dme-mir-3645- 12- and 20-way alignments

dme-mir-3645	chrX:5516313-5516449 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 5516358-5516379
   star strand at position 5516429-5516449
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:5516298-5516464 -	AAA--CAAATCGATATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGGCGCTGTTTACTGTTTA-------------CGATCGCACTGGAAGTGCGCTTTCCGGCGCCTTTGGAAGCCAGC------------------------------------------ACTCAAGTTTCCTTCATTGTTTTCCTTTCTT------------------TCCCCTCTCTCTCTCCC--------CGCAGGCAGCTTATACCGAG
droSim1	chrX:4275639-4275796 -	AAA--CAAATAGAAATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGGCGCTGTTTATTGTTTA-------------CGATCG---------TGCGCTATTCGGCGCCTTTGGAAGCCAGC------------------------------------------ACTCAAGTTTCCCTCATTGTTTTCCTTTCTT------------------CCCCCCCTCTCTCTCCC--------CGCAGGCAGCTTACACCGAG
droSec1	super_4:1240682-1240837 +	AAA--CAAATAGAAATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGGCGCTGTTTACTGTTTA-------------CGATCG---------TGCGCTATTCGGCGCCTTTGGAAGCCAGC------------------------------------------ACTCAAGTTTCCCTCATTGTTTTCCTTTCTT------------------TCCCC-CTCTCTCA-CC--------CGCAGGCAGCATACACCGAG
droYak2	chrX:2953226-2953406 +	AAA--CAAATCGATATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGATGCTGTTTACTGTTTACAACCGCT-------TTCGCACTGGAAGT-CGGTTTTCGGCGCCTTGGAAAACCAAC------------------------------------------ACTCAAGTTTCCTTCTTTGTTTTCCTTTTgTgTgggTgTgTgTgTTTgT-----------------gTgTgTGTCGCAGGCCGCTTACACCGAG
droEre2	scaffold_4690:2867616-2867787 -	AAA--CAAATCGATATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGGCGCTGTTTACTGTTTA-------------CGGTCGCACCGCAAGT-CGCTTTTCGGCGCCTTGGAAAACCAAC------------------------------------------ACTCAAGTTTgggTgTTTGTTTTggTTTgTTgTgggTgTgTgTgTgtgT-----------------gTg---TTCGCAGGCAGCTTACACCGAG
droAna3	scaffold_13117:2022232-2022400 +	AAAAACAAATCGATATGGTAAGTGCGTGAAGTAGGCAACATGACACT-T-------TGTATATT----------TGACAACAATTGAATGTTTA-------------CGGG--------ACCTC--CTATTTCCCGC-TTCGGCAGCAACG-------------ATGACGACGACG-----------------ACTCATGTTTTCCT--TTGTTTTGTTGT--------------------------------------------TTTTCAGGCAGCTTACACCGAG
dp4	chrXL_group1a:8129365-8129509 -	CAA--CAAATCGATATGGTAAGTGGGCT----------------GAA-CAGTAATT--------------------GATATCGTGGCCAATATATAGCCGCTAC--------GTATCG----------------------------------------------TATGGCTTTTCCACTGAGTTTTGCTGGGAGCTAATGTGTTCTT--TTGTTT--------------------------------------------GGT---TTTACAGGCAGCTTACACCGAG
droPer1	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12928:4987992-4988105 +	CGTT-TCAATCAATATGGTAAGTTGGCC----------------AAAATTGTTGTT--------GCT------------TTTA------CGACACGTACATTGTTTATAGT----------------------------------GTGT-TTATTCTTGCT---------------ACT---------------------------------TTT--------------------------------------------GCA---TTTACAGGCAGCTTACACCGAG
droMoj3	scaffold_6359:3485294-3485418 +	CATTTTTAATCAATATGGTAAGTTGGCA----------------CAG-CTGTTGCT--------ATT------------T---------------------------------------------------------TTTAGAGAGCAAAT-A-ATATGTTTCGTTTGTTTTTACAAT------------------------------------------TGTTGT----------------CTTTTTCTCTTGTTATT--------TACAGGCAGCATACACCGAG
droGri2	scaffold_14853:9687493-9687620 +	CAT--TAAATCAACATGGTAAGTTGTAT----------------AAA-T-------CTATTTTTGCAGCTATCTGCAGCATTGTGTGCACTATATACACATTAA------------------------------------TGAGTGTAA-TAA-TTTTGTT---------------GTT---------------------------------TTT--------------------------------------------GTT---TTTACAGGCAGCTTACACCGAG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:5516298-5516464 -	NA	A--AACAAATCGA-TATGGTGAGTGCAG-------GCTGTTTATTGCGG----------------------------------CGCTGTTTA-------CTGTTTACGAT-------C-------------------------------G-----------CACTGGAAGT--GCG-----------CTTTCCGGCG-----------CCTTTGGAAGCCAGCACTCAAGTTTCCTTCATTGTTTTC---CT---TTCTT---TCCCCTCTCTC---------TCTCCCCGCAGGCAGCTTATACCGAG
droSim1	chrX:4275639-4275796 -	1	A--AACAAATAGA-AATGGTGAGTGCAG-------GCTGTTTATTGCGG----------------------------------CGCTGTTTA-------TTGTTTACGAT-------C-------------------------------G-----------T-----------GCG-----------CTATTCGGCG-----------CCTTTGGAAGCCAGCACTCAAGTTTCCCTCATTGTTTTC---CT---TTCTT---CCCCCCCTCTC---------TCTCCCCGCAGGCAGCTTACACCGAG
droSec1	super_4:1240682-1240837 +	1	A--AACAAATAGA-AATGGTGAGTGCAG-------GCTGTTTATTGCGG----------------------------------CGCTGTTTA-------CTGTTTACGAT-------C-------------------------------G-----------T-----------GCG-----------CTATTCGGCG-----------CCTTTGGAAGCCAGCACTCAAGTTTCCCTCATTGTTTTC---CT---TTCTT---TCC-CCCTCTC----------TCACCCGCAGGCAGCATACACCGAG
droYak2	chrX:2953226-2953406 +	1	A--AACAAATCGA-TATGGTGAGTGCAG-------GCTGTTTATTGCGA----------------------------------TGCTGTTTA-------CTGTTTACAAC-------CGCTTTC-------------------------G-----------CACTGGAAGT---CG-----------GTTTTCGGCG-----------CCTTGGAAAACCAACACTCAAGTTTCCTTCTTTGTTTTC---CT---TTTCT---CTCCCTCTCTCTCTTTCTCTCTCTGTCGCAGGCCGCTTACACCGAG
droEre2	scaffold_4690:2867616-2867787 -	1	A--AACAAATCGA-TATGGTGAGTGCAG-------GCTGTTTATTGCGG----------------------------------CGCTGTTTA-------CTGTTTACGGT-------C-------------------------------G-----------CACCGCAAGT---CG-----------CTTTTCGGCG-----------CCTTGGAAAACCAACACTCAAGTTTCCCTCTTTGTTTTC---CT---TTCTT---CTCCCTCTCTCTCTCAC---TCTCTTCGCAGGCAGCTTACACCGAG
droEug1	scf7180000409095:554359-554525 -	1	A--AACAAATCGA-TATGGTGAGTGGT-GGTGCAGCCTGTTTACTGTTA--------------------------------GACTCAGTTAA-------CTGTTTATTTT-------G-------------------------------A-----------T-TTGGAACG---CC-----------CTTTTCGGCG-----------TCTT-GCCAACCGATACTCAAGTTTCCTTCTTTGTTTTC---CT---CTT---TCT-----CTCCG---------TTTCGTTGTAGGCAGCTTACACCGAG
droBia1	scf7180000302069:308686-308867 +	1	A--AACGAATAGA-GATGGTGAGTACGAG-CCGG-ACTGCTTATTGCGGCGCTGCTGCGGCT---------------------CGCTGTTTA-------CCGTTCACTAT-------TGGCCGTTTGCCATCGTCTC------------------------GAATGGAAGG---CC-----------GCCCTGGAAG-----------C-CT-GGGAATCGGTACTCAAGTGTCCCT--TC---------TT---TT---CTTT-------------------TCTCGTTGCAGGCGGCGTACACCGAG
droTak1	scf7180000415289:630465-630594 +	2	A--AACAAATCGA-TATGGTGAGTG---------------------------------------------------------------TTTA-------CTGTTTATTAT-------CGTGTGTGTT----------------------------------TATTGGAAGG---CC-----------GCTTT---------AACAGT----------AAGGGTACTAAT-------CCTTTGTTGTC---TT---TTCTTGTCT-------------------TCTCGTTGCAGGCAGCTTACACCGAG
droEle1	scf7180000491001:943150-943316 +	2	A--AACAAATCGA-TATGGTGAGCGCAA-------AGTGTTTAATGCAG----------------CACTGTTTGT--------TGTTGTTTA-------TTGTTTATTGT-------T-------------------------------G-----------T-TCGGAGCG---CC---------TTATTTTGGGCG-----------TGTTGTGAACGGAGCACTCAAGTTCTCTTCTTTGTTTTT---CT---TTT---TTT-------------------TTCCGATGCAGGCAGCTTACACCGAG
droRho1	scf7180000779976:765851-766001 +	2	A--AACAAATCGA-TATGGTGAGTGCAA-------AGTGTTTATTGCAG----------------------------------CACTGTTTA-------TTGTTTATTGT-------T-------------------------------G-----------T-TCGGAACG---CC---------T-TGTTCTGGCG-----------ACTT-GAGAACGGCTACTCAAGTTTATTTCTTTGTTTTT---CT---TT--------------------------TTTCGATGCAGGCAGCTTACACCGAG
droFic1	scf7180000454072:2595294-2595436 +	1	A--AACAAATCGA-TATGGTGAGTGGTC-------TGTGTTTACTGCAG----------------------------------CACTGTTTA-------C-GTTTGCTGT-------C-------------------------------G------------ACCGCAAGA---CC-----------GTTGGCGGCG-----------TCTT-GAAAACGGACACTCAGTTTCTGC--CTTCT-----------------GTTT-------------------TCTCGTTGCAGGCAGCTTACACCGAG
droKik1	scf7180000302469:622797-622953 +	1	A--AACCAATCGA-TATGGTGAGTGGG---TCGG-CCT-----------------------------------------------CCGTTTACTATTTATTGTTTATTGA-------G-----------------GC------------------------CAACGGCAGTGTGTG-----------ACTTTCGCCG-----------CC-T-GAAAACGGACACTCATGTTTT-TTCTTTGTTTTT---CTTGTT---TTTTT-------------------TTTCGTTGCAGGCAGCTTACACCGAG
droAna3	scaffold_13117:2022234-2022400 +	1	A--AACAAATCGA-TATGGTAAGTGCGTGA-----AGTAGGCAACATGA----------------CACTTTGTATAT-TTGACAACAATTGA-------ATGTTTACG---------------------------------------------------------GGACCT----CC--------T-ATTTCC--CGCTTCGGCAGCAACGATGACGACGACGACTCATGTTTTCC--TTTGTTTTG---TT---GT------------------------------TTTTCAGGCAGCTTACACCGAG
droBip1	scf7180000396425:45801-45969 -	1	AAAAACAAATCGA-TATGGTAAGTGCGTGA-----AGTAGGCAACATGA----------------CACTTTGTATAT-TTAATAACAATTGA-------ATGTTTACG---------------------------------------------------------GGAGCT---CC---------T-ATTTCC--CGCTTCGCCAGCAACGATGACGACGTCGACTCATGTTTTCC--TTTGTTTTG---TT---GT------------------------------TTTTCAGGCAGCTTACACCGAG
dp4	chrXL_group1a:8129365-8129509 -	1	C--AACAAATCGA-TATGGTAAGTGGG---CTGA-ACA-----GTA---------------------ATTGA-----------TATCGTG---------------------------------------------GCCAATATATAGCCGCTACGTATCGT---------------ATGGCTTTT--CCACTGAGTT-----------TTGCTGGGAGCT------AATGTGTTCT--TTTGTT---------------------------------------TGGTTTTACAGGCAGCTTACACCGAG
droPer1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12928:4987995-4988105 +	1	T-----CAATCAA-TATGGTAAGTTGG---CCAAAATTGTT-GTTGC-----------------------------TTTTACGACACGTACA-------TTGTTTATAGT-----------------------------------------------------------------------------------------------------------------------------------GTGTTTATTCTTGCTA---CTTT-------------------TGCATTTACAGGCAGCTTACACCGAG
droMoj3	scaffold_6359:3485302-3485418 +	1	---------TCAA-TATGGTAAGTTGG---CACA-GCTGTT--------------------------------------------------G-------CTATTTTTTA-------GAGAGCAAATA-----------------------ATATGTTTCGT---------------TT---------------------------------------------------GTTTTTACAATTGTTGTC---TT-TTT-------------CTCTT---------GTTATTTACAGGCAGCATACACCGAG
droGri2	scaffold_15252:11712567-11712737 +	6	T--ACCCTATAACCTATAATGAATGTAT-------AAGAAACTTGACAG---AGTTGCAAAACGATATTTAATGCAT-TGGAAAAAAGTCC----------GTTTTCTGTCTATAGAAGAGACTGTT----------------------------------ATAAGT------------------------------------------------TAGCTCGTATTTCAATTTCTACGATTAATATA---CC---CCCTT---TCT-CACTCTT---------TTT--------------TTTAATGGG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

AAA--CAAATCGATATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGGCGCTGTTTACTGTTTA-------------CGATCGCACTGGAAGTGCGCTTTCCGGCGCCTTTGGAAGCCAGC------------------------------------------ACTCAAGTTTCCTTCATTGTTTTCCTTTCTT------------------TCCCCTCTCTCTCTCCC--------CGCAGGCAGCTTATACCGAG

Size

Hit Count

Total Norm

droSim1

AAA--CAAATAGAAATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGGCGCTGTTTATTGTTTA-------------CGATCG---------TGCGCTATTCGGCGCCTTTGGAAGCCAGC------------------------------------------ACTCAAGTTTCCCTCATTGTTTTCCTTTCTT------------------CCCCCCCTCTCTCTCCC--------CGCAGGCAGCTTACACCGAG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................................................................TATTGTTTA-------------CGATCG---------TGCGCT...............................................................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
...........................................................................................................CGATCG---------TGCGCTATTCGGC........................................................................................................................................................	19	1	2.00	0.00	0.00	2.00	0.00
.................GTGAGTGC-------------------AGG-C-------TGTTTATT----------GC...................................................................................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
.....................................................................................TATTGTTTA-------------CGATCG---------TGCGCTT..............................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
..............................................................TT----------GCGGCGCTGTTTATTGTTTA-------------CGA.................................................................................................................................................................................	25	1	2.00	0.00	0.00	0.00	2.00
............................................................................................TG-------------CGATCG---------TGCGCTGTTCGGCG.......................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.............................................................................GCGCTGTTTATTGTTTA-------------CGATCG---------.....................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.................GTGAGTGC-------------------AGG-C-------TGTTTAT................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................TTGTTTA-------------CGATCG---------TGCGCTATTCGGC........................................................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
..................TGAGTGC-------------------AGG-C-------TGTTTATT----------GC...................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................TTA-------------CGATCG---------TGCGCTATTCGGT........................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........TAGAAATGGTGAGTGC-------------------AGG-C-------T......................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................TTCGGCGCCTTTGGAAGAC...........................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................TTA-------------CGATCG---------TGCGCTATTCGG.........................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................ATTCGGCGCCTTTGGAAGCC...........................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................TTA-------------CGATCG---------TGCGCTATTCGGCGC......................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
.................GTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGGCA...............................................................................................................................................................................................................	26	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................GTTTA-------------CGATCG---------TGCGCTATTCGGCGCCTT...................................................................................................................................................	29	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................CTTTGGAAGCCAGC------------------------------------------ACTCAAGT......................................................................................	22	1	1.00	0.00	0.00	1.00	0.00

droSec1

AAA--CAAATAGAAATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGGCGCTGTTTACTGTTTA-------------CGATCG---------TGCGCTATTCGGCGCCTTTGGAAGCCAGC------------------------------------------ACTCAAGTTTCCCTCATTGTTTTCCTTTCTT------------------TCCCC-CTCTCTCA-CC--------CGCAGGCAGCATACACCGAG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................................................................................ACTGTTTA-------------CGATCG---------TGCGCTA..............................................................................................................................................................	21	1	2.00	2.00	0.00	0.00
..........................................................................................................................................TTTGGAAGCCAGC------------------------------------------ACTCAAGA......................................................................................	21	1	2.00	1.00	0.00	1.00
.................GTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGG.................................................................................................................................................................................................................	24	1	2.00	2.00	0.00	0.00
.........................................................................................................................................CTTTGGAAGCCAGC------------------------------------------ACTCAAG.......................................................................................	21	1	2.00	2.00	0.00	0.00
..........................................................................................................................................TTTGGAAGCCAGC------------------------------------------ACTCAAGT......................................................................................	21	1	2.00	2.00	0.00	0.00
.........................................................................................................................................CTTTGGAAGCCAGC------------------------------------------ACTCAAGT......................................................................................	22	1	2.00	1.00	1.00	0.00
.......................................................................................................................................GCCTTTGGAAGCCAGC------------------------------------------ACTCAAG.......................................................................................	23	1	1.00	0.00	0.00	1.00
.............................................................................................A-------------CGATCG---------TGCGCTGTTCGGCG.......................................................................................................................................................	21	1	1.00	1.00	0.00	0.00
........................................................................................TGTTTA-------------CGATCG---------TGCGCTATT............................................................................................................................................................	21	1	1.00	1.00	0.00	0.00
.....................................................................................................................................GCGCCTTTGGAAGCCAGC------------------------------------------ACTCAAG.......................................................................................	25	1	1.00	0.00	1.00	0.00
....................................................................................TTACTGTTTA-------------CGATCG---------TGCGCTATT............................................................................................................................................................	25	1	1.00	1.00	0.00	0.00
............................................................................................TA-------------CGATCG---------TGCGCTATTCGGCT.......................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
.................GTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGA.................................................................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00
..A--CAAGTAGAAGTGGTGAGTGC-------------------A..................................................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
..........................................................................................................................................TTTGGAAGCCAGC------------------------------------------ACTCAAG.......................................................................................	20	1	1.00	1.00	0.00	0.00
...........................................................................................................................................TTGGAAGCCAGC------------------------------------------ACTCAAGT......................................................................................	20	1	1.00	0.00	0.00	1.00
.....................................................................................TGCTGTTTA-------------CGATCG---------TGCGCTA..............................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
.......AATAGAAATGGTGAGTGC-------------------A..................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
......................................................................................ACCTTTTA-------------CGATCG---------TGCGCTAT.............................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
..A--CAAATAGAAATGGTGAG.........................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.........................................................................................................................................CTTTGGAAGCCAGC------------------------------------------ACTCAAGC......................................................................................	22	1	1.00	1.00	0.00	0.00
.........................................................................................................................................CTTTGGAAGCCAGC------------------------------------------ACTCTAG.......................................................................................	21	1	1.00	1.00	0.00	0.00
..............................................................................CGCTGTTTACTGTTTA-------------CGATC...............................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
...........................................................................CGTCGCTGTTTACTGTTTT-------------....................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

AAA--CAAATCGATATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGATGCTGTTTACTGTTTACAACCGCT-------TTCGCACTGGAAGT-CGGTTTTCGGCGCCTTGGAAAACCAAC------------------------------------------ACTCAAGTTTCCTTCTTTGTTTTCCTTTTgTgTgggTgTgTgTgTTTgT-----------------gTgTgTGTCGCAGGCCGCTTACACCGAG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.................GTGAGTGC-------------------AGG-C-------TGTTTATT----------GC...................................................................................................................................................................................................................	22	1	6.00	0.00	0.00	0.00	0.00	6.00
.................GTGAGTGC-------------------AGG-C-------TGTTTATT----------.....................................................................................................................................................................................................................	20	1	3.00	0.00	0.00	0.00	0.00	3.00

droEre2

AAA--CAAATCGATATGGTGAGTGC-------------------AGG-C-------TGTTTATT----------GCGGCGCTGTTTACTGTTTA-------------CGGTCGCACCGCAAGT-CGCTTTTCGGCGCCTTGGAAAACCAAC------------------------------------------ACTCAAGTTTgggTgTTTGTTTTggTTTgTTgTgggTgTgTgTgTgtgT-----------------gTg---TTCGCAGGCAGCTTACACCGAG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.................................................................................................................................................................................................................................TGTGTGTGTGTGTxTGT-----------------GTG---......................	19	20	1.00	0.00	0.20	0.00	0.80
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT-----------------GT..........................	21	8	2.00	0.00	0.00	0.38	1.63
.................................................................................................................................................................................................................................TGTGTGTGTGTGTGTGT-----------------GTG---T.....................	21	8	2.00	0.00	0.00	0.38	1.63
................................................................................................................................................................................................................................GTGGGTGTGTGGGTGGGT-----------------GTG---......................	21	1	14.00	0.00	0.00	0.00	14.00
................................................................................................................................................................................................................................GTGGGTGTGTGGGTGGGT-----------------GT..........................	20	1	11.00	0.00	1.00	0.00	10.00
...............................................................................................................................................................................................................................TGTGTGTGTGTGTxTGTGT-----------------G...........................	19	20	0.50	0.00	0.10	0.00	0.40
...................................................................................................................................................................................................................................TGTGTGTGTGTGTxT-----------------GTG---TG....................	19	20	0.50	0.00	0.10	0.00	0.40
................................................................................................................................................................................................................................GTGGGTGTGTGGGTGGGT-----------------G...........................	19	1	8.00	0.00	0.00	0.00	8.00
...................................................................................................................................................................................................................................TGTGTGTGTGTGTxT-----------------GTG---TGC...................	20	14	0.36	0.00	0.00	0.00	0.36
................................................................................................................................................................................................................................GTGGGTGTGTGGGTGGGT-----------------............................	18	1	5.00	0.00	0.00	0.00	5.00
.....................................................................................................................................................................................................................................TGTGTGTGTGTGT-----------------GTG---TG....................	18	12	0.42	0.00	0.00	0.17	0.25
...................................................................................................................................................................................................................................TGTGTGTGTGTGTGT-----------------GTG---......................	18	12	0.42	0.00	0.00	0.17	0.25
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTG..............................................	18	12	0.42	0.00	0.00	0.17	0.25
.................................................................................................................................................................................................................................TGTGTGTGTGTGTGTGT-----------------G...........................	18	12	0.42	0.00	0.00	0.17	0.25
................................................................................................................................................................................................................................GTGTGTGTGTGTGTGTGT-----------------GTG---T.....................	22	6	0.67	0.00	0.00	0.67	0.00
.....................................................................................................................................................................................................................................TGTGTGTGTGTGT-----------------GTG---TGTGC.................	21	11	0.27	0.09	0.00	0.18	0.00
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT-----------------GC..........................	21	11	0.27	0.09	0.00	0.18	0.00
.................................................................................................................................................................................................................................TGTGTGTGTGTGTGTGT-----------------GTG---C.....................	21	11	0.27	0.09	0.00	0.18	0.00
....................................................................................................................................................................................................................................GTGTGTGCGTGTGT-----------------GTG---T.....................	18	11	0.27	0.00	0.00	0.27	0.00
.............................................................................................................................................................................................................................GTGGTGCGTGTGTGTGTGTGT-----------------G...........................	22	1	3.00	0.00	0.00	0.00	3.00
....................................................................................................................................................................................................................................GTGTGTGTGTGCGT-----------------GTG---TC....................	19	9	0.33	0.11	0.00	0.00	0.22
......................................................................................................................................................................................................................................GTGCGTGTGTGT-----------------GTG---TTTG..................	19	8	0.38	0.00	0.13	0.00	0.25
................................................................................................................................................................................................................................GTGTGTGCGTGTGTGTGT-----------------............................	18	11	0.27	0.00	0.00	0.27	0.00
...................................................................................................................................................................................................................................TGTGTGTGTGTGTGT-----------------GTG---TGC...................	21	11	0.27	0.09	0.00	0.18	0.00
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT-----------------TTG---T.....................	23	6	0.50	0.00	0.00	0.50	0.00
.............................................................................................................................................................................................................................GTGGTGCGTGTGTGTGTGTGT-----------------GTG---TT....................	26	1	3.00	0.00	0.00	0.00	3.00
...................................................................................................................................................................................................................................TGTGTGTGTGTGTGT-----------------GTG---T.....................	19	10	0.30	0.00	0.00	0.00	0.30
..................................................................................................................................................................................................................................GTGTGTGCGTGTGTGT-----------------GT..........................	18	11	0.27	0.00	0.00	0.27	0.00
................................................................................................................................................................................................................................GTGTGTGTGTGTGTGTGT-----------------GT..........................	20	8	0.38	0.00	0.00	0.38	0.00
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT-----------------GTG---T.....................	23	6	0.50	0.00	0.00	0.50	0.00
..................................................................................................................................................................................................................................GTGTGTGTGTGTGTGT-----------------GTG---T.....................	20	8	0.38	0.00	0.00	0.38	0.00
................................................................................................................................................................................................................................GTGCGTGTGTGTGTGTTT-----------------G...........................	19	8	0.38	0.00	0.13	0.00	0.25
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT-----------------............................	19	10	0.30	0.00	0.00	0.00	0.30
.................................................................................................................................................................................................................................TGTGTGTGTGTGTGTGT-----------------GT..........................	19	10	0.30	0.00	0.00	0.00	0.30
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT-----------------GTG---TGC...................	25	6	0.50	0.00	0.00	0.00	0.50
...............................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT-----------------GTG---......................	22	7	0.43	0.00	0.00	0.29	0.14

droAna3

AAAAACAAATCGATATGGTAAGTGCGTGAAGTAGGCAACATGACACT-T-------TGTATATT----------TGACAACAATTGAATGTTTA-------------CGGG--------ACCTC--CTATTTCCCGC-TTCGGCAGCAACG-------------ATGACGACGACG-----------------ACTCATGTTTTCCT--TTGTTTTGTTGT--------------------------------------------TTTTCAGGCAGCTTACACCGAG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
......................................................................................................................................................G-------------ATGACGACGAGG-----------------ACGCAT........................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................................................GACG-------------ATGACGACGACG-----------------AG............................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
...................................................................................................................................................GACG-------------ATGATGACGACG-----------------AC............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................................................GACG-------------ATGACGATGACG-----------------AC............................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

dp4

CAA--CAAATCGATATGGTAAGTGGGCT----------------GAA-CAGTAATT--------------------GATATCGTGGCCAATATATAGCCGCTAC--------GTATCG----------------------------------------------TATGGCTTTTCCACTGAGTTTTGCTGGGAGCTAATGTGTTCTT--TTGTTT--------------------------------------------GGT---TTTACAGGCAGCTTACACCGAG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........GATATGGTAGCTGGGCT----------------G..................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...........GATATGGTAGATGGGCT----------------G..................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......AATCGATAAGGTAAATGGG.....................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........GATATGGTAGGTGGGCT----------------A..................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

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

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CGTT-TCAATCAATATGGTAAGTTGGCC----------------AAAATTGTTGTT--------GCT------------TTTA------CGACACGTACATTGTTTATAGT----------------------------------GTGT-TTATTCTTGCT---------------ACT---------------------------------TTT--------------------------------------------GCA---TTTACAGGCAGCTTACACCGAG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CATTTTTAATCAATATGGTAAGTTGGCA----------------CAG-CTGTTGCT--------ATT------------T---------------------------------------------------------TTTAGAGAGCAAAT-A-ATATGTTTCGTTTGTTTTTACAAT------------------------------------------TGTTGT----------------CTTTTTCTCTTGTTATT--------TACAGGCAGCATACACCGAG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
............................................................................................................................................AGAGAGTAAAT-A-ATATTTT..............................................................................................................................	19	1	88.00	68.00	1.00	3.00	16.00
............................................................................................................................................AGAGAGTAAAT-A-ATATTTTT.............................................................................................................................	20	1	9.00	9.00	0.00	0.00	0.00
............................................................................................................................................AGAGAGTAAAT-A-ATATTT...............................................................................................................................	18	1	6.00	0.00	0.00	0.00	6.00
.............................................................................................................................................GAGAGTAAAT-A-ATATTTTT.............................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................................................................AGAGTAAAT-A-ATATTTTT.............................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droGri2

CAT--TAAATCAACATGGTAAGTTGTAT----------------AAA-T-------CTATTTTTGCAGCTATCTGCAGCATTGTGTGCACTATATACACATTAA------------------------------------TGAGTGTAA-TAA-TTTTGTT---------------GTT---------------------------------TTT--------------------------------------------GTT---TTTACAGGCAGCTTACACCGAG

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																None	None
UNAFold Image																None	None