13	0.00	0.00	0.13	0.00	0.00
....................................................................................................................................................................................CTC--GTTCTCTCTCTCTCT...................................	18	3	0.33	0.00	0.00	0.00	0.00	0.33
............................................................................................................................................................................................CTCTCTCTCTCTCTCTCTCT...........................	20	5	0.20	0.00	0.00	0.00	0.00	0.20
...................................................................................................................................................................................TCTC--TCTCTTTCTCTCTCT...................................	19	7	0.14	0.00	0.00	0.00	0.14	0.00
............................................................................................................................................................................................CTCTCTCTCTCTCTGTCTCT...........................	20	6	0.17	0.00	0.17	0.00	0.00	0.00
...................................................................................................................................................................................TCTC--TCTCTCTCTCTCGCTG..................................	20	3	0.33	0.00	0.00	0.00	0.00	0.33
..............................................................................................................................................................................................CTCTCTCTCTGTCACTCTC---.......................	19	4	0.25	0.00	0.00	0.00	0.00	0.25
.....................................................................................................................................................................................TC--TCTCTCTCTCTCTTTGTC................................	20	3	0.33	0.00	0.00	0.33	0.00	0.00
......................................................................................................................................................................................C--TCGTTCTCTCTCTCTCT.................................	18	3	0.33	0.00	0.00	0.00	0.00	0.33
........................................................................................................................................................................................................ATCGCTCTC---GTACGCAGG..............	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................CATATxTC--TCTCTCTCTCTCTCT...................................	22	2	0.50	0.00	0.50	0.00	0.00	0.00
....................................................................................................................................................................................CTC--TTTCTCTCTCTCTCT...................................	18	8	0.13	0.00	0.00	0.13	0.00	0.00
.................................................................................................................................................................................TCTCTC--TCTCTCTCTGTCTCTCT.................................	23	4	0.25	0.00	0.00	0.00	0.00	0.25
......................................................................................................................................................................................C--TCTCTCTCTCTCTCTCTCT...............................	20	5	0.20	0.00	0.00	0.00	0.00	0.20
...................................................................................................................................................................................TCTC--TxACTCTCACTCTCTCTC................................	21	2	0.50	0.00	0.00	0.00	0.00	0.50

droWil1

GAGAACACA---AGGGTGAGTGG------------------------------------------------GAGGA---------------------GAGAT-GAGAG----GAGAATGGACT-------------------------------------------TTAACCGCCATTATTTC--------------------T--TTC---TTCCACAGGGAAGTGAACTACAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........A---AGGGTGGGTxG------------------------------------------------GAGGA---------------------GA........................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
.........................................................................AGA---------------------GAGAT-GAGAG----AAGAA......................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
....ACACA---AGGGGGAGAGG------------------------------------------------GA..................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................AGAA---------------------GAGAT-GAGAT----GAGA.......................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...................GTCG------------------------------------------------GTGGA---------------------GAGAT-GAGA................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................AAGAG-GAGAG----GAGAATGGA..................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................GAGAT-GAGAx----GAGAATGAA..................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droVir3

GAAAACACA---CGAGTAAGTGG------------------------------------------------AA--------------------------------------------------------------------------------------------C-------AT----------------------------TTTCTATCCAACAGCAGTCAAGCGAAATACAG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...................................................................................................................................................................................................................CAACAACAGTCxAGCGAAA.....	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

GAAAACACA---AGAGTGAGTGA------------------------------------------------CAAGA---------------------TTTAT-ATATA----TTTATAGGAAT-------------------------------ATAATACTAATTCTTATCTACGTTATTCCCGTCT--------------CACTCAA---TCAATTAGTCGAGCCGAATACAT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........................................................................AGA---------------------TTAAT-ATATA----TATAT......................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................................TGATAGGAAT-------------------------------ATTATACT.........................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droGri2

GAAAACAGA---GGAGTAAGTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACAGTCGAGCGAAATACAG

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
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UNAFold Image																				None