dme-mir-4982- 12- and 20-way alignments

dme-mir-4982	chr2R:14607673-14607792 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 14607740-14607761
   star strand at position 14607703-14607723
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:14607658-14607807 +	TTTTGA--GTCG-AAAGGACC-AACTTT-GC----------------------------------TGGCATTCGGT-GGCCAA----TAATGCAATTGCATGTCCTTGTTG----------CTGTTGCAATG----------------------------------------------------------TTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC--------------------C---GCTGCTGCTGCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC
droSim1	chr2R:13317687-13317836 +	TTTCGA--GTCG-AAAGGACC-AACTTT-GC----------------------------------TGGCATTCGCT-GGCCAA----TAATGCAATTGCGTGTCCTTGTTG----------CTGTTGCAATG----------------------------------------------------------TTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC--------------------C---GCTGCTGCTGCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC
droSec1	super_1:12115359-12115508 +	TTTCGA--ATCG-AAAGGACC-AACTTT-GC----------------------------------TGGCATTCGCT-GGCCAA----TAATGCAATTGCATGTCCTTGTTG----------CAGTTGCAATG----------------------------------------------------------TTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC--------------------C---GCTGCTGCTGCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC
droYak2	chr2R:14591968-14592143 -	TTTCGG--GTCG-AAAGGACC-AACTTTTGT----------------------------------TGGCATTCGCT-GGCCAA----TAATGCAATTGCGTGTCCTTGTTG----------CTGTTGCAATG----------------------------------------------------------TTGCAACTTGCAACTGGAATTGCAATTGCATTTCTAGTTGCTTCTCCTCTTTTTCCT--GCT---GCTCCTACTCCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC
droEre2	scaffold_4845:8798992-8799150 +	TTTCGC--GTCG-AAAGGACC-AACTTT-GC----------------------------------TGGCACTCGCT-GGCCAA----TAATGCAATTGCGTGTCATTGTTG----------CTGTTGCAATG----------------------------------------------------------TTG-------CAACTGGAATTGCAATTGCATTTCTAGTTGCTC-----------CTCATGCT---GCTGCTGCTCCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC
droAna3	scaffold_13266:17767267-17767393 -	TTCTGA--AAGG-GAAGAGCCTTAGATT-ATATTGAAGATTCTATTCTGGCACGGACCAGGACTCTGTCATACTCT-AATC----------------ATATTTAAT-----ACATTTAGTATTATAGCTT----------------------AGT---------------------------------------------------------------------------C--------------------C---TTTGCTAGTCCTTCAGTG----------------------------------------
dp4	chr3:3450112-3450236 -	TGTTGC--ATGA-AGAGGACCCAACTTT-CCA---------------------------------GGAGATTTTCT-GGCAGC----TAATGCAATTGTGGTGCAT-----AGTTTCGGAGCTGTGGCATT-----------------------------------------------------------------------------------------------------------------CTC--ACA---GTTGCTGCAGCTCAAGTG---GCA-----ATTAGAAGG---------------ATCTG
droPer1	super_2:3643182-3643306 -	TGTTGC--ATGA-AGAGGACCCAACTTT-CCA---------------------------------TGAGATTTTCT-GGCCGC----TAATGCAATTGTGGTGCAT-----AGTTTCGGAGCTGGGGCATT-----------------------------------------------------------------------------------------------------------------CTC--ACA---GTTGCTGCAGCTCAAGTG---GCA-----ATTAGAAGG---------------ATCTG
droWil1	scaffold_180697:2056860-2057011 +	TTTTTT--ATTC-AAGCTCGG-AATTTA-GC----------------------------------TAGCTGTAGCTGGGCCAATAGCTAATCCAATTGCATGACAT-----TTCC-----------CCTT----------------------GGT---CCT---TGGATGGTTCTCTGTGTCTGTCCATGTTT-------CTG-----------------------------------------------CTAGCGCTGCTG--CCTCAAGTG---GCA-----ATTAT-TAG-------------ACAACTT
droVir3	scaffold_12875:14126484-14126664 -	GTTATTATATTGCAGAGAACG-AAC------------------------------------------GCATTGAAT-GACGA----------CAAGTGTGCGCTCCTTTTG----------GC-TTGCACAGTTGCATTAATATTGCGCTGTTGTTGTCGTTGCTTTACGGCTCTCTCT------------------------------------------CTCTCTCTGC--------------CT---CTATCGCTGCATTCGTTTGAGCG---CCA-----ATTAGGCAAAACTTCGCGACAGTTTTCTG
droMoj3	scaffold_6496:24608469-24608630 -	TTTGCT--GG----------G-AACGCC-GT----------------------------------TAGCAACAGCTG------------TTGTTAT----TGGCTTTGTGG----------TCGGCATAA--AAG-----------------------------TAGTCAG--AGCTGTATTTGGCTTCGTGC-------CAGCTGGCATCGCAGCGATATTGCTAGTTGT--------------------T---GCTGCTGTGGCCTGTGTGCTGGCAACAACATCAGCTG--------------TTGTCTT
droGri2	scaffold_15245:17121602-17121640 +	TTTTGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGC--------------------G---GCTCTTGACGGTAGAACA---GTA-----GTTGTCT----------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:14607658-14607807 +	NA	TTTT-GAGTC--------------GAAAGGA-CCAAC-TTTGCTGGCATT--------CGGTGGCCAATAATGCAATTGCATGTCC--------------------------TTGTT--------------------------G------CTGTTGCA-----ATG---------------------------TTGCAGCTGGAATTGCAATTGC---ATTTCTAGT------T---GCC------------GCTG--CTGCTGCTCGAGTGGCAATTA--GCTGGGTGTCTC
droSim1	chr2R:13317686-13317836 +	2	TTTTCGAGTC--------------GAAAGGA-CCAAC-TTTGCTGGCATT--------CGCTGGCCAATAATGCAATTGCGTGTCC--------------------------TTGTT--------------------------G------CTGTTGCA-----ATG---------------------------TTGCAGCTGGAATTGCAATTGC---ATTTCTAGT------T---GCC------------GCTG--CTGCTGCTCGAGTGGCAATTA--GCTGGGTGTCTC
droSec1	super_1:12115359-12115508 +	3	TTTC-GAATC--------------GAAAGGA-CCAAC-TTTGCTGGCATT--------CGCTGGCCAATAATGCAATTGCATGTCC--------------------------TTGTT--------------------------G------CAGTTGCA-----ATG---------------------------TTGCAGCTGGAATTGCAATTGC---ATTTCTAGT------T---GCC------------GCTG--CTGCTGCTCGAGTGGCAATTA--GCTGGGTGTCTC
droYak2	chr2R:14591968-14592144 -	7	TTTTCGGGTC--------------GAAAGGA-CCAACTTTTGTTGGCATT--------CGCTGGCCAATAATGCAATTGCGTGTCC--------------------------TTGTT--------------------------G------CTGTTGCA-----ATGTTGCAACTTGCA--------------------ACTGGAATTGCAATTGC---ATTTCTAGTTGCTTCTCCTCTTTTT---CCTGCTGCTC--CTACTCCTCGAGTGGCAATTA--GCTGGGTGTCTC
droEre2	scaffold_4845:8798992-8799150 +	3	TTTC-GCGTC--------------GAAAGGA-CCAAC-TTTGCTGGCACT--------CGCTGGCCAATAATGCAATTGCGTGTCA--------------------------TTGTT--------------------------G------CTGTTGCA-----ATG---------------------------TTGCAACTGGAATTGCAATTGC---ATTTCTAGTTGCTCCTCATGCT------------GCTG--CTGCTCCTCGAGTGGCAATTA--GCTGGGTGTCTC
droEug1	scf7180000409663:750613-750768 -	8	TTTTTCCTTC--------------GAAAGGA-CCAAC-TTCGATGAGATT--------TGCTGGCTAGAAATGCAATTGCGTGTCC--------------------------TTGTT--------------------------G------CAGTTGCACAGCCATG---------------------------TTGC------ACTTGTAATTGC---AATTCTAGTTGCTGTT---TGT------------GCCG--CTGCTGCTCGAGTGGCAATTA--GCAGGGTGTCTC
droBia1	scf7180000302292:1790364-1790532 -	5	CGCC-GCGGA--------------AGAAGGA-CCAAC-TTCGATGGCATT--------TGCTGGCCAATAATGTAATTTCGTGTCC--------------------------TTGCT--------------------------G------CACTTGCAACGACAAG-------TTGCAA-T-GCCC------------GCTGCACTTGTAATTGC---AGTTCTAGTTGCT------GCC------GCT---GCTGGCCTGCTGCTCGAGTGGCAATTA--GCAGGGTGTCTC
droTak1	scf7180000415991:23390-23548 +	2	TTGA---GGG--------------AAAAGGA-CCAAC-TTCGATGAGATT--------AGCTGGCGAATAATGCAATCGCGTGACC--------------------------TTGTT--------------------------G------CAGTTGCATTGGCAAG-------TTGCAAGTTGCTC------------GCTGCCCCAGCAAATGC---AATTCTAGT------T---GC---------------AG--CTGCTGCTCGAGTGGCAATTA--GCAGGGTGTCTC
droEle1	scf7180000490996:1014509-1014655 -	7	TCCC-GGCTC----------------AAAGC-TCACC-TTCTTCTGCACT--------GGCTTGGCCATCA-GCTGTTGC-TG--------------------------------TT--------------------------G------CTGTTG-------ATG-------CTGCTG-C-TG---------TTGCAGTTGCTGCTGCAGTTGC---TGTTGCTGT------T---GCT------------GCTG--CTGCTGCTGCAGCGGGTAGTA--GCCATGCGGCAG
droRho1	scf7180000766409:161897-162055 -	2	TTGC-TAGAA--------------AAAATAGGCAAAC-TTCGATGAGCTT--------TGCTGGAAAATAATGCAATTGCGTGTTC--------------------------GTGCT--------------------------G------TAGTTGAAATGGCATG-------TTGCAA-T-GCTT------------ACTGCACTTGTAAGTGC---AATTTCAGT------T---GC---------------AG--CTGCTGCTCTAGTGGCAATTA--GCAGGGTGTCTC
droFic1	scf7180000453811:359819-359967 -	7	TTCC-GAGGA--------------AAAAGGG-ACAAC-TTCGATGACATT--------TACTGGCCAATAATGCAATTGCGTG----------------------------------------------------------------------TTGCAATGGCAAG-------TTGCAA-C-ACTA------------GTTTCACTTGCAAGTGC---AATTTTCGT------T---GCA------------ACTG--CTGCTGCTCGAGAAGCAATTA--GCAGGGTGTCTC
droKik1	scf7180000302682:297395-297515 +	3	TTTT-G------------------AAAAGGA-CAAAG-TTCGATGCGATTTGCTCTTTCGCTGGCCCATAATGCAATTGCA---GC--------------------------TTGGC--------------------------T------CTGTTGCA-----ATA-----------------TTC------------GGTGCCCTT------------------------------------------------------TAACCCAAGAGGCAATTA--GCTGGGCGTCTC
droAna3	scaffold_13334:1368045-1368196 +	1	TTTT-GAGCT--------------G------------------------------------------------CAGTTGC------------------------AGATAAAGTTACAGTTGTTGTTGCTACTT---TCACGTTGTTGTTGTTGTTGT-------TG---------------------------CGGCAGCTGCAGTTGCAGTTGC---AGTTGCAAT------T---GTTGCTGCAGCT---GTTGGCC--TAATGAGAGTGGCCAGCAATGCGGCACGAATC
droBip1	scf7180000396006:46261-46375 +	1	T-----------------------------------------------------------------------GCACTTGC-TGTAC--------------------------CTGTT--------------------------G------CA------C----ATGTTG----CACCTG-T-TGCTG------CTGCTGCTGCACTTGCACTTGCTGCACTTGCACT------T---GCT------------GTTG--CTGCTGCTGAGGTGGCAGATA--GCCGGGTGC-TT
dp4	chrXL_group3a:862470-862596 -	14	A----------------------------------AC-TCTGCTGCCAGT--------AGTTGGCCATTGAGAAAATTGTGTGCCCTGGAATTTAATTCATTGCAAACAA-ATTGCT--------------------------G------CTGCT----------------------------------------------G---CTGCTGCTGC---TGCTGTTGT------T---GCT------------GCTG--CTGCCGTTGCAGTGGCAATT---------------
droPer1	super_15:2034074-2034206 +	3	A----------------------------------AC-TCTGCTGCCAGT--------AGTTGGCCATTGAGAAAATTGTGTGCCCTGGAATTTAATTCATTGCAAACAA-ATTGCT--------------------------G------CTGCT-------------------------------------------GCCGCTGCTGCTGTTGT---TGTTGTGGT------T---GCT------------GCTG--CTGCCGTTGCAGTGGCAATT---------------
droWil1	scaffold_181096:6674642-6674780 +	22	CTTG-GTGCCGTATCAAAGCTGGCATATAGT-TCAAC-TTCTTCA----T--------CGGTGGCAT-----------------------------------------CAC-----------------------------------------GTTGCAGTTG-TTG-------TTGTTG-T-TGTTGTTGCTGTTGCAGCTGTTGTTGTTGCTGT---TGTTGTTGC------T---GCA------------GCTG--CTGCTGCTCAAGTG---------------------
droVir3	scaffold_12822:1548557-1548661 -	15	TGTT---------------------------------------------------------------------------------G--------------------------CTGCT--------------------------G------CTGTTGCAATTG-TTG-------CTGCAG-C-TGTT------------GTTGCTGTTGCAGCTGC---AGCTGTAAC------TGTTGCT------------GCTG--CTGGGCATAGAGCTGCTCCTG--GT--AGTGCTTG
droMoj3	scaffold_6540:8945968-8946087 +	11	AGCC--------------------AGCATCG-ACAAC-TTGGCTGCAATT--------CA--------------------------------------------------GGTTGCAGCTACTGCTGTTGCCTGTTGCCTGTTG------CCGTTGCC-------G---------------------------TTGCTGCTGCAGTTGCAGTTGC---AGTTGTAGT------T---ACC------------GTTG--CAATTGC----------------------------
droGri2	scaffold_15245:16288597-16288735 +	30	TGTT-G--------------------------TCAGC-GTTGTCGT--TG--------TGCTTGTTGATTTTCCAGTTGCT----G--------------------------CTGTT--------------------------G------CTGTTGCAGTTGC-AG-------TTGCA--------------------GCTGTTGCTGCTGTTGC---AGTTGCAGTTGTTGCT---GC---------------TG--CTGCTGTTGTTGTTGGTGTTG--TC-GGTGGTGTC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TTTTGA--GTCG-AAAGGACC-AACTTT-GC----------------------------------TGGCATTCGGT-GGCCAA----TAATGCAATTGCATGTCCTTGTTG----------CTGTTGCAATG----------------------------------------------------------TTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC--------------------C---GCTGCTGCTGCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC

Size

Hit Count

Total Norm

droSim1

TTTCGA--GTCG-AAAGGACC-AACTTT-GC----------------------------------TGGCATTCGCT-GGCCAA----TAATGCAATTGCGTGTCCTTGTTG----------CTGTTGCAATG----------------------------------------------------------TTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC--------------------C---GCTGCTGCTGCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................................................................................................................................................CAGCTxGAATTGCAATGGC..............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

TTTCGA--ATCG-AAAGGACC-AACTTT-GC----------------------------------TGGCATTCGCT-GGCCAA----TAATGCAATTGCATGTCCTTGTTG----------CAGTTGCAATG----------------------------------------------------------TTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC--------------------C---GCTGCTGCTGCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............................................................................................................................................................................................................................................................................TG---GCA-----GTTAGCTGG-------------TTGT...	18	1	3.00	0.00	0.00	3.00
..................................................................................................................................................................................................................................................................GCAGCTGCTCGAGxG---GCA-----AT...........................	19	1	1.00	0.00	1.00	0.00
..............................................................................................................................GCAATG----------------------------------------------------------CTT-------CAGCTGGAA........................................................................................................	18	1	1.00	0.00	1.00	0.00
...................................................................................................ATGTxCTTGATG----------CAGTTGC.........................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TTTCGG--GTCG-AAAGGACC-AACTTTTGT----------------------------------TGGCATTCGCT-GGCCAA----TAATGCAATTGCGTGTCCTTGTTG----------CTGTTGCAATG----------------------------------------------------------TTGCAACTTGCAACTGGAATTGCAATTGCATTTCTAGTTGCTTCTCCTCTTTTTCCT--GCT---GCTCCTACTCCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..TCGG--GTAG-AAAGGACC-AT.................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.TTCGG--CTCG-xAAGGACC-A..................................................................................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................................................................................................................TG---GCA-----GTTAGCTGG-------------TTGT...	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TTTCGC--GTCG-AAAGGACC-AACTTT-GC----------------------------------TGGCACTCGCT-GGCCAA----TAATGCAATTGCGTGTCATTGTTG----------CTGTTGCAATG----------------------------------------------------------TTG-------CAACTGGAATTGCAATTGCATTTCTAGTTGCTC-----------CTCATGCT---GCTGCTGCTCCTCGAGTG---GCA-----ATTAGCTGG-------------GTGTCTC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................................................................................................................................................................................................................................................................TG---GCA-----GTTAGCTGG-------------TTGT...	18	1	4.00	0.00	0.00	0.00	4.00
..................................................................................................CGTGTCATCGTTG----------ATGTTGC.........................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................CGGGTCATCGTTG----------CTGTT...........................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................CGGGTCATCGTTG----------CTGTTGC.........................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................................................................................................AAGCT---GCTGCTGCTCCTCCA...........................................	20	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................CGTGTCTTTGTTG----------CTGTC...........................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................CTCATGCT---GCTGCTCGTC................................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

TTCTGA--AAGG-GAAGAGCCTTAGATT-ATATTGAAGATTCTATTCTGGCACGGACCAGGACTCTGTCATACTCT-AATC----------------ATATTTAAT-----ACATTTAGTATTATAGCTT----------------------AGT---------------------------------------------------------------------------C--------------------C---TTTGCTAGTCCTTCAGTG----------------------------------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...TGA--AAGG-GAAGGGCATT..................................................................................................................................................................................................................................................................................................	17	1	12.00	0.00	0.00	12.00	0.00
.....A--AAGG-GAAGGGCCTTTG................................................................................................................................................................................................................................................................................................	17	1	8.00	0.00	0.00	8.00	0.00
....GA--AAGG-GAAGAGCATTTGA...............................................................................................................................................................................................................................................................................................	19	1	7.00	7.00	0.00	0.00	0.00
....GA--AAGG-GAAGAGCATTTGAT..............................................................................................................................................................................................................................................................................................	20	1	3.00	3.00	0.00	0.00	0.00
....GA--AAGG-GAAGGGCCTTTGAT..............................................................................................................................................................................................................................................................................................	20	1	3.00	3.00	0.00	0.00	0.00
...TGA--AAGG-GAAGGGCAT...................................................................................................................................................................................................................................................................................................	16	1	3.00	0.00	0.00	3.00	0.00
...TGA--AAGG-GAAGAGCATTTG................................................................................................................................................................................................................................................................................................	19	1	3.00	3.00	0.00	0.00	0.00
....GA--AAGG-GAAGGGCATT..................................................................................................................................................................................................................................................................................................	16	1	3.00	0.00	0.00	3.00	0.00
.....A--AAGG-GAAGGGCCTTTGA...............................................................................................................................................................................................................................................................................................	18	1	3.00	3.00	0.00	0.00	0.00
.....A--AAGG-GAAGAGCATTTGA...............................................................................................................................................................................................................................................................................................	18	1	2.00	1.00	0.00	1.00	0.00
.....A--AAGG-GAAGGGCATTAG................................................................................................................................................................................................................................................................................................	17	1	2.00	0.00	0.00	2.00	0.00
...TGA--AAGG-GAAGAGCATTTGAT..............................................................................................................................................................................................................................................................................................	21	1	2.00	2.00	0.00	0.00	0.00
.....A--AAGG-GAAGGGCATTAGA...............................................................................................................................................................................................................................................................................................	18	1	2.00	2.00	0.00	0.00	0.00
....GA--AAGG-GAAGAGCATTTG................................................................................................................................................................................................................................................................................................	18	1	2.00	2.00	0.00	0.00	0.00
...TGA--AAGG-GAAGAGCATTT.................................................................................................................................................................................................................................................................................................	18	1	2.00	2.00	0.00	0.00	0.00
....GA--AAGG-GAAGAGCATTT.................................................................................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
....GA--AAGG-GAAGGGCGTTAG................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
........AAGG-GAAGGGCATTAGAT..............................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....A--AAGG-GAAGGGCATTAGAT..............................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.....A--AAGG-GAAGAGCATTAGA...............................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...TGA--AAGG-GAAGAGCATTTGA...............................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...TGA--AAGG-GAAGGGCCTTT.................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....A--AAGG-GAAGCGCCTTTG................................................................................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
.....A--AAGG-GAAGAGCATTTG................................................................................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................ATACTTCAT-----ACATTTAGT.................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....GA--AAGG-GAAGGGCATTAGAT..............................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..TTGA--AAGG-GAAGGGCCTT..................................................................................................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
....................CTTGGATT-xTATTGAAGA..................................................................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
..............................................CTGGCACGGACTTGGA...........................................................................................................................................................................................................................................................	16	1	1.00	0.00	0.00	1.00	0.00
...TGA--AAGG-GAAGCGCAT...................................................................................................................................................................................................................................................................................................	16	1	1.00	0.00	0.00	1.00	0.00
.....A--AAGG-GAAGGGCCTTAGATC-............................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
........AAGG-GAAGGGCCTTTGA...............................................................................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
....GA--AAGG-GAAGGGCCTTTG................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
........AAGG-GAAGCGCCTTTGA...............................................................................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00

dp4

TGTTGC--ATGA-AGAGGACCCAACTTT-CCA---------------------------------GGAGATTTTCT-GGCAGC----TAATGCAATTGTGGTGCAT-----AGTTTCGGAGCTGTGGCATT-----------------------------------------------------------------------------------------------------------------CTC--ACA---GTTGCTGCAGCTCAAGTG---GCA-----ATTAGAAGG---------------ATCTG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..................................................................................................................TTCGGGGCTGTGGAATT-----------------------------------------------------------------------------------------------------------------CTC--................................................................	20	1	1.00	0.00	0.00	0.00	1.00

droPer1

TGTTGC--ATGA-AGAGGACCCAACTTT-CCA---------------------------------TGAGATTTTCT-GGCCGC----TAATGCAATTGTGGTGCAT-----AGTTTCGGAGCTGGGGCATT-----------------------------------------------------------------------------------------------------------------CTC--ACA---GTTGCTGCAGCTCAAGTG---GCA-----ATTAGAAGG---------------ATCTG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................................................................................................................TTTCGGAGCTGGGGCCTG-----------------------------------------------------------------------------------------------------------------.....................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

TTTTTT--ATTC-AAGCTCGG-AATTTA-GC----------------------------------TAGCTGTAGCTGGGCCAATAGCTAATCCAATTGCATGACAT-----TTCC-----------CCTT----------------------GGT---CCT---TGGATGGTTCTCTGTGTCTGTCCATGTTT-------CTG-----------------------------------------------CTAGCGCTGCTG--CCTCAAGTG---GCA-----ATTAT-TAG-------------ACAACTT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........................................................................................................AT-----TTxC-----------CCTT----------------------GGT---CAT---TGG..................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

GTTATTATATTGCAGAGAACG-AAC------------------------------------------GCATTGAAT-GACGA----------CAAGTGTGCGCTCCTTTTG----------GC-TTGCACAGTTGCATTAATATTGCGCTGTTGTTGTCGTTGCTTTACGGCTCTCTCT------------------------------------------CTCTCTCTGC--------------CT---CTATCGCTGCATTCGTTTGAGCG---CCA-----ATTAGGCAAAACTTCGCGACAGTTTTCTG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..................................................................................................................................................CGCTGTTGTTGTTGCTGC.....................................................................................................................................................	18	2	1.50	0.00	0.00	0.00	0.00	1.50
..................................................................................................................................................CGATGTCGTTGTCGTTGCT....................................................................................................................................................	19	1	3.00	0.00	0.00	0.00	0.00	3.00
..........................................................................................................................................TAATAxTGCGCCGTTGTTGTCG.........................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................................................................GCGCTGTTGTTGTTGTTGT.....................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
.....................................................................................................................................................TGTTGTTGTTGTTGCTTT..................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00	0.00
.......................................................................................................................................................................TCAGCTCTCTCT------------------------------------------CTCTCTCT....................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
...................................................................................................................................................GCTGTTGTTGGTGTTGCT....................................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33	0.00
...................................................................................................................................................GCTGTTGTTGTTGTTGTTT...................................................................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00	0.00
.....................................................................................................................................................................................................................................................CT---CTATCGCAGCATTCGTG..............................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...........................................................................................................................................................................CTCTCTCT------------------------------------------CTCTCTCTCT--------------CT---CT.............................................................	22	12	0.08	0.00	0.00	0.00	0.08	0.00
............................................................................................................................................................................TCTCCCT------------------------------------------CTCTCTCTGT--------------CT---C..............................................................	20	4	0.25	0.00	0.00	0.25	0.00	0.00
....................................................................................................................................................CGGTTGTTGTCGTTGTTT...................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

TTTGCT--GG----------G-AACGCC-GT----------------------------------TAGCAACAGCTG------------TTGTTAT----TGGCTTTGTGG----------TCGGCATAA--AAG-----------------------------TAGTCAG--AGCTGTATTTGGCTTCGTGC-------CAGCTGGCATCGCAGCGATATTGCTAGTTGT--------------------T---GCTGCTGTGGCCTGTGTGCTGGCAACAACATCAGCTG--------------TTGTCTT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
....................................................................................................................................................................................................................CAGTGATATTGCTATTTGT--------------------..............................................................	19	1	5.00	3.00	1.00	1.00	0.00
...................................................................................................................................................................................................................................TTGT--------------------T---GCTGCTGTCGCG..............................................	17	1	1.00	0.00	1.00	0.00	0.00
.....................................................................AACAGCTG------------TCGTTAT----TTGCT................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................................................................................................................................TGTGGCCTGTGTGxTGGAAAC................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................TTGTGG----------TGGGCATCA--AAG-----------------------------.....................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droGri2

TTTTGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGC--------------------G---GCTCTTGACGGTAGAACA---GTA-----GTTGTCT----------------------

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

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

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image