dme-mir-2499- Best orthologs

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

Notes: Seems to be lost in dp4-droGri2.

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:19451026-19451151 +		1	CTTTGGGCGTTCGCCTCCT--------------TG--------CTGTGGGTGTGGTTGCGTGCGTAGACGTCAGCGCAATGCCTTTG---TTTGGCGGCATGCGGA-----------------TGACATTCACGTC-----------CGTATCCGCACACACATCCGCATCCA------TA---------------------------------------TATC
droSim1	chrX:15016847-15016968 +	LASTZ	1	CTTTGGGCGTTCGCCTCCT--------------TG--------CTG--TGGGTGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTG---TTTGGCGGCATGTGGA-----------------TGACGTTCATGTC-----------CACATCCGCACACACATCCGCATCCA------TA-----------------------------------------TC
droSec1	super_8:1733318-1733439 +	LASTZ	1	CTTTGGGCGTTCGCCTCCG--------------TG--------CTG--TGGGTGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTG---TTTGGCGGCATGTGGA-----------------TGACGTTCATGTC-----------CACATCCGCACACACATCCGCATCCA------TA-----------------------------------------TC
droYak2	chrX:11887438-11887559 -	LASTZ	1	CTTTGGGCGCTCTCCTCCT--------------TG--------CTG--TGAGCGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTTGTCGGCATGCGGA-----------------TGGCGTACACGTC-----------CACATCCGCACACACACACGCATCTG------TA-----------------------------------------TC
droEre2	scaffold_4690:9687367-9687488 +	LASTZ	1	CTTTGGGCGCTCCTTTCCT--------------GG--------CTG--TGAGTGGGTGCGTGCGTTTATGTCAGCGCAATGCTTTTG---TTTGGCGGCATGCGGA-----------------TGGCATACACGTC-----------CACATCCGCACACACATCCGCATCCG------TA-----------------------------------------TC
droEug1	scf7180000409109:1918-2066 -	LASTZ	4	CTCT-----------------------------TT--------CTG--TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTTGCCGGCATGCGGA-----------------TGGCGTACACGTC-----------CACATCCGCGCACACATTCGCAACAATATCCGCATATGGATTTACAACTGCAGCCCTATCCACACAGG-----CATT
droBia1	scf7180000302069:1153003-1153157 -	LASTZ	4	CCGTTT----------CCG-------------CAC--------CTG--TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTGGATGGCATGCGGA-----------------TGGCGTACACGTC-----------CACATCCGCGCACATATTCGCATCAGCTTCCGCTTCCGCATTCACGGCTGCAGCCCTATCCGCACGGA-----CATC
droTak1	scf7180000415169:846463-846599 -	LASTZ	4	CT-------------------------------------------G--TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTTGTCGGCATGCGGA-----------------TGGCGTATACGTC-----------CTCATCCGCACACACATCCGCATCGGCATCCACA------TTTGCAACTGCAGCCATATCCGCGCACA-----CATC
droEle1	scf7180000490751:1116747-1116877 +	LASTZ	4	CTTCACGCC------GG----------------AT--------TTT--TGTGTGTGTGATGGGGTTGGAGTCAGCGCAATGCCATTG---TTTGCCGTCATGCGGC-----------------TGGCTCGCAGATA-----------GACATCCACATCCACATCCGCATCCG------CA------T-TACAAGTGCAGCAAA-----------------CTT
droRho1	scf7180000761121:191845-191991 -	LASTZ	4	TGGAGGTCCTTCAGATCCAG------------TTT--------CTG--CGTGTGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTG---TTTGCCGGCATGTGGC-----------------TGCCGTGCACGTC-----------CACATCCGCATCCGCACCCGCATCCGCATCCGCA------T-TACAAGTGCAGCAAC-----------------ATC
droFic1	scf7180000454073:1729690-1729845 +	LASTZ	4	CTGTAAATGTATCTGGATT-TGTTTCGGTTAATTCATCTGCATTTG--TGTGCGTGTTTCGACGTTGGCGTCAGCGCAGTGCCATTGTTATTTGCCGGCATGCGGT-----------------TGGCGTGCGCGTC-----------GACATCCGCATTTCTATAC--------------------------------AACCATTTCTACTCCTG-----AATT
droKik1	scf7180000302517:1182226-1182359 +	LASTZ	4	CCCCGCTCCTCCACCACCA-------------CCC--------ATG--TGTGCGTGTGTTATCGTTGGTGTCAGCGCAATGCCGTTG---TTTGCCGGCATGCAGC-----------------TAATGTCAATGTC-----------TACATCCGCACCCGCACTCGCACATC------TA------------GATGCAGTTA------------------GTC
droAna3	scaffold_13417:2469661-2469798 -	LASTZ	1	CGACTT----------CTG-------------TGT--------GTG--TGTGCGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTG---TTTGCCGGCATGCGGC-----------------TGGCGTGCACGTC-----------TACATCCGCACCTGCATCCACAT-------------------AGCAGCTGCAACAACAAACAC---GGCACTCCGTC
droBip1	scf7180000395874:42023-42130 -	LASTZ	4	TCCTGTG---------------------------T--------GTG--TGTGCGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTG---TTTACCGGCATGCGGC-----------------TGGCGTGCACGTC-----------TACATCCGCACCTGCATTCACATA-G------CA-----------------------------------------GC
dp4	chrXL_group1e:12520639-12520746 -	LASTZ	0	TTTTTGAGT------GTGTG------------TTT--------GTA--TTTATTTATTTTTGTGTGGACTTCACTGCATTGTCATTG---ATTGGCGG-------C-----------------TGTCGTGCAGGAC-----------AATGTG--AAACATCATTCGACA-------------------------------------------CA-----AATC
droPer1	Unknown		0	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown		0	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_13042:909712-909778 -	LASTZ	0	------------------------------------------------------------------------------AGGCCATTGTTA-TGGCAGGTGGGCAGG-----------------TGTCATCAATAGC-----------CGCATCCA--GGCACATCCGCATCCA------CA-----------------------------------------T-
droMoj3	scaffold_6328:2902676-2902778 -	LASTZ	0	CTGTGGGCTTTAGGCCAAT--------------TG--------ATA--TGGTCGTG---------------------------------------TGGCATGAGGCAGGTGTCAGCAGGTGGCAGCAATTCGGAACCATTGTGTGCCCACATCCGCATTTGCAA----------------------------------------------------------GC
droGri2	scaffold_15081:2046312-2046418 -	LASTZ	0	TGTTGCA---------------------------G--------TTG--CATTTGAATGTAGGTGTTGTCATT-------------AT---TTTGAGGGCATGCGGCAGGTGTCAACG------------CCACGTC-----------CTCATTTGCATCCGCTTCCGCATCCGCATCCGCT-----------------------------------------GT

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	CTTTGGGCGT----------------------TCGCCTCC--TTG-CTG----TGGGTGTGGTTGCGTGCGTAGACGTCAGCGCAATGCCTTTGT---TTGGCGGCATGCGGATGACATTCACGTCCGTATCCGCACACACATCCGCATCC--------------AT----------------------------A-----TATC
droSim1	CTTTGGGCGT----------------------TCGCCTCC--TTG-CTG------TGGGTGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTGT---TTGGCGGCATGTGGATGACGTTCATGTCCACATCCGCACACACATCCGCATCC--------------AT-----------------------------------ATC
droSec1	CTTTGGGCGT----------------------TCGCCTCC--GTG-CTG------TGGGTGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTGT---TTGGCGGCATGTGGATGACGTTCATGTCCACATCCGCACACACATCCGCATCC--------------AT-----------------------------------ATC
droYak2	CTTTGGGCGC----------------------TCTCCTCC--TTG-CTG------TGAGCGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTGT---TTGTCGGCATGCGGATGGCGTACACGTCCACATCCGCACACACACACGCATCT--------------GT-----------------------------------ATC
droEre2	CTTTGGGCGC----------------------TCCTTTCC--TGG-CTG------TGAGTGGGTGCGTGCGTTTATGTCAGCGCAATGCTTTTGT---TTGGCGGCATGCGGATGGCATACACGTCCACATCCGCACACACATCCGCATCC--------------GT-----------------------------------ATC
droEug1	CTCT---------------------------------------TT-CTG------TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTGT---TTGCCGGCATGCGGATGGCGTACACGTCCACATCCGCGCACACATTCGCAACAATATCCGCATATGG--ATTTACAACTGCAGCCCTATCCACACAGG-----CATT
droBia1	CCGTTT--------------------------------CC--GCACCTG------TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTGT---TGGATGGCATGCGGATGGCGTACACGTCCACATCCGCGCACATATTCGCATCAGCTTCCGCTTCCGC--ATTCACGGCTGCAGCCCTATCCGCACGGA-----CATC
droTak1	C----------------------------------------------TG------TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTGT---TTGTCGGCATGCGGATGGCGTATACGTCCTCATCCGCACACACATCCGCATCGGCATCCAC--------ATTTGCAACTGCAGCCATATCCGCGCACA-----CATC
droEle1	CTTCACGC------------------------------CGGATT---TT------TGTGTGTGTGATGGGGTTGGAGTCAGCGCAATGCCATTGT---TTGCCGTCATGCGGCTGGCTCGCAGATAGACATCCACATCCACATCCGCATCC--------------GCA-TTACAAGTGCAGCAAA-----------------CTT
droRho1	TGGAGGTCCT----------------------TCAGATCCAGTTT-CTG------CGTGTGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTGT---TTGCCGGCATGTGGCTGCCGTGCACGTCCACATCCGCATCCGCACCCGCATCCGCATCCGC--------A-TTACAAGTGCAGCAAC-----------------ATC
droFic1	CTGTAAATGTATCTGGATTTGTTTCGGTTAATTCATCT----------GCATTTGTGTGCGTGTTTCGACGTTGGCGTCAGCGCAGTGCCATTGTTATTTGCCGGCATGCGGTTGGCGTGCGCGTCGACATCCGCATTTCTATAC----------------------------------AACCATTTCTACTCCTG-----AATT
droKik1	CCCCGCTCCT----------------------CCACCACC--ACCCATG------TGTGCGTGTGTTATCGTTGGTGTCAGCGCAATGCCGTTGT---TTGCCGGCATGCAGCTAATGTCAATGTCTACATCCGCACCCGCACTCGCACAT--------------CT------AGATGCAGTTA------------------GTC
droAna3	CGAC---------------------------------------TT-CTGTGTGTGTGTGCGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTGT---TTGCCGGCATGCGGCTGGCGTGCACGTCTACATCCGCACCTGCATCCACAT---------------------AGCAGCTGCAACAACAAACAC---GGCACTCCGTC
droBip1	TCCTGTGTG--------------------------------------TG------TGTGCGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTGT---TTACCGGCATGCGGCTGGCGTGCACGTCTACATCCGCACCTGCATTCACATA---------------GC-----------------------------------AGC

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

Small RNA-seq read pileup

Species

Alignment

droSim1

CTTTGGGCGTTCGCCTCCT--------------TG--------CTG--TGGGTGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTG---TTTGGCGGCATGTGGA-----------------TGACGTTCATGTC-----------CACATCCGCACACACATCCGCATCCA------TA-----------------------------------------TC	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
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------C............................................................................	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
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------CA...........................................................................	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
..................................................................................................CATGTGGA-----------------TGACGTTCATGTC-----------CAC..........................................................................	24	1	3.00	0.00	0.00	3.00	0.00
..................................................................................................CATGTGGA-----------------TGACGTTCATGTC-----------CA...........................................................................	23	1	3.00	0.00	0.00	3.00	0.00
..................................................................................................CATGTGGA-----------------TGACGTTCATGTC-----------C............................................................................	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
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------T............................................................................	21	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................ATGTGGA-----------------TGACxTTCAAGT.........................................................................................	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
..................................................................................................CATGTGGA-----------------TGACGTTCATGTC-----------.............................................................................	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
................................................................................GCATTTG---ATTGGCGGCATG..........................................................................................................................	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
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------.............................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACCTTCATG..........................................................................................	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

CTTTGGGCGTTCGCCTCCG--------------TG--------CTG--TGGGTGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTG---TTTGGCGGCATGTGGA-----------------TGACGTTCATGTC-----------CACATCCGCACACACATCCGCATCCA------TA-----------------------------------------TC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................GCAGGCGTGGAGGTCAGT.....................................................................................................................................................	18	1	247.00	86.00	89.00	72.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------CA...........................................................................	22	1	225.00	167.00	20.00	38.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------C............................................................................	21	1	134.00	124.00	4.00	6.00
..................................................................................................CATGTGGA-----------------TGACGTTCATGTC-----------CA...........................................................................	23	1	128.00	61.00	36.00	31.00
.............................................G--TGGGTGGGTGGAGGCGA...............................................................................................................................................................	18	1	121.00	0.00	0.00	121.00
........................................................GGCAGGCGTGGAGGTCAG......................................................................................................................................................	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
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------.............................................................................	20	1	17.00	17.00	0.00	0.00
..................................................................................................CATGTGGA-----------------TGACGTTCATGTC-----------C............................................................................	22	1	17.00	7.00	3.00	7.00
...........................................................AGGCGTGGACGTCAGCACAATGCC.............................................................................................................................................	24	1	14.00	8.00	4.00	2.00
........................................................GGCAGGCGTGGAGGTCAGC.....................................................................................................................................................	19	1	6.00	5.00	1.00	0.00
..................................................................................................CATGTGGA-----------------TGACGTTCATGTC-----------.............................................................................	21	1	5.00	3.00	2.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGT.........................................................................................	19	1	5.00	4.00	0.00	1.00
....................................................................................................TGTGGA-----------------TGACGTTCATGTC-----------CA...........................................................................	21	1	5.00	5.00	0.00	0.00
.............................................G--TGGGTGGGTGGAGGCGG...............................................................................................................................................................	18	1	4.00	0.00	0.00	4.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------CAC..........................................................................	23	1	4.00	2.00	1.00	1.00
............................................CG--TGGGTGGGTGGAGGCG................................................................................................................................................................	18	1	3.00	0.00	0.00	3.00
..................................................................................................CATGTGGA-----------------TGACGTTCATGTC-----------CAC..........................................................................	24	1	3.00	2.00	0.00	1.00
...................................................................................................ATGGGGA-----------------TGACGTTCATGTC-----------CA...........................................................................	22	1	3.00	3.00	0.00	0.00
...........................................................AGGCGTGGACGTCAGCACAAT................................................................................................................................................	21	1	2.00	2.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------CT...........................................................................	22	1	2.00	1.00	0.00	1.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------T............................................................................	21	1	2.00	2.00	0.00	0.00
..................................................................................................CATGTGGA-----------------TGACGTTCATTTC-----------CA...........................................................................	23	1	2.00	2.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGAC-----------C............................................................................	21	1	2.00	2.00	0.00	0.00
.................................................................................................GCATGTGGA-----------------TGACxTTCAAGT.........................................................................................	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
...................................................................................................ATGTGGA-----------------TGACGTTCCTGTC-----------C............................................................................	21	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGCTCATGTC-----------CA...........................................................................	22	1	1.00	1.00	0.00	0.00
...................................................................................................ATGGGGA-----------------TGACGGTCATGTC-----------CA...........................................................................	22	1	1.00	1.00	0.00	0.00
....................................................................................................AGTGGA-----------------TGACGTTCATGTC-----------CA...........................................................................	21	1	1.00	1.00	0.00	0.00
.........................................................GCAGGCGTGGATGTCAGT.....................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
...................................................................................................ATGTGGC-----------------TGACGTTCATGTC-----------CA...........................................................................	22	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGAAGTTCATGTC-----------C............................................................................	21	1	1.00	1.00	0.00	0.00
....................................................................................................TGTGGA-----------------TGACGTTCATGTC-----------.............................................................................	19	1	1.00	1.00	0.00	0.00
..................................................................................................CATGTGGA-----------------TGACGTTCGTGTC-----------CAC..........................................................................	24	1	1.00	0.00	0.00	1.00
...................................................................................................ATGTGGA-----------------TGCCGTTCATGTC-----------C............................................................................	21	1	1.00	1.00	0.00	0.00
........................................................TGCAGGCGTGGAGGTCAGT.....................................................................................................................................................	19	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTGCATGTC-----------CA...........................................................................	22	1	1.00	0.00	1.00	0.00
.......................................................GGGCAGGCGTGGAGGTCA.......................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATCTC-----------C............................................................................	21	1	1.00	1.00	0.00	0.00
...................................................................................................ATATGGA-----------------TGACGTTCATGCC-----------CA...........................................................................	22	1	1.00	1.00	0.00	0.00
..................................................................................................CATGTGGA-----------------TGGCGTTCATGTC-----------CA...........................................................................	23	1	1.00	1.00	0.00	0.00
..................................................................................................CATGTGGA-----------------TGACGGGCATG..........................................................................................	19	1	1.00	0.00	1.00	0.00
.......................................................AGGCAGGCGTGGACGTCA.......................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGCC-----------CA...........................................................................	22	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------CC...........................................................................	22	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGGC-----------CA...........................................................................	22	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCACGTC-----------C............................................................................	21	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGAC-----------.............................................................................	20	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCGTGTC-----------.............................................................................	20	1	1.00	1.00	0.00	0.00
..TTGCGCxTTCGCCTCCG--------------TG--------C....................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00
...................................................................................................ATGTGGA-----------------TGACGCTCATGTC-----------CAC..........................................................................	23	1	1.00	1.00	0.00	0.00
...................................................................................................ATGAGGA-----------------TGACGTTCATGTC-----------CAC..........................................................................	23	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGTC-----------CATT.........................................................................	24	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTGGA-----------------TGACGCTCATGTC-----------C............................................................................	21	1	1.00	1.00	0.00	0.00
...................................................................................................ATGTCGA-----------------TGACGTTCATGTC-----------CAC..........................................................................	23	1	1.00	1.00	0.00	0.00
...........................................................AGGCGTGGACGTTAGCACAATG...............................................................................................................................................	22	1	1.00	0.00	1.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATA..........................................................................................	18	1	1.00	0.00	0.00	1.00
...........................................................AGGCGTGGACGTAAGCAAAATG...............................................................................................................................................	22	1	1.00	0.00	1.00	0.00
...................................................................................................ATGTGGA-----------------TGACGTTCATGAC-----------CA...........................................................................	22	1	1.00	1.00	0.00	0.00
...................................................................................................AAGTGGA-----------------TGACGTTCATGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	1.00
...........................................................AGGCGTGGACGTCAGCCCAATGC..............................................................................................................................................	23	1	1.00	0.00	1.00	0.00
......................................................AGTGCAGGCGTGGAGGTC........................................................................................................................................................	18	1	1.00	1.00	0.00	0.00
..................................................................................................CATGTGGA-----------------TGACGTTCATGTC-----------CAA..........................................................................	24	1	1.00	0.00	1.00	0.00
...................................................................................................ATGTGGA-----------------CGACGTTCATGTC-----------CA...........................................................................	22	1	1.00	1.00	0.00	0.00
............................................................GGCGTGGACGTCAGCACAATG...............................................................................................................................................	21	1	1.00	1.00	0.00	0.00

droYak2

CTTTGGGCGCTCTCCTCCT--------------TG--------CTG--TGAGCGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTTGTCGGCATGCGGA-----------------TGGCGTACACGTC-----------CACATCCGCACACACACACGCATCTG------TA-----------------------------------------TC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CACA.........................................................................	24	1	126.00	0.00	0.00	124.00	2.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CA...........................................................................	22	1	80.00	1.00	2.00	76.00	1.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CAC..........................................................................	23	1	40.00	0.00	0.00	40.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------C............................................................................	21	1	37.00	0.00	1.00	33.00	1.00	2.00
..................................................................................................CATGCGGA-----------------TGGCGTACACGTC-----------CA...........................................................................	23	1	14.00	0.00	0.00	14.00	0.00	0.00
..................................................................................................CATGCGGA-----------------TGGCGTACACGTC-----------C............................................................................	22	1	8.00	0.00	0.00	8.00	0.00	0.00
..................................................................................................CATGCGGA-----------------TGGCGTACACGTC-----------CAC..........................................................................	24	1	7.00	0.00	0.00	7.00	0.00	0.00
..................................................................................................CATGCGGA-----------------TGGCGTACACGTC-----------CACA.........................................................................	25	1	7.00	1.00	0.00	6.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------.............................................................................	20	1	6.00	0.00	1.00	5.00	0.00	0.00
..................................................................................................CATGCGGA-----------------TGGCGTACACGTC-----------.............................................................................	21	1	4.00	0.00	0.00	4.00	0.00	0.00
....................................................................................................TGCGGA-----------------TGGCGTACACGTC-----------CAC..........................................................................	22	1	3.00	0.00	0.00	3.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGCC-----------CACA.........................................................................	24	1	2.00	0.00	0.00	2.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CCC..........................................................................	23	1	2.00	0.00	0.00	2.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CCCA.........................................................................	24	1	2.00	0.00	0.00	1.00	1.00	0.00
...................................................................................................ATGCGGT-----------------TGGCGTACACGTC-----------CAA..........................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CATT.........................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TAGCGTACACGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACCCCTC-----------CAC..........................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACCTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CT...........................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCTGA-----------------TGGCGTACACGTC-----------CAC..........................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACCCGTC-----------C............................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGCA-----------------TGGCGTACACGTC-----------CAC..........................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTAAACGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................................................CATGCGGA-----------------TGGCGTACACGCC-----------CACA.........................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................................................CATGCGGA-----------------TGGCGTACACGTT-----------.............................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACCCGTC-----------CC...........................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...................................................................................................ATGCCGA-----------------TGGCGTACACGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGCACACGTC-----------C............................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................TGCGGA-----------------TGGCGGACACGTC-----------C............................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................................CATGCGGA-----------------TGGCGTACACGTC-----------T............................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CC...........................................................................	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
...................................................................................................ATGCGGA-----------------TGGCGTGCACGTC-----------CACA.........................................................................	24	1	1.00	0.00	1.00	0.00	0.00	0.00
..................................................................................................CATGCGGA-----------------TTGCGTACACGTC-----------CA...........................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CCCC.........................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................AAATGCGGA-----------------TGGCGTACACGTC-----------C............................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................................................CATGCGGA-----------------TGGCGTACACGT.........................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACATC-----------C............................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ACGCGGA-----------------TGGCGTACACGTC-----------C............................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACAAGTC-----------CG...........................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CTCA.........................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
...................................................................................................ATGCGGA-----------------CGGCGTACACGTC-----------CACA.........................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CACAT........................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------CATTT........................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCGTACACGTC-----------T............................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................TGCGGA-----------------TGGCGTACACGTC-----------CACA.........................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

CTTTGGGCGCTCCTTTCCT--------------GG--------CTG--TGAGTGGGTGCGTGCGTTTATGTCAGCGCAATGCTTTTG---TTTGGCGGCATGCGGA-----------------TGGCATACACGTC-----------CACATCCGCACACACATCCGCATCCG------TA-----------------------------------------TC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................................................................................................ATGCGGA-----------------TGGCATACACGTC-----------CA...........................................................................	22	1	88.00	0.00	11.00	0.00	77.00
...................................................................................................ATGCGGA-----------------TGGCATACACGTC-----------CACA.........................................................................	24	1	27.00	0.00	5.00	0.00	22.00
...................................................................................................ATGCGGA-----------------TGGCATACACGTC-----------C............................................................................	21	1	21.00	0.00	1.00	0.00	20.00
...................................................................................................ATGCGGA-----------------TGGCATACACGTC-----------CAC..........................................................................	23	1	17.00	1.00	4.00	0.00	12.00
...................................................................................................ATGCGGA-----------------TGGCATACACGTC-----------.............................................................................	20	1	4.00	0.00	1.00	0.00	3.00
..................................................................................................CATGCGGA-----------------TGGCATACACGTC-----------CA...........................................................................	23	1	3.00	0.00	0.00	0.00	3.00
..................................................................................................CATGCGGA-----------------TGGCATACACGTC-----------C............................................................................	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
...................................................................................................ATGCTGA-----------------TGGCATACACGTC-----------CACA.........................................................................	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
...................................................................................................ATGCGGA-----------------TGGCATATACGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.............TTTCCT--------------GG--------CTG--TGAGTGGGTG......................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCTGA-----------------TGGCATACACGTC-----------C............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGCATACACCTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGCATACACTTC-----------CACA.........................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGAATACACGTC-----------CACA.........................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGCATACACGTC-----------CCCA.........................................................................	24	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCTGA-----------------TGGCATACACGTC-----------CAC..........................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGG-----------------TGGCATACACGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGCATACACGTC-----------CACC.........................................................................	24	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCATCCACGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TTGCATACACGTC-----------CACA.........................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...............TCCT--------------GG--------CTG--TGAGTGGGTG......................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATTCGGA-----------------TGTCATACACGTC-----------CACA.........................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGCATACACGC.........................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATTCGGA-----------------TGGCATACACGTC-----------C............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGC-----------------TGGCATACACGTC-----------C............................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................ATGCGGA-----------------TGGCATACACATC-----------CA...........................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................CATGCGGA-----------------TGGCATCCACGTC-----------CA...........................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.............................................G--TGAGTGTGTGTGTGCGT...............................................................................................................................................................	18	8	0.13	0.00	0.00	0.00	0.13
...................................................................................................ATTCGGA-----------------TGGCATACACGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGAGGA-----------------TGGCATACACGTC-----------CAC..........................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGCATACAAGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGTCATACACGTC-----------CA...........................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGCATACACGTC-----------CACTA........................................................................	25	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................ATACGGA-----------------TGGCATACACGTC-----------CACA.........................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGCATACACGTC-----------CAT..........................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................ATGCGGA-----------------TGGCATACACGTA-----------C............................................................................	21	1	1.00	0.00	0.00	0.00	1.00

droEug1

CTCT-----------------------------TT--------CTG--TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTTGCCGGCATGCGGA-----------------TGGCGTACACGTC-----------CACATCCGCGCACACATTCGCAACAATATCCGCATATGGATTTACAACTGCAGCCCTATCCACACAGG-----CATT

Size

Hit Count

Total Norm

droBia1

CCGTTT----------CCG-------------CAC--------CTG--TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTGGATGGCATGCGGA-----------------TGGCGTACACGTC-----------CACATCCGCGCACATATTCGCATCAGCTTCCGCTTCCGCATTCACGGCTGCAGCCCTATCCGCACGGA-----CATC

Size

Hit Count

Total Norm

droTak1

CT-------------------------------------------G--TGAGTGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTG---TTTGTCGGCATGCGGA-----------------TGGCGTATACGTC-----------CTCATCCGCACACACATCCGCATCGGCATCCACA------TTTGCAACTGCAGCCATATCCGCGCACA-----CATC

Size

Hit Count

Total Norm

droEle1

CTTCACGCC------GG----------------AT--------TTT--TGTGTGTGTGATGGGGTTGGAGTCAGCGCAATGCCATTG---TTTGCCGTCATGCGGC-----------------TGGCTCGCAGATA-----------GACATCCACATCCACATCCGCATCCG------CA------T-TACAAGTGCAGCAAA-----------------CTT

Size

Hit Count

Total Norm

droRho1

TGGAGGTCCTTCAGATCCAG------------TTT--------CTG--CGTGTGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTG---TTTGCCGGCATGTGGC-----------------TGCCGTGCACGTC-----------CACATCCGCATCCGCACCCGCATCCGCATCCGCA------T-TACAAGTGCAGCAAC-----------------ATC

Size

Hit Count

Total Norm

droFic1

CTGTAAATGTATCTGGATT-TGTTTCGGTTAATTCATCTGCATTTG--TGTGCGTGTTTCGACGTTGGCGTCAGCGCAGTGCCATTGTTATTTGCCGGCATGCGGT-----------------TGGCGTGCGCGTC-----------GACATCCGCATTTCTATAC--------------------------------AACCATTTCTACTCCTG-----AATT

Size

Hit Count

Total Norm

droKik1

CCCCGCTCCTCCACCACCA-------------CCC--------ATG--TGTGCGTGTGTTATCGTTGGTGTCAGCGCAATGCCGTTG---TTTGCCGGCATGCAGC-----------------TAATGTCAATGTC-----------TACATCCGCACCCGCACTCGCACATC------TA------------GATGCAGTTA------------------GTC

Size

Hit Count

Total Norm

droAna3

CGACTT----------CTG-------------TGT--------GTG--TGTGCGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTG---TTTGCCGGCATGCGGC-----------------TGGCGTGCACGTC-----------TACATCCGCACCTGCATCCACAT-------------------AGCAGCTGCAACAACAAACAC---GGCACTCCGTC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
......................................................TGTGTTGGCGTTGGCGTCAG......................................................................................................................................................	20	1	121.00	102.00	14.00	5.00	0.00
......................................................TGTGTTGGCGTTGGCGTCAGCG....................................................................................................................................................	22	1	118.00	94.00	14.00	10.00	0.00
......................................................TGTGTTGGCGTTGGCGTCAGC.....................................................................................................................................................	21	1	89.00	75.00	6.00	8.00	0.00
......................................................TGTGTTGGCGTTGGCGTCA.......................................................................................................................................................	19	1	40.00	33.00	4.00	3.00	0.00
......................................................TGTGTTGGCGTTGGCGTCAGT.....................................................................................................................................................	21	1	21.00	20.00	1.00	0.00	0.00
..................................................................................................CATGCGGC-----------------TGGCGTGCACGTC-----------T............................................................................	22	1	16.00	13.00	3.00	0.00	0.00
......................................................TGTGTTGGCGTTGGCGTCAGCT....................................................................................................................................................	22	1	16.00	15.00	0.00	1.00	0.00
..................................................................................................CATGCGGC-----------------TGGCGTGCACGTC-----------TA...........................................................................	23	1	11.00	7.00	3.00	1.00	0.00
.................AG-------------TGT--------GTG--TGTGTGTGTG......................................................................................................................................................................	18	27	0.41	0.04	0.37	0.00	0.00
..................G-------------TGT--------GTG--TGTGTGTGTGT.....................................................................................................................................................................	18	20	0.50	0.00	0.50	0.00	0.00
..................................................................................................CATGCGGC-----------------TGGCGTGCACGTC-----------.............................................................................	21	1	9.00	6.00	0.00	3.00	0.00
......................................................TGTGTTGGCGTTGGCGTCAGA.....................................................................................................................................................	21	1	8.00	8.00	0.00	0.00	0.00
.................AG-------------TGT--------GTG--TGTGTGTGTGT.....................................................................................................................................................................	19	22	0.36	0.00	0.36	0.00	0.00
..................................................................................................CATGCGGC-----------------TGGCGTGCACGT.........................................................................................	20	1	7.00	4.00	2.00	1.00	0.00
.................TG-------------TGT--------GTG--TGTGTGTGTG......................................................................................................................................................................	18	23	0.30	0.00	0.30	0.00	0.00
.................TG-------------TGT--------GTG--TGTGTGTGTGT.....................................................................................................................................................................	19	19	0.32	0.00	0.32	0.00	0.00
.................................GT--------GTG--TGTGTGTGTGTTG...................................................................................................................................................................	18	12	0.42	0.00	0.42	0.00	0.00
.....T----------GTG-------------TGT--------GTG--TGTGGGTG........................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00
..ACTT----------CTG-------------TGT--------GTG--TGTGCG..........................................................................................................................................................................	19	1	3.00	0.00	3.00	0.00	0.00
......................................................TGTGTTGGCGTTGGCGTCAGTT....................................................................................................................................................	22	1	3.00	3.00	0.00	0.00	0.00
................................TGT--------GTG--TGTGTGTGTGTTGGTG................................................................................................................................................................	22	7	0.43	0.00	0.43	0.00	0.00
................................TGT--------GTG--TGTGTGTGTGTT....................................................................................................................................................................	18	10	0.30	0.00	0.30	0.00	0.00
.................GG-------------TGT--------GTG--TGTGTGTGTGT.....................................................................................................................................................................	19	21	0.14	0.05	0.10	0.00	0.00
..................G-------------TGT--------GTG--TGTGCGTGTGT.....................................................................................................................................................................	18	7	0.43	0.00	0.43	0.00	0.00
...................................................................................................ATGCGGC-----------------TGGCGTGCACGTC-----------T............................................................................	21	1	3.00	3.00	0.00	0.00	0.00
..................G-------------TGG--------GTG--TGTGGGTGTGT.....................................................................................................................................................................	18	7	0.43	0.14	0.29	0.00	0.00
................................AGT--------GTG--TGTGTGTGTGTT....................................................................................................................................................................	18	13	0.23	0.00	0.23	0.00	0.00
.................TG-------------TGT--------GTG--TGTGTGGGTG......................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00
..................................................................................................CATGCGGC-----------------TGGCGTGCACGTC-----------TTT..........................................................................	24	1	3.00	1.00	0.00	2.00	0.00

droBip1

TCCTGTG---------------------------T--------GTG--TGTGCGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTG---TTTACCGGCATGCGGC-----------------TGGCGTGCACGTC-----------TACATCCGCACCTGCATTCACATA-G------CA-----------------------------------------GC

Size

Hit Count

Total Norm

dp4

TTTTTGAGT------GTGTG------------TTT--------GTA--TTTATTTATTTTTGTGTGGACTTCACTGCATTGTCATTG---ATTGGCGG-------C-----------------TGTCGTGCAGGAC-----------AATGTG--AAACATCATTCGACA-------------------------------------------CA-----AATC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
TGTTTGTGT------GTGTG------------TTT--------GT...................................................................................................................................................................................	19	44	0.05	0.02	0.00	0.02	0.00
.............................................A--TTTATGTATTTTTGTTT...............................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
......ATT------GTGTG------------TGT--------GTA--TTTA............................................................................................................................................................................	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

------------------------------------------------------------------------------AGGCCATTGTTA-TGGCAGGTGGGCAGG-----------------TGTCATCAATAGC-----------CGCATCCA--GGCACATCCGCATCCA------CA-----------------------------------------T-	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...............................................................................................................................ATCGATCGC-----------CGCATCCA--GG.................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
....................................................................................................................................................................................A-----------------------------------------G-	22	15	0.07	0.07	0.00	0.00	0.00	0.00
....................................................................................................................................................................................G-----------------------------------------T-	21	3	0.33	0.00	0.00	0.33	0.00	0.00
.....................................................................................TGTTA-TGGCGGGTGGGTAGG-----------------.....................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

CTGTGGGCTTTAGGCCAAT--------------TG--------ATA--TGGTCGTG---------------------------------------TGGCATGAGGCAGGTGTCAGCAGGTGGCAGCAATTCGGAACCATTGTGTGCCCACATCCGCATTTGCAA----------------------------------------------------------GC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TGTTGCA---------------------------G--------TTG--CATTTGAATGTAGGTGTTGTCATT-------------AT---TTTGAGGGCATGCGGCAGGTGTCAACG------------CCACGTC-----------CTCATTTGCATCCGCTTCCGCATCCGCATCCGCT-----------------------------------------GT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:15:55 EDT

dme-mir-2499

chrX:19451041-19451136 +

Known_mirbase

intergenic

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup