dme-mir-4976- 12- and 20-way alignments

dme-mir-4976	chr2R:2723037-2723140 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 2723098-2723119
   star strand at position 2723058-2723077
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:2723022-2723155 -	ACATCATCGATTATTGTCGATGCCGGCGTTTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTCCGCG---T--CTGGTCCACG
droSim1	chr2R:1535693-1535826 -	ACATCATCGATTATTGTCGATGCCGGCGTTTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTTGCTCCGCG---T--CTGGTCCACG
droSec1	super_1:401443-401575 -	ACATCATCGATTATTGTCGATGCCGGCGTTTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAA-GCGTCGTCTCGCTTCGCG---T--CTGGTCCACG
droYak2	chr2L:15457678-15457811 -	ACATCATCGATTATTGTCGATGCCGGCGTTTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGTTTGTGTTGTCTGCATTCAGCTCGGTGGATGTCAGCCATCGGTGGAAGGCGTCGTCGCGCTCCGCG---T--CTGGTCCACG
droEre2	scaffold_4929:19824507-19824640 +	ACATCATCGATTATGGTCGATGGCGGCGTCTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCACGGAGTTCGTGTTGTCGGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCGCGCTCCGCG---T--CCGGTCCACG
droAna3	scaffold_13266:9050244-9050380 -	ACATCATCGATTATTGTCGATGTTGGCGTTTC---CTGCT------C------------------------------------------------------------------------------CAAGTTATCGTCAAGCGGGTTTGTGTTGTCGCCATTTAGCTCCGTAGATGTCAGCCACCGGTGGAAGGCGTCATCCAGCTCCTCGGGGT--CATGTCCACT
dp4	chr3:994566-994696 -	ACATCATCGATTATTGTCGATGCTGCTGTTTC---CTGCT------C------------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTCCTTG---C--C---ACCGCT
droPer1	super_2:1175582-1175712 -	ACATCATCGATTATTGTCGATGCTGCTGTTTC---CTGCT------C------------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTCCTTG---C--C---ACCGCT
droWil1	scaffold_180745:52392-52524 +	ACATCATCGATTATCGTTGATGCTGATGTTTTTTCCTGCT------C------------------------------------------------------------------------------CAAGCTAACGTCCAGTGTATTGGTATTTTCAACATTCAGCTCTGTGGATGTTAGCCAACGATGAAATGCATCATCAT----CTTG---TTCC--ATCATCT
droVir3	scaffold_12875:15675060-15675224 -	ACATCATCGATTATTGTTGATGCTGGCGTTTC---CTGTT------CGACAGCAAgTGgTGgTGgTGg---------------------------------------TGgTGggGgtGgTGgTGgCAAGCTATCGTCGAGCGTGTTTGTGCTGTCAACATTCAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCGTCAGCTTCCT-------------CAATT
droMoj3	scaffold_6496:8124753-8124946 +	ACATCATCGATTATTGTTGATGCTGGTGTTTCCTGCTGCTGAACGGCAAgTGt------TGgTGgTGgTggGtgGGgTggGGgTGtTGgTGgTGgTGgTTgTGgTTgTGgTTgTGgTGgTGgTGTCAAGCTATCGTCGAGCGTGTTTGTGCTGTCAACATTGAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCGTC--------------------------
droGri2	scaffold_15245:12478490-12478641 -	ACATCATCGATTATTGTTGATGCTGATGTTTC---CTGCT------CAATTGTAGgTTgTGgTGgtGg---------------------------------------TGgtGgTGgTGgTGgTGgCAAGTTATCGTCAAACATATTTGTACTGTCAATATTGAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCATC--------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:2723022-2723155 -	NA	ACATCATCGATTATTGTCGATG-----CCGGCGTT---TCCCGCTC---------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTCCGC------GTCTGGT----------------CC-ACG
droSim1	chr2R:1535693-1535826 -	55	ACATCATCGATTATTGTCGATG-----CCGGCGTT---TCCCGCTC---------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTTGCTCCGC------GTCTGGT----------------CC-ACG
droSec1	super_1:401443-401575 -	65	ACATCATCGATTATTGTCGATG-----CCGGCGTT---TCCCGCTC---------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAA-GCGTCGTCTCGCTTCGC------GTCTGGT----------------CC-ACG
droYak2	chr2L:15457678-15457811 -	80	ACATCATCGATTATTGTCGATG-----CCGGCGTT---TCCCGCTC---------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGTTTGTGTTGTCTGCATTCAGCTCGGTGGATGTCAGCCATCGGTGGAAGGCGTCGTCGCGCTCCGC------GTCTGGT----------------CC-ACG
droEre2	scaffold_4929:19824507-19824640 +	73	ACATCATCGATTATGGTCGATG-----GCGGCGTC---TCCCGCTC---------------------------------------------------------------------------CAGGCTGTCGTCCACGGAGTTCGTGTTGTCGGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCGCGCTCCGC------GTCCGGT----------------CC-ACG
droEug1	scf7180000409672:4743216-4743349 -	347	ACATCATCGATTATTGTCGATG-----CCGGCGTT---TCCTGCTC---------------------------------------------------------------------------CACGTTATCGTCAAGCGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCATCGATGGAAGGCGTCGTCGGGTTCCGC------GTCAGGT----------------CC-ATT
droBia1	scf7180000302292:3421528-3421661 +	70	ACATCATCGATTATTGTCGATG-----CCGGCGTT---TCCTGCTC---------------------------------------------------------------------------CAAGTTGTCGTCGAGCGAGTCCGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCACCGGTGGAAGGCGTCGTCGGTCTCCGC------GGCGGGT----------------CC-ACT
droTak1	scf7180000415420:352514-352653 +	114	ACATCATCGATTATTGTCGATG-----CCGGCGTT---TCCTGCTC---------------------------------------------------------------------------CAGGTTATCGTCGAGTGAGTTTGTGTTGTCAGCGTTCAGTTCGGTGGATGTCAACCATCGGTGGAAGGCGTCATCGGCCTCCGGCTCCGTCTTGGGT----------------CC-ACT
droEle1	scf7180000491217:258006-258145 +	76	ACATCATCGATTATTGTCGATG-----CCGGCGTT---TCCTGCTC---------------------------------------------------------------------------CAAGTTATCGTCGAGCGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGAAAGGCGTCGTCAGGCTCAGGGGCGTTGTCAGGT----------------CC-ACT
droRho1	scf7180000779196:89887-90023 -	120	ACATCATCGATTATTGTCGATG-----CCGGCGTT---TCCTGCTC---------------------------------------------------------------------------CAAGTTATCGTCGAGCGCGTTTGTGTTGGCAGCATTCAGCTCGGTGGATGTCAGCCATCGATGAAAGGCGTCGTCAGGCTGCGC---GTCGTCAGGT----------------CC-ACT
droFic1	scf7180000453955:564801-564935 +	87	ACATCATCGATTATTGTCGATG-----GCGGCGTT---TCCTGCTC---------------------------------------------------------------------------CGAGTTGTCGTCCAGCGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCATCGGTGGAAGGCGTCATCGGGCTCCGC------GTCATGT----------------CCTGCG
droKik1	scf7180000302630:16328-16464 -	108	ACATCATCGATTATTGTCGACG-----CTGGCGTT---TCCTGCTC---------------------------------------------------------------------------CGAGTTGTCGTCGGGCGAGTTTGTGTTGTCAGCGTTCAGCTCTGTGGACGTCAGCCATCGGTGGAACGCGTCGTCGACCTCCTC---CGCGTCATGT----------------CC-ACG
droAna3	scaffold_13266:9050244-9050380 -	96	ACATCATCGATTATTGTCGATG-----TTGGCGTT---TCCTGCTC---------------------------------------------------------------------------CAAGTTATCGTCAAGCGGGTTTGTGTTGTCGCCATTTAGCTCCGTAGATGTCAGCCACCGGTGGAAGGCGTCATCCAGCTCCTC---GGGGTCATGT----------------CC-ACT
droBip1	scf7180000396427:194063-194199 -	110	ACATCATCGATTATTGTCGATG-----CTGGCGTT---TCCTGCTC---------------------------------------------------------------------------CAAGTTGTCGTCGAGCGGGTTCGTGTTGTCGCCATTCAGCTCGGTGGATGTCAGCCATCGATGGAAGGCGTCATCCGACTCCTC---CGGGTCGTGT----------------CC-ACT
dp4	chr3:994566-994696 -	206	ACATCATCGATTATTGTCGATG-----CTGCTGTT---TCCTGCTC---------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTCCTT------GCC---A----------------CC-GCT
droPer1	super_2:1175582-1175712 -	146	ACATCATCGATTATTGTCGATG-----CTGCTGTT---TCCTGCTC---------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTCCTT------GCC---A----------------CC-GCT
droWil1	scaffold_180745:52392-52526 +	175	ACATCATCGATTATCGTTGATG-----CTGATGTTTTTTCCTGCTC---------------------------------------------------------------------------CAAGCTAACGTCCAGTGTATTGGTATTTTCAACATTCAGCTCTGTGGATGTTAGCCAACGATGAAATGCATCATCATCTTGTTC---C--ATCATCT----------------TC----
droVir3	scaffold_12970:7508989-7509113 -	914	-CAGCACCGAGCT--GGC-ATT-----CTGGCTGT---G-ATGCTCCAGCTGTGCGGCCGCCACATTTGCAGCATTCAGTTTGGCAGCCGCTG-------------------------------------------------------------------------------CTGC-TGCTGCGGCAGCTGCTGCTG-CTGCCGC-----GGCCGCGG----------------CC-ACT
droMoj3	scaffold_6328:978242-978368 -	1166	ACTGCAACGCTT-TTGCCGACGCACAGCTGGCGTT---GC-TGCTG-----------------CTGCTGCTGCTGGCGGAGCAACGGCAGACAACGCTC----------------------C-------------TGCTGCTGCTGCTGT---------------------------------------------CG-CTGCTGC-----AGCTGCAGCCGCTCTGCTTGTGGTC-----
droGri2	scaffold_15245:12478490-12478641 -	1025	ACATCATCGATTATTGTTGATG-----CTGATGTT---TCCTGCTC------------------------------------AATTGTAGCTTCTGCTGCAGCTGCAGCTGCTGCTGCTGCCAAGTTATCGTCAAACATATTTGTACTGTCAATATTGAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCATC--------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ACATCATCGATTATTGTCGATGCCGGCGTTTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTCCGCG---T--CTGGTCCACG

Size

Hit Count

Total Norm

droSim1

ACATCATCGATTATTGTCGATGCCGGCGTTTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTTGCTCCGCG---T--CTGGTCCACG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	22	1	173.00	0.00	66.00	105.00	2.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAG..................................................................................	21	1	40.00	0.00	22.00	18.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGG.................................................................................	22	1	13.00	0.00	4.00	8.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGC.................................................................................	22	1	13.00	0.00	7.00	6.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGG....................................................................................	19	1	8.00	0.00	4.00	4.00	0.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAG..................................................................................	20	1	7.00	0.00	4.00	3.00	0.00
.......................................T------C------------------------------------------------------------------------------CATGCTGTCGTCCATGGAGT.................................................................................	22	1	6.00	0.00	3.00	3.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGA...................................................................................	20	1	5.00	0.00	4.00	1.00	0.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	21	1	4.00	0.00	1.00	3.00	0.00
..............................................................................................................................AGGCTGTCGTCCATGGAGT.................................................................................	19	1	3.00	0.00	1.00	2.00	0.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTT................................................................................	22	1	3.00	0.00	1.00	2.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGTCTGTCGTCCATGGAGT.................................................................................	22	1	2.00	0.00	0.00	2.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGA.................................................................................	22	1	2.00	0.00	1.00	1.00	0.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGG.................................................................................	21	1	2.00	0.00	2.00	0.00	0.00
.............................................................................................................................CAGGCTGTCGTCCATGGAGT.................................................................................	20	1	2.00	0.00	1.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGT.................................................................................	22	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................................................................CTCGGTGGATGTCAGCCAGCT.........................................	21	1	1.00	0.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGTGT.................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.......................................T------T------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................CAGGCTGTCGTCCATGGAG..................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGGGT.................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CGGGCTGTCGTCCATGGAGT.................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGGCGTCCATGGAG..................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGG....................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGGCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CACGCTGTCGTCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAC..................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGCCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTT................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGCCTGTCGTCCATGGA...................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................CAGGCTGTCGTCCATGGAGTT................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGCGT.................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................C------------------------------------------------------------------------------CATGCTGTCGTCCATGGAGG.................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGCCTGTCGTCCATGGAGC.................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGGCCATGGAG..................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCGTGG....................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................C------C------------------------------------------------------------------------------CACGCTGTCGTCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00	0.00

droSec1

ACATCATCGATTATTGTCGATGCCGGCGTTTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAA-GCGTCGTCTCGCTTCGCG---T--CTGGTCCACG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	22	1	2582.00	1627.00	18.00	937.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAG..................................................................................	21	1	330.00	198.00	2.00	130.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGA.................................................................................	22	1	16.00	9.00	0.00	7.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	21	1	13.00	11.00	0.00	2.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGA...................................................................................	20	1	13.00	9.00	0.00	4.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGAAGT.................................................................................	22	1	13.00	12.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGCAGT.................................................................................	22	1	12.00	12.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGC.................................................................................	22	1	9.00	6.00	0.00	3.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGTAGT.................................................................................	22	1	8.00	6.00	0.00	2.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGG....................................................................................	19	1	7.00	1.00	0.00	6.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAG..................................................................................	20	1	5.00	2.00	0.00	3.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGCCGTCCATGGAGT.................................................................................	22	1	5.00	3.00	0.00	2.00
.............................................................................................................................CAGGCTGTCGTCCATGGAGT.................................................................................	20	1	5.00	1.00	0.00	4.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTT................................................................................	22	1	5.00	5.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCGTGGAGT.................................................................................	22	1	5.00	3.00	0.00	2.00
.......................................C------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	22	1	5.00	4.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGCCCATGGAGT.................................................................................	22	1	4.00	4.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGAAG..................................................................................	21	1	4.00	4.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCCGTCGTCCATGGAGT.................................................................................	22	1	4.00	0.00	0.00	4.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGCGT.................................................................................	22	1	4.00	4.00	0.00	0.00
.......................................G------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	22	1	3.00	0.00	0.00	3.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAAT.................................................................................	22	1	3.00	2.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGGGT.................................................................................	22	1	3.00	1.00	0.00	2.00
.......................................T------C------------------------------------------------------------------------------CAGGCTxTCGTCCATGGAGT.................................................................................	21	1	3.00	1.00	0.00	2.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCCTCCATGGAG..................................................................................	21	1	3.00	3.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCTTCCATGGAGT.................................................................................	22	1	3.00	3.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGTAG..................................................................................	21	1	3.00	3.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGGCGTCCATGGAGT.................................................................................	22	1	2.00	2.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCTATGGAGT.................................................................................	22	1	2.00	0.00	0.00	2.00
.......................................T------C------------------------------------------------------------------------------CAGGATGTCGTCCATGGAGT.................................................................................	22	1	2.00	2.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAAGCTGTCGTCCATGGAGT.................................................................................	22	1	2.00	1.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CATGCTGTCGTCCATGGAGT.................................................................................	22	1	2.00	0.00	0.00	2.00
.......................................T------C------------------------------------------------------------------------------CAGACTGTCGTCCATGGAGT.................................................................................	22	1	2.00	1.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTTGTCCATGGAGT.................................................................................	22	1	2.00	2.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCATCCATGGAGT.................................................................................	22	1	2.00	2.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATAGAGT.................................................................................	22	1	2.00	1.00	0.00	1.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGTT..................................................................................	20	1	2.00	2.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CACGCTGTCGTCCATGGAGT.................................................................................	22	1	2.00	2.00	0.00	0.00
.......................................T------A------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	22	1	2.00	0.00	0.00	2.00
.......................................A------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	22	1	2.00	0.00	0.00	2.00
.......................................T------C------------------------------------------------------------------------------CAGGCTCTCGTCCATGGAGT.................................................................................	22	1	2.00	2.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCAGTCGTCCATGGAGT.................................................................................	22	1	2.00	1.00	0.00	1.00
..............................................................................................................................AGGCTGTCGTCCATGGAGT.................................................................................	19	1	2.00	2.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCAATGGAGT.................................................................................	22	1	2.00	1.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTAGTCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGTCTGTCGTCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00
......................................CT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	23	1	1.00	0.00	0.00	1.00
.....................................TCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	24	1	1.00	0.00	0.00	1.00
.....................................................................................................................................................................TCGGTGGATGTCAGCCAGCGGT.......................................	22	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGTTGTCGTCCATGGAG..................................................................................	21	1	1.00	0.00	0.00	1.00
.............................................................................................................................CAGGCTGTCGTCCATGGAG..................................................................................	19	1	1.00	0.00	0.00	1.00
.................................................................................................................................................TTGTGTTGTCAGCATTCAGC.............................................................	20	1	1.00	0.00	0.00	1.00
.CAACATCGATTTTTGTCGA..............................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGCCTGTCGCCCATGGAGT.................................................................................	22	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGCAG..................................................................................	21	1	1.00	1.00	0.00	0.00
......................................AT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGT.................................................................................	23	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAT..................................................................................	21	1	1.00	1.00	0.00	0.00
.....................................................................................................................................................................TCGGTGGATGTCAGCCAGCGA........................................	21	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTC................................................................................	23	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGGCCATGGAGT.................................................................................	22	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAC..................................................................................	21	1	1.00	0.00	0.00	1.00
.....................................................................................................................................................................TCGGTGGATGTCAGCCAGCG.........................................	20	1	1.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------AAGGCTGTCGTCCATGGAG..................................................................................	21	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGATGTCGTCCATGGAG..................................................................................	21	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCACGGAGT.................................................................................	22	1	1.00	1.00	0.00	0.00
.....................................................................................................................................................................TCGGTGGATGTCAGCCAGCGTT.......................................	22	1	1.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGT....................................................................................	19	1	1.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAAA.................................................................................	22	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGT...................................................................................	20	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------TAGGCTGTCGTCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00
...........................................................................................................................................................................GATGTCAxCCATCGGTGGAA-..................................	19	1	1.00	0.00	1.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGTTGTCGTCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00
...............................................................................................................................AGCTGTCGTCCATGAAGT.................................................................................	18	1	1.00	0.00	1.00	0.00
..............................................C------------------------------------------------------------------------------CAxGCTGTCGTCCATGAAGTT................................................................................	21	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGG.................................................................................	22	1	1.00	0.00	0.00	1.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTT...............................................................................	23	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCAATGGAG..................................................................................	21	1	1.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCCTGGAGT.................................................................................	22	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGCCCATGGAGTT................................................................................	23	1	1.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTTCATGGAGT.................................................................................	22	1	1.00	1.00	0.00	0.00
...............................................................................................................................................................TTCAGCTCGGTGGATGTCAGC..............................................	21	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCxTCCATGGAGT.................................................................................	21	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CGGGCTGTCGTCCATGGAG..................................................................................	21	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTTTCGTCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTT................................................................................	23	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATGGTG..................................................................................	21	1	1.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCCTCCATGGAGT.................................................................................	22	1	1.00	0.00	0.00	1.00

droYak2

ACATCATCGATTATTGTCGATGCCGGCGTTTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGTTTGTGTTGTCTGCATTCAGCTCGGTGGATGTCAGCCATCGGTGGAAGGCGTCGTCGCGCTCCGCG---T--CTGGTCCACG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGT.................................................................................	22	1	9.00	0.00	0.00	1.00	1.00	7.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGTT................................................................................	23	1	4.00	0.00	0.00	0.00	0.00	4.00
..............................................................................................................................................................................GTCTGCCATCGGTxGAAGGC................................	19	1	2.00	0.00	1.00	1.00	0.00	0.00
...........................................................................................................................................................................GATGTCAxCCATCGGTGGAAT..................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................GTGGxCGGCGTCGTCGC........................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGTT................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGG.................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCATTCAGT.................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCTTCCATTTAGT.................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

ACATCATCGATTATGGTCGATGGCGGCGTCTC---CCGCT------C------------------------------------------------------------------------------CAGGCTGTCGTCCACGGAGTTCGTGTTGTCGGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCGCGCTCCGCG---T--CCGGTCCACG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCACGGAGT.................................................................................	22	1	21.00	0.00	3.00	0.00	18.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCACGGAGT.................................................................................	21	1	2.00	0.00	1.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCACGGAG..................................................................................	21	1	2.00	0.00	0.00	0.00	2.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCACGGGG..................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCACTGAGT.................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------CAGACTGTCGTCCACGGAGT.................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------TAGGCTGTCGTCTACGGAGT.................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................C------------------------------------------------------------------------------CAGGCTGTCGTCCACGGAGTT................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCACGTAGT.................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.......................................T------C------------------------------------------------------------------------------TAGGCTGTCGTCCCCGGAGT.................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................T------C------------------------------------------------------------------------------CAGGCTGTCGTCCCCGGAGT.................................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droAna3

ACATCATCGATTATTGTCGATGTTGGCGTTTC---CTGCT------C------------------------------------------------------------------------------CAAGTTATCGTCAAGCGGGTTTGTGTTGTCGCCATTTAGCTCCGTAGATGTCAGCCACCGGTGGAAGGCGTCATCCAGCTCCTCGGGGT--CATGTCCACT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................................................................................................................................................................GGTGGAAGGCGTCAACCT........................	18	1	1.00	1.00	0.00	0.00	0.00
..............................TC---CTGCT------C------------------------------------------------------------------------------CAATTTATCTTCA........................................................................................	21	1	1.00	0.00	0.00	0.00	1.00

dp4

ACATCATCGATTATTGTCGATGCTGCTGTTTC---CTGCT------C------------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTCCTTG---C--C---ACCGCT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
....................................................................................................................................TTGTCCGGGGTGTTTGTGC...........................................................................	19	1	2.00	0.00	2.00	0.00	0.00

droPer1

ACATCATCGATTATTGTCGATGCTGCTGTTTC---CTGCT------C------------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTCCTTG---C--C---ACCGCT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.............................................................................................................................CTAGGCATCGTCTGGCGT...................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...........TATTGTTGTTGCTGCTGT.....................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
...........TATTGTCGATGCTGCTGAT....................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................................................CATCCGCCGTGTTTGTGCT..........................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
........................GTTGxTTC---CTGCT------C------------------------------------------------------------------------------CGAGG................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
........................GCTGATCC---CTGCT------C------------------------------------------------------------------------------CGAG.................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.........ATTATCGTxGATGCTGCTGT.....................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................TCCGTCGATGxCTGCCACC..........................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.CATCATCGATTxGTGTCGA..............................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

ACATCATCGATTATCGTTGATGCTGATGTTTTTTCCTGCT------C------------------------------------------------------------------------------CAAGCTAACGTCCAGTGTATTGGTATTTTCAACATTCAGCTCTGTGGATGTTAGCCAACGATGAAATGCATCATCAT----CTTG---TTCC--ATCATCT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.............................................................................................................................................................CATACAGGTCTGTGGATGTT.................................................	20	1	6.00	0.00	6.00	0.00	0.00
..............................................................................................................................................................ATACAGGTCTGTGGATGTT.................................................	19	1	4.00	1.00	3.00	0.00	0.00
.............................................................................................................................................................CATACAGGTCTGTGGATGT..................................................	19	1	2.00	0.00	2.00	0.00	0.00
..................GATGCGGATGTTTTCTCC..............................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................................................................................CT	18	36	0.03	0.00	0.03	0.00	0.00
..............................................................................................................................................................................................................................ATTT	19	8	0.13	0.00	0.13	0.00	0.00
................................................................................................................................................................................................................................TT	19	32	0.03	0.00	0.00	0.03	0.00
.................................................................................................................................................................................................................................T	18	50	0.02	0.00	0.02	0.00	0.00
..............................................................................................................................................................................................................................TTCT	18	49	0.02	0.00	0.02	0.00	0.00
..............................................................................................................................................................ATACAGGTCTGTGGATGT..................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

ACATCATCGATTATTGTTGATGCTGGCGTTTC---CTGTT------CGACAGCAAgTGgTGgTGgTGg---------------------------------------TGgTGggGgtGgTGgTGgCAAGCTATCGTCGAGCGTGTTTGTGCTGTCAACATTCAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCGTCAGCTTCCT-------------CAATT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..........................................................GTGGTGGGGG---------------------------------------TGGTGGGGGT.............................................................................................................	20	3	1.67	1.67	0.00	0.00	0.00	0.00
...................................................................G---------------------------------------TGGTGGGGGTGGTGGGGGT....................................................................................................	20	3	1.67	1.67	0.00	0.00	0.00	0.00

droMoj3

ACATCATCGATTATTGTTGATGCTGGTGTTTCCTGCTGCTGAACGGCAAgTGt------TGgTGgTGgTggGtgGGgTggGGgTGtTGgTGgTGgTGgTTgTGgTTgTGgTTgTGgTGgTGgTGTCAAGCTATCGTCGAGCGTGTTTGTGCTGTCAACATTGAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCGTC--------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.............................................................................................TGTGGTTGTGGTTGTGATTGTGG..............................................................................................................	23	2	34.50	34.50	0.00	0.00	0.00
...................................................................................................TGTGGTTGTGGTTGTGATTGTGG........................................................................................................	23	2	34.50	34.50	0.00	0.00	0.00
.............................................................................................TGTGGTTGTGGTTGTGATTGTGGT.............................................................................................................	24	2	21.50	21.50	0.00	0.00	0.00
...................................................................................................TGTGGTTGTGGTTGTGATTGTGGT.......................................................................................................	24	2	21.50	21.50	0.00	0.00	0.00
.................................................................................GGTGGTGGTGGTGGTGGTGGTGGT.........................................................................................................................	24	6	4.00	4.00	0.00	0.00	0.00
...........................................................................GGTGGTGGTGGTGGTGGTGGTGGT...............................................................................................................................	24	6	4.00	4.00	0.00	0.00	0.00
.......................................................................................GGTGGTGGTGGTGGTGGTGGTGGT...................................................................................................................	24	6	4.00	4.00	0.00	0.00	0.00
..................................................................................................TTGTGGTTGTGGTTGTGATTGTGG........................................................................................................	24	2	11.00	11.00	0.00	0.00	0.00
............................................................................................TTGTGGTTGTGGTTGTGATTGTGG..............................................................................................................	24	2	11.00	11.00	0.00	0.00	0.00
..................................................................................................TTGTGGTTGTGGTTGTGATTGTGGT.......................................................................................................	25	2	4.00	4.00	0.00	0.00	0.00
............................................................................................TTGTGGTTGTGGTTGTGATTGTGGT.............................................................................................................	25	2	4.00	4.00	0.00	0.00	0.00
............................................................................................TTGTGGTTGTGGTTGTGATTGTG...............................................................................................................	23	2	4.00	4.00	0.00	0.00	0.00
..................................................................................................TTGTGGTTGTGGTTGTGATTGTG.........................................................................................................	23	2	4.00	4.00	0.00	0.00	0.00
...................................................................................................TGTGGTTGTGGTTGTGATTGTG.........................................................................................................	22	2	2.00	2.00	0.00	0.00	0.00
.............................................................................................TGTGGTTGTGGTTGTGATTGTG...............................................................................................................	22	2	2.00	2.00	0.00	0.00	0.00
...................................................GT------GGGTGGTGGTGGGGGG.......................................................................................................................................................	18	1	3.00	2.00	1.00	0.00	0.00

droGri2

ACATCATCGATTATTGTTGATGCTGATGTTTC---CTGCT------CAATTGTAGgTTgTGgTGgtGg---------------------------------------TGgtGgTGgTGgTGgTGgCAAGTTATCGTCAAACATATTTGTACTGTCAATATTGAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCATC--------------------------

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