dme-mir-2499- 12- and 20-way alignments

dme-mir-2499	chrX:19451041-19451136 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 19451100-19451123
   star strand at position 19451062-19451085
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:19451026-19451151 +	CTTTGGGCGTTCGCCTCCTTGCTGTGGGT----GTGGTT--------GCGTGCGTAGACGTCAGCGCAATGCCTTTGTTTGGCGGCAT----GCGGATG---ACATTCACGTCCGTATCCGCACACACATCC-----GCATCCATATATC
droSim1	chrX:15016847-15016968 +	CTTTGGGCGTTCGCCTCCTTGCTGTGGGT------GGGT--------GCAGGCGTGGACGTCAGCACAATGCCTTTGTTTGGCGGCAT----GTGGATG---ACGTTCATGTCCACATCCGCACACACATCC-----GCATCCA--TATC
droSec1	super_8:1733318-1733439 +	CTTTGGGCGTTCGCCTCCGTGCTGTGGGT------GGGT--------GCAGGCGTGGACGTCAGCACAATGCCTTTGTTTGGCGGCAT----GTGGATG---ACGTTCATGTCCACATCCGCACACACATCC-----GCATCCA--TATC
droYak2	chrX:11887438-11887559 -	CTTTGGGCGCTCTCCTCCTTGCTGTGAGC------GGGT--------GCGTGCGTTGACGTCAGCGCAATGCCTTTGTTTGTCGGCAT----GCGGATG---GCGTACACGTCCACATCCGCACACACACAC-----GCATCTG--TATC
droEre2	scaffold_4690:9687367-9687488 +	CTTTGGGCGCTCCTTTCCTGGCTGTGAGT------GGGT--------GCGTGCGTTTATGTCAGCGCAATGCTTTTGTTTGGCGGCAT----GCGGATG---GCATACACGTCCACATCCGCACACACATCC-----GCATCCG--TATC
droAna3	scaffold_13417:2469681-2469798 -	CGAC-----------T----TCTGTGTGTGTGTGCGTGT--------GTTGGCGTTGGCGTCAGCGCAATGCCATTGTTTGCCGGCAT----GCGGCTG---GCGTGCACGTCTACATCCGCACCTGCATCCACATAGCAGCTG--CAAC
dp4	chrXL_group1e:12520647-12520746 -	TTTTTGA------------------GTGTGTGTTTGTATTTATTTATTTTTGTGTGGACTTCACTGCATTGTCATTGATTGGCGGC-----------TG---TCGTGCAGGACAATGTGA--AACATCATTC-----GA-----------
droPer1	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_13042:909711-909778 -	--------------------------------------------------------------------AGGCCATTGTT--ATGGCAGGTGGGCAGGTG---TCATCAATAGCCGCATCC--AGGCACATCC-----GCATCCA--CATC
droMoj3	scaffold_6328:2902689-2902778 -	CTGTGGGCTTTAGGCCAATTGATATGGTC------GTGT--------------------------------------------GGCAT----GAGGCAGGTGTCA---GCA-GGTGGCAGCAATTCGGAACCATTGTGTGCCCA--CATC
droGri2	scaffold_15081:2046324-2046418 -	TGTTG-------------------CAGTTGCATTTGAAT--------GTAGGTGTTGTCAT------TA-------TTTTGAGGGCAT----GCGGCAG---GTGTCAACG-CCACGTCCTCATTTGCATCC-----GCTTCCG--CATC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:19451026-19451151 +	NA	CTTTGGGCGTTCGCCTCCT--------------TG--------CTGTGGGTGTGGTTGCGTGCGTAGACGTCAGCGCAATGCCTTTG---TTTGGCGGCATGCGGA-----------------TGACATTCACGTC-----------CGTATCCGCACACACATCCGCATCCA------TA---------------------------------------TATC
droSim1	chrX:15016847-15016968 +	1	CTTTGGGCGTTCGCCTCCT--------------TG--------CTG--TGGGTGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTG---TTTGGCGGCATGTGGA-----------------TGACGTTCATGTC-----------CACATCCGCACACACATCCGCATCCA------TA-----------------------------------------TC
droSec1	super_8:1733318-1733439 +	1	CTTTGGGCGTTCGCCTCCG--------------TG--------CTG--TGGGTGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTG---TTTGGCGGCATGTGGA-----------------TGACGTTCATGTC-----------CACATCCGCACACACATCCGCATCCA------TA-----------------------------------------TC
droYak2	chrX:11887438-11887559 -	2	CTTTGGGCGCTCTCCTCCT--------------TG--------CTG--TGAGCGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTTGTCGGCATGCGGA-----------------TGGCGTACACGTC-----------CACATCCGCACACACACACGCATCTG------TA-----------------------------------------TC
droEre2	scaffold_4690:9687367-9687488 +	2	CTTTGGGCGCTCCTTTCCT--------------GG--------CTG--TGAGTGGGTGCGTGCGTTTATGTCAGCGCAATGCTTTTG---TTTGGCGGCATGCGGA-----------------TGGCATACACGTC-----------CACATCCGCACACACATCCGCATCCG------TA-----------------------------------------TC
droEug1	scf7180000409109:1918-2066 -	1	CTCT-----------------------------TT--------CTG--TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTTGCCGGCATGCGGA-----------------TGGCGTACACGTC-----------CACATCCGCGCACACATTCGCAACAATATCCGCATATGGATTTACAACTGCAGCCCTATCCACACAGG-----CATT
droBia1	scf7180000302069:1153003-1153157 -	2	CCGTTT----------CCG-------------CAC--------CTG--TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTGGATGGCATGCGGA-----------------TGGCGTACACGTC-----------CACATCCGCGCACATATTCGCATCAGCTTCCGCTTCCGCATTCACGGCTGCAGCCCTATCCGCACGGA-----CATC
droTak1	scf7180000415169:846463-846599 -	1	CT-------------------------------------------G--TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTTGTCGGCATGCGGA-----------------TGGCGTATACGTC-----------CTCATCCGCACACACATCCGCATCGGCATCCACA------TTTGCAACTGCAGCCATATCCGCGCACA-----CATC
droEle1	scf7180000490751:1116747-1116877 +	2	CTTCACGCC------GG----------------AT--------TTT--TGTGTGTGTGATGGGGTTGGAGTCAGCGCAATGCCATTG---TTTGCCGTCATGCGGC-----------------TGGCTCGCAGATA-----------GACATCCACATCCACATCCGCATCCG------CA------T-TACAAGTGCAGCAAA-----------------CTT
droRho1	scf7180000761121:191845-191991 -	1	TGGAGGTCCTTCAGATCCAG------------TTT--------CTG--CGTGTGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTG---TTTGCCGGCATGTGGC-----------------TGCCGTGCACGTC-----------CACATCCGCATCCGCACCCGCATCCGCATCCGCA------T-TACAAGTGCAGCAAC-----------------ATC
droFic1	scf7180000454073:1729690-1729845 +	1	CTGTAAATGTATCTGGATT-TGTTTCGGTTAATTCATCTGCATTTG--TGTGCGTGTTTCGACGTTGGCGTCAGCGCAGTGCCATTGTTATTTGCCGGCATGCGGT-----------------TGGCGTGCGCGTC-----------GACATCCGCATTTCTATAC--------------------------------AACCATTTCTACTCCTG-----AATT
droKik1	scf7180000302517:1182226-1182359 +	2	CCCCGCTCCTCCACCACCA-------------CCC--------ATG--TGTGCGTGTGTTATCGTTGGTGTCAGCGCAATGCCGTTG---TTTGCCGGCATGCAGC-----------------TAATGTCAATGTC-----------TACATCCGCACCCGCACTCGCACATC------TA------------GATGCAGTTA------------------GTC
droAna3	scaffold_13417:2469661-2469798 -	1	CGACTT----------CTG-------------TGT--------GTG--TGTGCGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTG---TTTGCCGGCATGCGGC-----------------TGGCGTGCACGTC-----------TACATCCGCACCTGCATCCACAT-------------------AGCAGCTGCAACAACAAACAC---GGCACTCCGTC
droBip1	scf7180000395874:42023-42130 -	1	TCCTGTG---------------------------T--------GTG--TGTGCGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTG---TTTACCGGCATGCGGC-----------------TGGCGTGCACGTC-----------TACATCCGCACCTGCATTCACATA-G------CA-----------------------------------------GC
dp4	chrXL_group1e:12520639-12520746 -	2	TTTTTGAGT------GTGTG------------TTT--------GTA--TTTATTTATTTTTGTGTGGACTTCACTGCATTGTCATTG---ATTGGCGG-------C-----------------TGTCGTGCAGGAC-----------AATGTG--AAACATCATTCGACA-------------------------------------------CA-----AATC
droPer1	Unknown	NA	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	NA	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_13042:909712-909778 -	1	------------------------------------------------------------------------------AGGCCATTGTTA-TGGCAGGTGGGCAGG-----------------TGTCATCAATAGC-----------CGCATCCA--GGCACATCCGCATCCA------CA-----------------------------------------T-
droMoj3	scaffold_6328:2902676-2902778 -	1	CTGTGGGCTTTAGGCCAAT--------------TG--------ATA--TGGTCGTG---------------------------------------TGGCATGAGGCAGGTGTCAGCAGGTGGCAGCAATTCGGAACCATTGTGTGCCCACATCCGCATTTGCAA----------------------------------------------------------GC
droGri2	scaffold_15081:2046312-2046418 -	1	TGTTGCA---------------------------G--------TTG--CATTTGAATGTAGGTGTTGTCATT-------------AT---TTTGAGGGCATGCGGCAGGTGTCAACG------------CCACGTC-----------CTCATTTGCATCCGCTTCCGCATCCGCATCCGCT-----------------------------------------GT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CTTTGGGCGTTCGCCTCCTTGCTGTGGGT----GTGGTT--------GCGTGCGTAGACGTCAGCGCAATGCCTTTGTTTGGCGGCAT----GCGGATG---ACATTCACGTCCGTATCCGCACACACATCC-----GCATCCATATATC

Size

Hit Count

Total Norm

droSim1

CTTTGGGCGTTCGCCTCCTTGCTGTGGGT------GGGT--------GCAGGCGTGGACGTCAGCACAATGCCTTTGTTTGGCGGCAT----GTGGATG---ACGTTCATGTCCACATCCGCACACACATCC-----GCATCCA--TATC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.................................................AGGCGTGGACGTCAGCACAATGCC.............................................................................	24	1	26.00	0.00	1.00	25.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGTCC....................................	21	1	6.00	0.00	0.00	6.00	0.00
...............................................GCAGGCGTGGAGGTCAGT.....................................................................................	18	1	6.00	1.00	1.00	4.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGTCCA...................................	22	1	4.00	1.00	0.00	3.00	0.00
.................................................AGGCGTGGACGTCAGCACAATGC..............................................................................	23	1	4.00	0.00	0.00	4.00	0.00
.....................................................................................CAT----GTGGATG---ACGTTCATGTCCAC..................................	24	1	3.00	0.00	0.00	3.00	0.00
.....................................................................................CAT----GTGGATG---ACGTTCATGTCCA...................................	23	1	3.00	0.00	0.00	3.00	0.00
.....................................................................................CAT----GTGGATG---ACGTTCATGTCC....................................	22	1	3.00	0.00	2.00	0.00	1.00
.................................................AGGCGTGGACGTCAGCACC..................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGTCT....................................	21	1	1.00	0.00	0.00	1.00	0.00
......................................................................................AT----GTGGATG---ACxTTCAAGT......................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................AGGCGTGGACGGCGGCACAATGC..............................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................CAT----GTGGATG---ACGTTCATGTC.....................................	21	1	1.00	0.00	0.00	1.00	0.00
.................................................AGTCGTGGACGTCAGCACAATGC..............................................................................	23	1	1.00	0.00	1.00	0.00	0.00
......................................................................GCATTTGATTGGCGGCAT----G.........................................................	19	1	1.00	0.00	1.00	0.00	0.00
.................................................AGGCGTGGACGTCAGCACAATGCCT............................................................................	25	1	1.00	0.00	0.00	1.00	0.00
...............................................GCAGGCGTGGAGGTCAGG.....................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGTC.....................................	20	1	1.00	0.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACCTTCATG.......................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................AGGCGTGGACGTCAGCACAGTGCC.............................................................................	24	1	1.00	0.00	0.00	1.00	0.00
.................................................AGGCGTGGACGTCAGCACAATG...............................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.................................................AGGCGTGGACGTCAGCACAA.................................................................................	20	1	1.00	0.00	0.00	1.00	0.00

droSec1

CTTTGGGCGTTCGCCTCCGTGCTGTGGGT------GGGT--------GCAGGCGTGGACGTCAGCACAATGCCTTTGTTTGGCGGCAT----GTGGATG---ACGTTCATGTCCACATCCGCACACACATCC-----GCATCCA--TATC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............................................GCAGGCGTGGAGGTCAGT.....................................................................................	18	1	247.00	86.00	89.00	72.00
......................................................................................AT----GTGGATG---ACGTTCATGTCCA...................................	22	1	225.00	167.00	20.00	38.00
......................................................................................AT----GTGGATG---ACGTTCATGTCC....................................	21	1	134.00	124.00	4.00	6.00
.....................................................................................CAT----GTGGATG---ACGTTCATGTCCA...................................	23	1	128.00	61.00	36.00	31.00
.......................GTGGGT------GGGT--------GGAGGCGA...............................................................................................	18	1	121.00	0.00	0.00	121.00
......................................G--------GCAGGCGTGGAGGTCAG......................................................................................	18	1	32.00	22.00	6.00	4.00
.................................................AGGCGTGGACGTCAGCACAATGC..............................................................................	23	1	22.00	14.00	5.00	3.00
.................................................AGGCGTGGACGTCAGCACAATG...............................................................................	22	1	18.00	13.00	2.00	3.00
......................................................................................AT----GTGGATG---ACGTTCATGTC.....................................	20	1	17.00	17.00	0.00	0.00
.....................................................................................CAT----GTGGATG---ACGTTCATGTCC....................................	22	1	17.00	7.00	3.00	7.00
.................................................AGGCGTGGACGTCAGCACAATGCC.............................................................................	24	1	14.00	8.00	4.00	2.00
......................................G--------GCAGGCGTGGAGGTCAGC.....................................................................................	19	1	6.00	5.00	1.00	0.00
.....................................................................................CAT----GTGGATG---ACGTTCATGTC.....................................	21	1	5.00	3.00	2.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGT......................................	19	1	5.00	4.00	0.00	1.00
.......................................................................................T----GTGGATG---ACGTTCATGTCCA...................................	21	1	5.00	5.00	0.00	0.00
.......................GTGGGT------GGGT--------GGAGGCGG...............................................................................................	18	1	4.00	0.00	0.00	4.00
......................................................................................AT----GTGGATG---ACGTTCATGTCCAC..................................	23	1	4.00	2.00	1.00	1.00
......................CGTGGGT------GGGT--------GGAGGCG................................................................................................	18	1	3.00	0.00	0.00	3.00
.....................................................................................CAT----GTGGATG---ACGTTCATGTCCAC..................................	24	1	3.00	2.00	0.00	1.00
......................................................................................AT----GGGGATG---ACGTTCATGTCCA...................................	22	1	3.00	3.00	0.00	0.00
.................................................AGGCGTGGACGTCAGCACAAT................................................................................	21	1	2.00	2.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGTCCT...................................	22	1	2.00	1.00	0.00	1.00
......................................................................................AT----GTGGATG---ACGTTCATGTCT....................................	21	1	2.00	2.00	0.00	0.00
.....................................................................................CAT----GTGGATG---ACGTTCATTTCCA...................................	23	1	2.00	2.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGACC....................................	21	1	2.00	2.00	0.00	0.00
....................................................................................GCAT----GTGGATG---ACxTTCAAGT......................................	20	1	1.00	1.00	0.00	0.00
...............................................GCAGGCGTGGAGGTCAGGA....................................................................................	19	1	1.00	1.00	0.00	0.00
................................................CAGGCGTGGAGGTCAGTA....................................................................................	18	1	1.00	0.00	0.00	1.00
......................................................................................AT----GTGGATG---ACGTTCCTGTCC....................................	21	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGCTCATGTCCA...................................	22	1	1.00	1.00	0.00	0.00
......................................................................................AT----GGGGATG---ACGGTCATGTCCA...................................	22	1	1.00	1.00	0.00	0.00
.......................................................................................A----GTGGATG---ACGTTCATGTCCA...................................	21	1	1.00	1.00	0.00	0.00
...............................................GCAGGCGTGGATGTCAGT.....................................................................................	18	1	1.00	0.00	0.00	1.00
......................................................................................AT----GTGGCTG---ACGTTCATGTCCA...................................	22	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---AAGTTCATGTCC....................................	21	1	1.00	1.00	0.00	0.00
.......................................................................................T----GTGGATG---ACGTTCATGTC.....................................	19	1	1.00	1.00	0.00	0.00
.....................................................................................CAT----GTGGATG---ACGTTCGTGTCCAC..................................	24	1	1.00	0.00	0.00	1.00
......................................................................................AT----GTGGATG---CCGTTCATGTCC....................................	21	1	1.00	1.00	0.00	0.00
......................................T--------GCAGGCGTGGAGGTCAGT.....................................................................................	19	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTGCATGTCCA...................................	22	1	1.00	0.00	1.00	0.00
.....................................GG--------GCAGGCGTGGAGGTCA.......................................................................................	18	1	1.00	0.00	1.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATCTCC....................................	21	1	1.00	1.00	0.00	0.00
......................................................................................AT----ATGGATG---ACGTTCATGCCCA...................................	22	1	1.00	1.00	0.00	0.00
.....................................................................................CAT----GTGGATG---GCGTTCATGTCCA...................................	23	1	1.00	1.00	0.00	0.00
.....................................................................................CAT----GTGGATG---ACGGGCATG.......................................	19	1	1.00	0.00	1.00	0.00
.....................................AG--------GCAGGCGTGGACGTCA.......................................................................................	18	1	1.00	0.00	1.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGCCCA...................................	22	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGTCCC...................................	22	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGGCCA...................................	22	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCACGTCC....................................	21	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGAC.....................................	20	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCGTGTC.....................................	20	1	1.00	1.00	0.00	0.00
..TTGCGCxTTCGCCTCCGTGC................................................................................................................................	19	1	1.00	0.00	0.00	1.00
......................................................................................AT----GTGGATG---ACGCTCATGTCCAC..................................	23	1	1.00	1.00	0.00	0.00
......................................................................................AT----GAGGATG---ACGTTCATGTCCAC..................................	23	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGTCCATT.................................	24	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTGGATG---ACGCTCATGTCC....................................	21	1	1.00	1.00	0.00	0.00
......................................................................................AT----GTCGATG---ACGTTCATGTCCAC..................................	23	1	1.00	1.00	0.00	0.00
.................................................AGGCGTGGACGTTAGCACAATG...............................................................................	22	1	1.00	0.00	1.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATA.......................................	18	1	1.00	0.00	0.00	1.00
.................................................AGGCGTGGACGTAAGCAAAATG...............................................................................	22	1	1.00	0.00	1.00	0.00
......................................................................................AT----GTGGATG---ACGTTCATGACCA...................................	22	1	1.00	1.00	0.00	0.00
......................................................................................AA----GTGGATG---ACGTTCATGTCCA...................................	22	1	1.00	0.00	0.00	1.00
.................................................AGGCGTGGACGTCAGCCCAATGC..............................................................................	23	1	1.00	0.00	1.00	0.00
....................................AGT--------GCAGGCGTGGAGGTC........................................................................................	18	1	1.00	1.00	0.00	0.00
.....................................................................................CAT----GTGGATG---ACGTTCATGTCCAA..................................	24	1	1.00	0.00	1.00	0.00
......................................................................................AT----GTGGACG---ACGTTCATGTCCA...................................	22	1	1.00	1.00	0.00	0.00
..................................................GGCGTGGACGTCAGCACAATG...............................................................................	21	1	1.00	1.00	0.00	0.00

droYak2

CTTTGGGCGCTCTCCTCCTTGCTGTGAGC------GGGT--------GCGTGCGTTGACGTCAGCGCAATGCCTTTGTTTGTCGGCAT----GCGGATG---GCGTACACGTCCACATCCGCACACACACAC-----GCATCTG--TATC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................................AT----GCGGATG---GCGTACACGTCCACA.................................	24	1	126.00	0.00	0.00	124.00	2.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCA...................................	22	1	80.00	1.00	2.00	76.00	1.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCAC..................................	23	1	40.00	0.00	0.00	40.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCC....................................	21	1	37.00	0.00	1.00	33.00	1.00	2.00
.....................................................................................CAT----GCGGATG---GCGTACACGTCCA...................................	23	1	14.00	0.00	0.00	14.00	0.00	0.00
.....................................................................................CAT----GCGGATG---GCGTACACGTCC....................................	22	1	8.00	0.00	0.00	8.00	0.00	0.00
.....................................................................................CAT----GCGGATG---GCGTACACGTCCAC..................................	24	1	7.00	0.00	0.00	7.00	0.00	0.00
.....................................................................................CAT----GCGGATG---GCGTACACGTCCACA.................................	25	1	7.00	1.00	0.00	6.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTC.....................................	20	1	6.00	0.00	1.00	5.00	0.00	0.00
.....................................................................................CAT----GCGGATG---GCGTACACGTC.....................................	21	1	4.00	0.00	0.00	4.00	0.00	0.00
.......................................................................................T----GCGGATG---GCGTACACGTCCAC..................................	22	1	3.00	0.00	0.00	3.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGCCCACA.................................	24	1	2.00	0.00	0.00	2.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCCC..................................	23	1	2.00	0.00	0.00	2.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCCCA.................................	24	1	2.00	0.00	0.00	1.00	1.00	0.00
......................................................................................AT----GCGGTTG---GCGTACACGTCCAA..................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCATT.................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATA---GCGTACACGTCCA...................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACCCCTCCAC..................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACCTCCA...................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCT...................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCTGATG---GCGTACACGTCCAC..................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACCCGTCC....................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGCATG---GCGTACACGTCCAC..................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTAAACGTCCA...................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................CAT----GCGGATG---GCGTACACGCCCACA.................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................CAT----GCGGATG---GCGTACACGTT.....................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACCCGTCCC...................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................AT----GCCGATG---GCGTACACGTCCA...................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGCACACGTCC....................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................................................T----GCGGATG---GCGGACACGTCC....................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................CAT----GCGGATG---GCGTACACGTCT....................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCC...................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................CGTGCGTTGACGTCAGCGCAATG...............................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................AT----GCGGATG---GCGTGCACGTCCACA.................................	24	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................................................................CAT----GCGGATT---GCGTACACGTCCA...................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCCCC.................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................................AAAT----GCGGATG---GCGTACACGTCC....................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................CAT----GCGGATG---GCGTACACGT......................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACATCC....................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AC----GCGGATG---GCGTACACGTCC....................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACAAGTCCG...................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCTCA.................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................AT----GCGGACG---GCGTACACGTCCACA.................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCACAT................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCCATTT................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCGTACACGTCT....................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................................................T----GCGGATG---GCGTACACGTCCACA.................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

CTTTGGGCGCTCCTTTCCTGGCTGTGAGT------GGGT--------GCGTGCGTTTATGTCAGCGCAATGCTTTTGTTTGGCGGCAT----GCGGATG---GCATACACGTCCACATCCGCACACACATCC-----GCATCCG--TATC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................AT----GCGGATG---GCATACACGTCCA...................................	22	1	88.00	0.00	11.00	0.00	77.00
......................................................................................AT----GCGGATG---GCATACACGTCCACA.................................	24	1	27.00	0.00	5.00	0.00	22.00
......................................................................................AT----GCGGATG---GCATACACGTCC....................................	21	1	21.00	0.00	1.00	0.00	20.00
......................................................................................AT----GCGGATG---GCATACACGTCCAC..................................	23	1	17.00	1.00	4.00	0.00	12.00
......................................................................................AT----GCGGATG---GCATACACGTC.....................................	20	1	4.00	0.00	1.00	0.00	3.00
.....................................................................................CAT----GCGGATG---GCATACACGTCCA...................................	23	1	3.00	0.00	0.00	0.00	3.00
.....................................................................................CAT----GCGGATG---GCATACACGTCC....................................	22	1	3.00	0.00	0.00	0.00	3.00
................................................CGTGCGTTTATGTCAGCGCAATG...............................................................................	23	1	2.00	0.00	0.00	0.00	2.00
......................................................................................AT----GCTGATG---GCATACACGTCCACA.................................	24	1	2.00	0.00	0.00	0.00	2.00
................................................CGTGCGTTTATGTCAGCGCAATGC..............................................................................	24	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATATACGTCCA...................................	22	1	1.00	0.00	0.00	0.00	1.00
.............TTTCCTGGCTGTGAGT------GGGT--------G......................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCTGATG---GCATACACGTCC....................................	21	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATACACCTCCA...................................	22	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATACACTTCCACA.................................	24	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GAATACACGTCCACA.................................	24	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATACACGTCCCCA.................................	24	1	1.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCTGATG---GCATACACGTCCAC..................................	23	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGGTG---GCATACACGTCCA...................................	22	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATACACGTCCACC.................................	24	1	1.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCATCCACGTCCA...................................	22	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATT---GCATACACGTCCACA.................................	24	1	1.00	0.00	0.00	0.00	1.00
...............TCCTGGCTGTGAGT------GGGT--------G......................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----TCGGATG---TCATACACGTCCACA.................................	24	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATACACGC......................................	19	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----TCGGATG---GCATACACGTCC....................................	21	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGCTG---GCATACACGTCC....................................	21	1	1.00	0.00	1.00	0.00	0.00
......................................................................................AT----GCGGATG---GCATACACATCCA...................................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................CAT----GCGGATG---GCATCCACGTCCA...................................	23	1	1.00	0.00	1.00	0.00	0.00
.......................GTGAGT------GTGT--------GTGTGCGT...............................................................................................	18	10	0.10	0.00	0.00	0.00	0.10
......................................................................................AT----TCGGATG---GCATACACGTCCA...................................	22	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GAGGATG---GCATACACGTCCAC..................................	23	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATACAAGTCCA...................................	22	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---TCATACACGTCCA...................................	22	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATACACGTCCACTA................................	25	1	1.00	0.00	1.00	0.00	0.00
......................................................................................AT----ACGGATG---GCATACACGTCCACA.................................	24	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATACACGTCCAT..................................	23	1	1.00	0.00	0.00	0.00	1.00
......................................................................................AT----GCGGATG---GCATACACGTAC....................................	21	1	1.00	0.00	0.00	0.00	1.00

droAna3

CGAC-----------T----TCTGTGTGTGTGTGCGTGT--------GTTGGCGTTGGCGTCAGCGCAATGCCATTGTTTGCCGGCAT----GCGGCTG---GCGTGCACGTCTACATCCGCACCTGCATCCACATAGCAGCTG--CAAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................................TGT--------GTTGGCGTTGGCGTCAG......................................................................................	20	1	121.00	102.00	14.00	5.00	0.00
....................................TGT--------GTTGGCGTTGGCGTCAGCG....................................................................................	22	1	118.00	94.00	14.00	10.00	0.00
....................................TGT--------GTTGGCGTTGGCGTCAGC.....................................................................................	21	1	89.00	75.00	6.00	8.00	0.00
....................................TGT--------GTTGGCGTTGGCGTCA.......................................................................................	19	1	40.00	33.00	4.00	3.00	0.00
....................................TGT--------GTTGGCGTTGGCGTCAGT.....................................................................................	21	1	21.00	20.00	1.00	0.00	0.00
.....................................................................................CAT----GCGGCTG---GCGTGCACGTCT....................................	22	1	16.00	13.00	3.00	0.00	0.00
....................................TGT--------GTTGGCGTTGGCGTCAGCT....................................................................................	22	1	16.00	15.00	0.00	1.00	0.00
......................AGTGTGTGTGTGTGTGT--------G......................................................................................................	18	16	0.69	0.06	0.63	0.00	0.00
.....................................................................................CAT----GCGGCTG---GCGTGCACGTCTA...................................	23	1	11.00	7.00	3.00	1.00	0.00
.......................GTGTGTGTGTGTGTGT--------GT.....................................................................................................	18	13	0.77	0.00	0.77	0.00	0.00
.....................................................................................CAT----GCGGCTG---GCGTGCACGTC.....................................	21	1	9.00	6.00	0.00	3.00	0.00
....................................TGT--------GTTGGCGTTGGCGTCAGA.....................................................................................	21	1	8.00	8.00	0.00	0.00	0.00
......................AGTGTGTGTGTGTGTGT--------GT.....................................................................................................	19	14	0.57	0.00	0.57	0.00	0.00
.....................................................................................CAT----GCGGCTG---GCGTGCACGT......................................	20	1	7.00	4.00	2.00	1.00	0.00
......................TGTGTGTGTGTGTGTGT--------G......................................................................................................	18	13	0.54	0.00	0.54	0.00	0.00
......................TGTGTGTGTGTGTGTGT--------GT.....................................................................................................	19	11	0.55	0.00	0.55	0.00	0.00
.........................GTGTGTGTGTGTGT--------GTTG...................................................................................................	18	7	0.71	0.00	0.71	0.00	0.00
..AC-----------T----TCTGTGTGTGTGTGCG..................................................................................................................	19	1	3.00	0.00	3.00	0.00	0.00
........................TGTGTGTGTGTGTGT--------GTTGGTG................................................................................................	22	6	0.50	0.00	0.50	0.00	0.00
........................TGTGTGTGTGTGTGT--------GTT....................................................................................................	18	7	0.43	0.00	0.43	0.00	0.00
......................GGTGTGTGTGTGTGTGT--------GT.....................................................................................................	19	13	0.23	0.08	0.15	0.00	0.00
......................................................................................AT----GCGGCTG---GCGTGCACGTCT....................................	21	1	3.00	3.00	0.00	0.00	0.00
.......................GTGGGTGTGTGGGTGT--------GT.....................................................................................................	18	8	0.38	0.13	0.25	0.00	0.00
........................AGTGTGTGTGTGTGT--------GTT....................................................................................................	18	8	0.38	0.00	0.38	0.00	0.00
....................TGTGTGTGTGTGTGGGTG................................................................................................................	18	18	0.17	0.00	0.17	0.00	0.00
....................................TGT--------GTTGGCGTTGGCGTCAGTT....................................................................................	22	1	3.00	3.00	0.00	0.00	0.00
.......................GTGTGTGTGTGCGTGT--------GT.....................................................................................................	18	5	0.60	0.00	0.60	0.00	0.00
......................TGTGTGTGTGTGTGTGT--------GC.....................................................................................................	19	14	0.21	0.00	0.21	0.00	0.00
.......................GTGTGTGTGTGTGTGT--------GC.....................................................................................................	18	17	0.18	0.00	0.18	0.00	0.00
......................TGTGTGTGTGTGTGGGT--------G......................................................................................................	18	18	0.17	0.00	0.17	0.00	0.00
.....................................................................................CAT----GCGGCTG---GCGTGCACGTCTTT..................................	24	1	3.00	1.00	0.00	2.00	0.00

dp4

TTTTTGA------------------GTGTGTGTTTGTATTTATTTATTTTTGTGTGGACTTCACTGCATTGTCATTGATTGGCGGC-----------TG---TCGTGCAGGACAATGTGA--AACATCATTC-----GA-----------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
TGTTTGT------------------GTGTGTGTTTGT.................................................................................................................	19	22	0.09	0.05	0.00	0.05	0.00
.....................................ATTTATGTATTTTTGTTT...............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......A------------------TTGTGTGTGTGTATTTA............................................................................................................	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

--------------------------------------------------------------------AGGCCATTGTT--ATGGCAGGTGGGCAGGTG---TCATCAATAGCCGCATCC--AGGCACATCC-----GCATCCA--CATC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
........................................................................................................ATCGATCGCCGCATCC--AGG.........................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
...........................................................................TGTT--ATGGCGGGTGGGTAGG.....................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

CTGTGGGCTTTAGGCCAATTGATATGGTC------GTGT--------------------------------------------GGCAT----GAGGCAGGTGTCA---GCA-GGTGGCAGCAATTCGGAACCATTGTGTGCCCA--CATC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TGTTG-------------------CAGTTGCATTTGAAT--------GTAGGTGTTGTCAT------TA-------TTTTGAGGGCAT----GCGGCAG---GTGTCAACG-CCACGTCCTCATTTGCATCC-----GCTTCCG--CATC

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