dme-mir-976- Best orthologs

dme-mir-976	chrX:19452928-19453024 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 19452987-19453008
   star strand at position 19452950-19452971
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:19452913-19453039 +		1	AACGG------------------------CGGTG-----------------GTG-GGCATCGCCATGCAGTGCCGCGGCATTGGTGAGGC-CATCTCCAATGG-ATTAGTT---------CTCAACATTGGATTAGTTATCATCAATGCCGGTGCACTGCACC--TAAC--AACATC---------------GCG------------------CCGG
droSim1	chrX:15018511-15018617 +	LASTZ	1	A----------------------------------------------------------------TGCAGTGTCGTGGCATTGGTGAGGA-CATCTCCAATGG-ATTGGTT---------CTCATCATTGGATTAGTTATCATCAATGCCGGTGCACTGCACTGCTGTC--AACTTC---------------GCG------------------CAAT
droSec1	super_8:1735239-1735349 +	LASTZ	1	TCC-----------------------------------------------------------GCATGCAGTGCCGTGGCATTGGTGAGGA-CATCTCCAATGG-CTTAGTT---------CTCATCATTGGATTAGTTATCATCAATGCCGGTGCACTGCAGC--TGTC--AACTTC---------------GCG------------------CAAT
droYak2	chrX:11885798-11885920 -	LASTZ	1	AGAGG---------------------------TG---------------A-GTG-AGAATC-GCATGCAGTGCCACGACATTGGTGAGGG-CATCTCCAATGG-G-GACCC---------GGCATCATTGGATTAGTTCTCATTAATGCCGGAGCACTGCACC--TACC--AACTTC---------------GCA------------------CGGT
droEre2	scaffold_4690:9688892-9689017 +	LASTZ	1	TCCAG------------------------AGGTG-----------------TGCCAGAATC-GCATGCAGTGCCTCGACATTGGTGAGGG-CATCTCCAATGG-G-GAGCC---------AGCATCATTGGATTAGTTCTCATTAATGCCGGAGCATGGCACC--TACG--AACTGA---------------GCA------------------TTTG
droEug1	scf7180000409230:879657-879763 -	LASTZ	4	A----------------------------------------------------------------TGCAGCGCCTTGACATTGGCGAGGC-CAACTCCAATGT-C-GAATC---------GAAATCATTGGATTAGTTCTCATCAATGACTGAGCCCTGTAAT--GACC--AACGTA---------------CCATA----------------TCTT
droBia1	scf7180000302069:1151015-1151142 -	LASTZ	4	ATCAA------------------------TGCTG-----------------GTG-GGGATGAGGAAGCACCGCCTCGGCATTGGTGAGGG-CACCTCCAATGG-C-GAGCC---------GGCATCATTGGATTAGTTCTCATTAATGGCGGAGTGCTGCACC--GACC--AACGCC---------------ACATA----------------CGGT
droTak1	scf7180000415169:844814-844944 -	LASTZ	4	TCTGG------------------------AGAGG-----------------AGGAGAAA-GAGGAAGCATCGCCTCGACATTATTGAGGG-CACCTCCAATGG-C-GAGCC---------GACATCATTGGATTAGTTCTCATTAATGGCGGAGCGCTGCACT--GACC--AACTGTTCGTC----------CAT------------------AAGG
droEle1	scf7180000490751:1118774-1118889 +	LASTZ	4	ATCAA------------------------TAC-------------------CTG------CACAAAGCATCGCCTCGCCATTGGTGAGGG-CACCTCCAATGG-C-GAGCC---------GGCTGCATTGGATTAGTTTTCATCAATGGCGGAGCCCTGCACT--GACC--AGCAGA------------------------------------CCGA
droRho1	scf7180000761121:190087-190218 -	LASTZ	4	AACCG------------------------C---------------------CTG------CAAACAGCATCACCTCGCCATTGGTGAGGG-CATCTCCAATGA-C-GAGTC---------GGCAGCATTGGATTAGTTCTCATTAATGGCGGAGCGGTGCACT--GACC--AGCAGACTGACCTCTCCGCTAGCA------------------CCAG
droFic1	scf7180000454073:1733903-1734027 +	LASTZ	4	ATCAC------------------------CGC-----------------------------AGACAGCGGCGCCCCGCCATTAATAAGGA-CCTCTCCAATGG-C-AGACC-------GTCGAATCATTGGATTAGTTCTCATTAATGGTGGAGTGCCGCACC--GACC--ACCACATTTTTTTC-------TAA------------------GTGC
droKik1	scf7180000302517:1183679-1183793 +	LASTZ	4	GC-------------------------------------------------------------GAGGCATTGCCTCGCCATTGGTGAGAG-CATCTCCAATGA-C-GGCAC-------TTGATTGCATTGGATTAGTTCTCATTGATGGCGGAGCATTGCACC--TACT--CCAGCAACGGC----------TAT------------------CCAG
droAna3	scaffold_13417:2467561-2467679 -	LASTZ	1	GCTAC------------------------CGATG-----------------CTC------CCCGAAGGAGCGCCTCGACATTGGTGAGTT-CATCTCCAATGG-T-CAGTA---------GCCCGCATTGGATTAGTTCTCATTGATGGCGAAGCGAGT--CC--TACC--CCCACA---------------CCA------------------GCGA
droBip1	scf7180000395874:39930-40044 -	LASTZ	4	GCTAG------------------------CGATG-----------------CTC------CGTGAAGGAGCGCCTCGCCATTGGTGGGGG-CGTCTCCAATGG-C-CAGAA---------GCCCGCATTGGATTAGTTCTCATTAATGGCGAAGCGAGTCCTT--CCTC-----------------------CAC------------------ACCA
dp4	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7956743-7956912 +	LASTZ	1	CTCTC----CCCTTCC--TTCTTACACAGGATTA-----------------TGT-AGGATT--ATGGCAACACCTCGATATTGGTGAGTTCCAGCTCCAATGTTATTGGAGCCCAACATTGAACACATTGGATTAGTTCTCATCGATGGCGAAGTGTTT--GT--GAGC--AATATC---------------GTATATTGTGCGTGCAGTGTATTGT
droVir3	scaffold_13042:906708-906880 -	LASTZ	1	ATCGTTATCGTTATCGTTATCGTTATCAGAATTAATTATCGTTGAAGTGCGTTC------TTTGGTGCAGCCCCTCGCGATTGATGATAG-CATCTCCAATGA-G-CA------------TATCACATTGGATTAGTTCTCATCGATGCCGATGCGCTGTACC--AGCAACAACAAC---------------AGG------AATAGCAACGGAAACA
droMoj3	scaffold_6328:2900970-2901098 -	LASTZ	1	TATCG-----TTATCGCTAG---------CGACG-----------------CTT------C-GGGTGCAGCCCCTCGCGATTGATGAAAG-CATCTCCAATGA-G-TA------------TTTCGCATTGGATTAGTTCTCATCGATGTCGATGCGCTGTATC--AGCAACAACAAC---------------AAC------------------ATGA
droGri2	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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	AACGG------------------------CGGTG-----------------GTG-GGCATCGCCATGCAGTGCCGCGGCATTGGTGAGGC-CATCTCCAATGG-ATTAGTT---------CTCAACATTGGATTAGTTATCATCAATGCCGGTGCACTGCACC--TAAC--AACATC---------------GCG------------------CCGG
droSim1	A----------------------------------------------------------------TGCAGTGTCGTGGCATTGGTGAGGA-CATCTCCAATGG-ATTGGTT---------CTCATCATTGGATTAGTTATCATCAATGCCGGTGCACTGCACTGCTGTC--AACTTC---------------GCG------------------CAAT
droSec1	TCC-----------------------------------------------------------GCATGCAGTGCCGTGGCATTGGTGAGGA-CATCTCCAATGG-CTTAGTT---------CTCATCATTGGATTAGTTATCATCAATGCCGGTGCACTGCAGC--TGTC--AACTTC---------------GCG------------------CAAT
droYak2	AGAGG---------------------------TG---------------A-GTG-AGAATC-GCATGCAGTGCCACGACATTGGTGAGGG-CATCTCCAATGG-G-GACCC---------GGCATCATTGGATTAGTTCTCATTAATGCCGGAGCACTGCACC--TACC--AACTTC---------------GCA------------------CGGT
droEre2	TCCAG------------------------AGGTG-----------------TGCCAGAATC-GCATGCAGTGCCTCGACATTGGTGAGGG-CATCTCCAATGG-G-GAGCC---------AGCATCATTGGATTAGTTCTCATTAATGCCGGAGCATGGCACC--TACG--AACTGA---------------GCA------------------TTTG
droEug1	A----------------------------------------------------------------TGCAGCGCCTTGACATTGGCGAGGC-CAACTCCAATGT-C-GAATC---------GAAATCATTGGATTAGTTCTCATCAATGACTGAGCCCTGTAAT--GACC--AACGTA---------------CCATA----------------TCTT
droBia1	ATCAA------------------------TGCTG-----------------GTG-GGGATGAGGAAGCACCGCCTCGGCATTGGTGAGGG-CACCTCCAATGG-C-GAGCC---------GGCATCATTGGATTAGTTCTCATTAATGGCGGAGTGCTGCACC--GACC--AACGCC---------------ACATA----------------CGGT
droTak1	TCTGG------------------------AGAGG-----------------AGGAGAAA-GAGGAAGCATCGCCTCGACATTATTGAGGG-CACCTCCAATGG-C-GAGCC---------GACATCATTGGATTAGTTCTCATTAATGGCGGAGCGCTGCACT--GACC--AACTGTTCGTC----------CAT------------------AAGG
droEle1	ATCAA------------------------TAC-------------------CTG------CACAAAGCATCGCCTCGCCATTGGTGAGGG-CACCTCCAATGG-C-GAGCC---------GGCTGCATTGGATTAGTTTTCATCAATGGCGGAGCCCTGCACT--GACC--AGCAGA------------------------------------CCGA
droRho1	AACCG------------------------C---------------------CTG------CAAACAGCATCACCTCGCCATTGGTGAGGG-CATCTCCAATGA-C-GAGTC---------GGCAGCATTGGATTAGTTCTCATTAATGGCGGAGCGGTGCACT--GACC--AGCAGACTGACCTCTCCGCTAGCA------------------CCAG
droFic1	ATCAC------------------------CGC-----------------------------AGACAGCGGCGCCCCGCCATTAATAAGGA-CCTCTCCAATGG-C-AGACC-------GTCGAATCATTGGATTAGTTCTCATTAATGGTGGAGTGCCGCACC--GACC--ACCACATTTTTTTC-------TAA------------------GTGC
droKik1	GC-------------------------------------------------------------GAGGCATTGCCTCGCCATTGGTGAGAG-CATCTCCAATGA-C-GGCAC-------TTGATTGCATTGGATTAGTTCTCATTGATGGCGGAGCATTGCACC--TACT--CCAGCAACGGC----------TAT------------------CCAG
droAna3	GCTAC------------------------CGATG-----------------CTC------CCCGAAGGAGCGCCTCGACATTGGTGAGTT-CATCTCCAATGG-T-CAGTA---------GCCCGCATTGGATTAGTTCTCATTGATGGCGAAGCGAGT--CC--TACC--CCCACA---------------CCA------------------GCGA
droBip1	GCTAG------------------------CGATG-----------------CTC------CGTGAAGGAGCGCCTCGCCATTGGTGGGGG-CGTCTCCAATGG-C-CAGAA---------GCCCGCATTGGATTAGTTCTCATTAATGGCGAAGCGAGTCCTT--CCTC-----------------------CAC------------------ACCA
droWil1	CTCTC----CCCTTCC--TTCTTACACAGGATTA-----------------TGT-AGGATT--ATGGCAACACCTCGATATTGGTGAGTTCCAGCTCCAATGTTATTGGAGCCCAACATTGAACACATTGGATTAGTTCTCATCGATGGCGAAGTGTTT--GT--GAGC--AATATC---------------GTATATTGTGCGTGCAGTGTATTGT
droVir3	ATCGTTATCGTTATCGTTATCGTTATCAGAATTAATTATCGTTGAAGTGCGTTC------TTTGGTGCAGCCCCTCGCGATTGATGATAG-CATCTCCAATGA-G-CA------------TATCACATTGGATTAGTTCTCATCGATGCCGATGCGCTGTACC--AGCAACAACAAC---------------AGG------AATAGCAACGGAAACA
droMoj3	TATCG-----TTATCGCTAG---------CGACG-----------------CTT------C-GGGTGCAGCCCCTCGCGATTGATGAAAG-CATCTCCAATGA-G-TA------------TTTCGCATTGGATTAGTTCTCATCGATGTCGATGCGCTGTATC--AGCAACAACAAC---------------AAC------------------ATGA

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				None
UNAFold Image															None	None				None

Small RNA-seq read pileup

Species

Alignment

droSim1

A----------------------------------------------------------------TGCAGTGTCGTGGCATTGGTGAGGA-CATCTCCAATGG-ATTGGTT---------CTCATCATTGGATTAGTTATCATCAATGCCGGTGCACTGCACTGCTGTC--AACTTC---------------GCG------------------CAAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................................................................................TTGGATTAGTTATCATCAATGCC...................................................................	23	1	999.00	0.00	36.00	958.00	5.00
...............................................................................................................................TTGGATTAGTTATCATCAATG.....................................................................	21	1	29.00	0.00	2.00	27.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGC....................................................................	22	1	22.00	0.00	1.00	21.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGCCT..................................................................	24	1	13.00	0.00	1.00	12.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGAC...................................................................	23	1	9.00	0.00	0.00	9.00	0.00
................................................................................................................................TGGATTAGTTATCATCAATGCC...................................................................	22	1	3.00	0.00	0.00	3.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGCCC..................................................................	24	1	2.00	0.00	0.00	2.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAA.......................................................................	19	1	2.00	0.00	0.00	2.00	0.00
................................................................................TTGGTGAGGT-CGTCTCCA......................................................................................................................	18	1	2.00	0.00	0.00	2.00	0.00
...............................................................................................................................TTGGATTAGTTATCATTAATGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGGTTAGTTATCATCAATGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGCCA..................................................................	24	1	1.00	0.00	0.00	1.00	0.00
............................................................................................................................................................CTGCAxTGCTGTC--ACCTTC---------------GC.......................	20	1	1.00	0.00	0.00	0.00	1.00
..............................................................................CATTGGTGAGGA-CATCTC........................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAATTATCATCAATGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGCTTAGTTATCATCAATGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
..............................................................................CATTGGTGAGGA-CATCTCCA......................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGACTAGTTATCATCAATGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................CACTGCAxTGCTGTC--ACCTT.........................................	19	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGTTATCATCAGTGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCA........................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGCT...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TCGGATTAGTTATCATCAATGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGTC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTGGTTATCATCAATGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................................ATTAGTTATCATCAATGCCGGAT...............................................................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTATAATCAATGC....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATCAGTTATCATCAATGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00
..............................................................................CATTGGTGAGGA-CATCTCT.......................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................ATTGGxT---------CTGATCATTGGA.....................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGGTATCATCAATGCC...................................................................	23	1	1.00	0.00	0.00	1.00	0.00

droSec1

TCC-----------------------------------------------------------GCATGCAGTGCCGTGGCATTGGTGAGGA-CATCTCCAATGG-CTTAGTT---------CTCATCATTGGATTAGTTATCATCAATGCCGGTGCACTGCAGC--TGTC--AACTTC---------------GCG------------------CAAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............................................................................................................................TTGGATTAGTTATCATCAATGCC...................................................................	23	1	35.00	25.00	5.00	5.00
...............................................................................................................................TTGGATTAGTTATCATCAATGC....................................................................	22	1	26.00	20.00	1.00	5.00
................................................................................................................................TGGATTAGTTATCATCAATGCC...................................................................	22	1	7.00	5.00	1.00	1.00
...............................................................................................................................TTGGATTAGTTATCATCAATG.....................................................................	21	1	6.00	4.00	1.00	1.00
................................................................................................................................TGGATTAGTTATCATCAATGC....................................................................	21	1	2.00	1.00	1.00	0.00
...............................................................................................................................TTGGATTATTTATCATCAATGC....................................................................	22	1	1.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGCA...................................................................	23	1	1.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGCT...................................................................	23	1	1.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCACTGCC...................................................................	23	1	1.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCAATGCCT..................................................................	24	1	1.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTATCCTCAAT......................................................................	20	1	1.00	1.00	0.00	0.00
................................................................................................................................GAGATTAGTTATCATCAATGCC...................................................................	22	1	1.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGTTATCATCAATGCAA..................................................................	24	1	1.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCACTGC....................................................................	22	1	1.00	1.00	0.00	0.00

droYak2

AGAGG---------------------------TG---------------A-GTG-AGAATC-GCATGCAGTGCCACGACATTGGTGAGGG-CATCTCCAATGG-G-GACCC---------GGCATCATTGGATTAGTTCTCATTAATGCCGGAGCACTGCACC--TACC--AACTTC---------------GCA------------------CGGT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...............................................................................................................................TTGGATTAGTTCTCATTAATGC....................................................................	22	2	65.50	0.00	0.00	20.50	2.00	43.00
................................................................................TTGGTGAGGG-CATCTCCAATGG-.................................................................................................................	22	2	32.50	0.00	0.00	31.50	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTAATG.....................................................................	21	2	28.50	0.00	0.50	24.00	0.50	3.50
...............................................................................................................................TTGGATTAGTTCTCATTAAT......................................................................	20	2	11.00	0.00	0.00	3.00	0.00	8.00
...............................................................................................................................TTGGATTAGTTCTCATTAATGCC...................................................................	23	2	8.00	0.00	0.00	0.00	0.00	8.00
................................................................................TTGGTGAGGG-CATCTCCAATG...................................................................................................................	21	2	7.50	0.00	0.00	7.00	0.50	0.00
...............................................................................................................................TTGGATTAGTTCTCATTAATGCT...................................................................	23	2	4.00	0.00	0.00	0.50	0.00	3.50
..............................................................................................................................ATTGGATTAGTTCTCATTAATG.....................................................................	22	2	2.50	0.00	0.00	2.00	0.00	0.50
..............................................................................................................................ATTGGATTAGTTCTCATTAAT......................................................................	21	2	2.50	0.00	0.00	1.00	0.50	1.00
...............................................................................ATTGGTGAGGG-CATCTCCAATG...................................................................................................................	22	2	1.50	0.00	0.00	1.00	0.50	0.00
...............................................................................ATTGGTGAGGG-CATCTCCAAT....................................................................................................................	21	2	1.00	0.00	0.00	0.50	0.50	0.00
...........................................................TC-GCATGCAGTGCCACGAC..........................................................................................................................................	19	2	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGTTCTCATTAATGCCT..................................................................	24	2	0.50	0.00	0.00	0.00	0.00	0.50
...............................................................................................................................TTGGATTAGTTCTCATTAATTC....................................................................	22	2	0.50	0.00	0.00	0.00	0.50	0.00
...............................................................................................................................TTGGATTAGGTCTCATTAATGC....................................................................	22	2	0.50	0.00	0.00	0.00	0.00	0.50
..............................................................................................................................ATTGGATTAGTTCTAATTAAT......................................................................	21	2	0.50	0.00	0.00	0.00	0.00	0.50
...............................................................................................................................TTGGATTAGTTCTCTTTACT......................................................................	20	2	0.50	0.00	0.00	0.00	0.50	0.00
...............................................................................................................................TTGGATTAGTTCTCATTAATGT....................................................................	22	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................CATTGGTGAGGT-CGTCTCC.......................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATG.....................................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
...............................................................................................................................TTGGATTAGTTCCCATTAATGCT...................................................................	23	2	0.50	0.00	0.00	0.00	0.00	0.50
...............................................................................................................................TTGGATTAATTCTCATTAAT......................................................................	20	2	0.50	0.00	0.00	0.00	0.00	0.50
...............................................................................ATTGGTGAGGT-CGTCTCCA......................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCACATTAATGC....................................................................	22	2	0.50	0.00	0.00	0.50	0.00	0.00
...............................................................................ATTGGTGAGGG-CATCTCCAATA...................................................................................................................	22	2	0.50	0.00	0.00	0.50	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCTTTAATGCT...................................................................	23	2	0.50	0.00	0.00	0.00	0.50	0.00
.............................................................................ACATTGGTGAGGT-CGTCTCC.......................................................................................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00
................................................................................TTGGTGAGGG-CATCTCCAATGA-.................................................................................................................	22	2	0.50	0.00	0.00	0.50	0.00	0.00
...............................................................................................................................TTGGATTCGTTCTCATTAATG.....................................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
...............................................................................ATTGGTGAGGG-CATCTCCTT.....................................................................................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATTAATGA....................................................................	23	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................CTTGGATTAGTTCTCATTAATGC....................................................................	23	2	0.50	0.00	0.00	0.50	0.00	0.00

droEre2

TCCAG------------------------AGGTG-----------------TGCCAGAATC-GCATGCAGTGCCTCGACATTGGTGAGGG-CATCTCCAATGG-G-GAGCC---------AGCATCATTGGATTAGTTCTCATTAATGCCGGAGCATGGCACC--TACG--AACTGA---------------GCA------------------TTTG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................................................................................................................TTGGATTAGTTCTCATTAATGC....................................................................	22	1	79.00	0.00	3.00	0.00	76.00
................................................................................TTGGTGAGGG-CATCTCCAATGG-.................................................................................................................	22	1	68.00	0.00	7.00	0.00	61.00
...............................................................................................................................TTGGATTAGTTCTCATTAATG.....................................................................	21	1	12.00	0.00	1.00	0.00	11.00
................................................................................TTGGTGAGGG-CATCTCCAATG...................................................................................................................	21	1	12.00	0.00	1.00	0.00	11.00
..............................................................................................................................ATTGGATTAGTTCTCATTAAT......................................................................	21	1	10.00	0.00	0.00	0.00	10.00
...............................................................................................................................TTGGATTAGTTCTCATTAAT......................................................................	20	1	8.00	0.00	1.00	0.00	7.00
...............................................................................ATTGGTGAGGG-CATCTCCAATG...................................................................................................................	22	1	5.00	0.00	0.00	0.00	5.00
..............................................................................................................................ATTGGATTAGTTCTCATTAATG.....................................................................	22	1	3.00	0.00	0.00	0.00	3.00
...............................................................................................................................TTGGCTTAGTTCTCATTAATGC....................................................................	22	1	2.00	0.00	0.00	0.00	2.00
...............................................................................ATTGGTGAGGG-CATCTCCAAT....................................................................................................................	21	1	2.00	0.00	0.00	0.00	2.00
................................................................................TTTGTGAGGG-CATCTCCAATGG-.................................................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
................................................................................TTGGTGATGG-CATCTCCAATGG-.................................................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
................................................................................TTGGTGAGTG-CATCTCCAATGG-.................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGTTCTCATTAATGCT...................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGGTTAGTTCTCATTAATGC....................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGTTCTCATTAATGCA...................................................................	23	1	1.00	0.00	0.00	0.00	1.00
................................................................................TTAGTGAGGG-CATCTCCAATGG-.................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................ATTGGATTATTTCTCATTAATG.....................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTATTTCTCATTAATGC....................................................................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TTGGTGAGGG-CATCTxCAATGG-.................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................TTGGTGCGGG-CATCTACAATGG-.................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................................................................TGAGGG-CATCTCCAAGGC-.................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
................................................................................TTGGTGATGG-CATCTCCAATG...................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................TTGGCGAGGG-CATCTCCAATG...................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................TTGGTGAGGG-CATCTCCAATGG-A-...............................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
..................................................................................GATGTGGG-CATCTCCAATGG-.................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................TTGGTGAGGG-CAGCTCCAATG...................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGTTCTCACTAATG.....................................................................	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................TTGGTGAGGC-CATCTCCAATGG-.................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TTGGTGAGGG-AATCTCCAATGG-.................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGTTCTCATTAATC.....................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTAGATTAGTTCTCATTAATGC....................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTTGATTAGTTCTCATTAATGC....................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droEug1

A----------------------------------------------------------------TGCAGCGCCTTGACATTGGCGAGGC-CAACTCCAATGT-C-GAATC---------GAAATCATTGGATTAGTTCTCATCAATGACTGAGCCCTGTAAT--GACC--AACGTA---------------CCATA----------------TCTT

Size

Hit Count

Total Norm

droBia1

ATCAA------------------------TGCTG-----------------GTG-GGGATGAGGAAGCACCGCCTCGGCATTGGTGAGGG-CACCTCCAATGG-C-GAGCC---------GGCATCATTGGATTAGTTCTCATTAATGGCGGAGTGCTGCACC--GACC--AACGCC---------------ACATA----------------CGGT

Size

Hit Count

Total Norm

droTak1

TCTGG------------------------AGAGG-----------------AGGAGAAA-GAGGAAGCATCGCCTCGACATTATTGAGGG-CACCTCCAATGG-C-GAGCC---------GACATCATTGGATTAGTTCTCATTAATGGCGGAGCGCTGCACT--GACC--AACTGTTCGTC----------CAT------------------AAGG

Size

Hit Count

Total Norm

droEle1

ATCAA------------------------TAC-------------------CTG------CACAAAGCATCGCCTCGCCATTGGTGAGGG-CACCTCCAATGG-C-GAGCC---------GGCTGCATTGGATTAGTTTTCATCAATGGCGGAGCCCTGCACT--GACC--AGCAGA------------------------------------CCGA

Size

Hit Count

Total Norm

droRho1

AACCG------------------------C---------------------CTG------CAAACAGCATCACCTCGCCATTGGTGAGGG-CATCTCCAATGA-C-GAGTC---------GGCAGCATTGGATTAGTTCTCATTAATGGCGGAGCGGTGCACT--GACC--AGCAGACTGACCTCTCCGCTAGCA------------------CCAG

Size

Hit Count

Total Norm

droFic1

ATCAC------------------------CGC-----------------------------AGACAGCGGCGCCCCGCCATTAATAAGGA-CCTCTCCAATGG-C-AGACC-------GTCGAATCATTGGATTAGTTCTCATTAATGGTGGAGTGCCGCACC--GACC--ACCACATTTTTTTC-------TAA------------------GTGC

Size

Hit Count

Total Norm

droKik1

GC-------------------------------------------------------------GAGGCATTGCCTCGCCATTGGTGAGAG-CATCTCCAATGA-C-GGCAC-------TTGATTGCATTGGATTAGTTCTCATTGATGGCGGAGCATTGCACC--TACT--CCAGCAACGGC----------TAT------------------CCAG

Size

Hit Count

Total Norm

droAna3

GCTAC------------------------CGATG-----------------CTC------CCCGAAGGAGCGCCTCGACATTGGTGAGTT-CATCTCCAATGG-T-CAGTA---------GCCCGCATTGGATTAGTTCTCATTGATGGCGAAGCGAGT--CC--TACC--CCCACA---------------CCA------------------GCGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............................................................................................................................TTGGATTAGTTCTCATTGATGG....................................................................	22	1	771.00	281.00	428.00	61.00	1.00
...............................................................................................................................TTGGATTAGTTCTCATTGATG.....................................................................	21	1	289.00	168.00	104.00	17.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATGT....................................................................	22	1	62.00	47.00	14.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATGGT...................................................................	23	1	33.00	14.00	18.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGAT......................................................................	20	1	18.00	13.00	1.00	4.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATTGATG.....................................................................	22	1	11.00	10.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATGGC...................................................................	23	1	10.00	6.00	4.00	0.00	0.00
...............................................................................................................................TTTGATTAGTTCTCATTGATGG....................................................................	22	1	9.00	0.00	9.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATGGA...................................................................	23	1	8.00	3.00	5.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATGGTT..................................................................	24	1	5.00	3.00	2.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATT.....................................................................	21	1	4.00	2.00	2.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTAATTGATGG....................................................................	22	1	4.00	1.00	3.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATTG....................................................................	22	1	4.00	1.00	3.00	0.00	0.00
...............................................................................................................................TTGGATTAGCTCTCATTGATGG....................................................................	22	1	3.00	0.00	1.00	2.00	0.00
...............................................................................................................................TGGGATTAGTTCTCATTGATGG....................................................................	22	1	3.00	3.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCAGTGATGG....................................................................	22	1	3.00	3.00	0.00	0.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATTGATGT....................................................................	23	1	3.00	3.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATA.....................................................................	21	1	3.00	1.00	2.00	0.00	0.00
...............................................................................................................................TTGGATTAGTCCTCATTGATGG....................................................................	22	1	3.00	3.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTATCATTGATGG....................................................................	22	1	3.00	2.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATAG....................................................................	22	1	3.00	1.00	2.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTTATTGATGG....................................................................	22	1	2.00	0.00	1.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATCG....................................................................	22	1	2.00	1.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGGTGG....................................................................	22	1	2.00	0.00	2.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTGTCATTGATGG....................................................................	22	1	2.00	2.00	0.00	0.00	0.00
...............................................................................................................................TTTGATTAGTTCTCATTGATG.....................................................................	21	1	2.00	0.00	2.00	0.00	0.00
...............................................................................................................................TTGGTTTAGTTCTCATTGATGG....................................................................	22	1	2.00	0.00	0.00	2.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATC.....................................................................	21	1	2.00	1.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTCATGG....................................................................	22	1	2.00	1.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTAATGC....................................................................	22	1	2.00	0.00	2.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCACATTGATGG....................................................................	22	1	2.00	1.00	1.00	0.00	0.00
...............................................................................................................................TTGGGTTAGTTCTCATTGATGG....................................................................	22	1	2.00	0.00	1.00	1.00	0.00
...............................................................................................................................TTGGATTAGCTCTCATTGATG.....................................................................	21	1	2.00	0.00	2.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTAATGG....................................................................	22	1	2.00	1.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTTTCATTGATGG....................................................................	22	1	2.00	0.00	2.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTATCATTGATGT....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGACTAGTTCTCATTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGCTTAGTTCTCATTGATGC....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGGTTAGTTCTCATTGATGC....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATTGA.......................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTGGTTCTCATTGATG.....................................................................	21	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TCGGATTAGTTCTCATTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTGTCATTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATAT....................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGGATGAGTTCTCATTGATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTGCTCATTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCACTGATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGCTGG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCACATTGAT......................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTTATGGT...................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGAxTAGTTCTCATTGATGG....................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGAGGG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCCTTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGTTTAGTTCTCATTGATG.....................................................................	21	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCCCATTGATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGA.......................................................................	19	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................GCCCGCACTGGATTATTT...............................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................CTGGATTAGTTCTCATTGATGG....................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TCGGATTAGTTCTCATTGATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTATCATTGATG.....................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTACTTCTCATTGATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................TTGATTAGTTCTCATTGATG.....................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTxxTTCTCATTGATG.....................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCACTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAATTCTCATTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTTGATTAGTTCTCATTGATGT....................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTTATGG....................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTTGATTAGTTCTCATTGATTG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTACTCATTGATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATTGATGA....................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGTATTAGTTCTCATTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATGGATGG....................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGCATTAGTTCTCATTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGTTGG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGCTTAGTTCTCATTGATGG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATTGAT......................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTCCTCATTGATG.....................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGTTG.....................................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................ATCGGATTAGTTCTCATTGATG.....................................................................	22	1	1.00	1.00	0.00	0.00	0.00

droBip1

GCTAG------------------------CGATG-----------------CTC------CGTGAAGGAGCGCCTCGCCATTGGTGGGGG-CGTCTCCAATGG-C-CAGAA---------GCCCGCATTGGATTAGTTCTCATTAATGGCGAAGCGAGTCCTT--CCTC-----------------------CAC------------------ACCA

Size

Hit Count

Total Norm

dp4

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

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

CTCTC----CCCTTCC--TTCTTACACAGGATTA-----------------TGT-AGGATT--ATGGCAACACCTCGATATTGGTGAGTTCCAGCTCCAATGTTATTGGAGCCCAACATTGAACACATTGGATTAGTTCTCATCGATGGCGAAGTGTTT--GT--GAGC--AATATC---------------GTATATTGTGCGTGCAGTGTATTGT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...............................................................................................................................TTGGATTAGTTCTCATCGATGG....................................................................	22	1	427.00	241.00	27.00	83.00	76.00
...............................................................................................................................TTGGATTAGTTCTCATCGATG.....................................................................	21	1	155.00	116.00	2.00	5.00	32.00
...............................................................................................................................TTGGATTAGTTCTCATCGAT......................................................................	20	1	32.00	27.00	0.00	1.00	4.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGGT...................................................................	23	1	13.00	3.00	2.00	5.00	3.00
...............................................................................................................................TTGGATTAGTTCTCATCGA.......................................................................	19	1	8.00	1.00	0.00	0.00	7.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGT....................................................................	22	1	7.00	5.00	0.00	1.00	1.00
...............................................................................................................................TTGGATTAGTTCTCATTGATGG....................................................................	22	1	4.00	4.00	0.00	0.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATCGATG.....................................................................	22	1	4.00	3.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGTTCTCATCGG.......................................................................	19	1	3.00	0.00	0.00	0.00	3.00
...............................................................................................................................CTGGATTAGTTCTCATCGATGG....................................................................	22	1	2.00	0.00	1.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCCCATCGATGG....................................................................	22	1	2.00	0.00	0.00	2.00	0.00
...............................................................................................................................TTGGATTAGTTCTTATCGATGG....................................................................	22	1	2.00	1.00	0.00	1.00	0.00
......................................................................................................TTATTGGAGCCCAACATTGAACACA..........................................................................................	25	1	2.00	0.00	0.00	0.00	2.00
...............................................................................................................................ATGGATTAGTTCTCATCGATGG....................................................................	22	1	2.00	0.00	0.00	2.00	0.00
...............................................................................................................................TTGGATTAATTCTCATCGATGG....................................................................	22	1	2.00	1.00	1.00	0.00	0.00
..................................................................................................AAAGTTATTGGAGCCAAA.....................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
...............................................................................................................................TTGGGTTAGTTCTCATCGATGG....................................................................	22	1	2.00	1.00	0.00	1.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATCGAT......................................................................	21	1	2.00	2.00	0.00	0.00	0.00
...............................................................................................................................TTGGCTTAGTTCTCATCGATGG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTTGATTAGTTCTCATCGATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................AATTCTCATCGATGGCGT.................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGC....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATAG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTxGTTCTCATCGATG.....................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCCATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGGTGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGAGG.....................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTAGATTAGTTCTCATCGATGG....................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..................................................................................GGTxAATTCCAGCTCCAAT....................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTATCATCGATGG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGACGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCGCATCGATGG....................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGCATTAGTTCTCATCGATGG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTxATCGATGG....................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................GTTTTCATCGATGCCGAAG...............................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGCTCTCATCGATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................................................................................................TGT	19	2	0.50	0.50	0.00	0.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATCGATGG....................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTTGTTCTCATCGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTxxTTCTCATCGATGG....................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGGA...................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGACTAGTTCTCATCGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGG....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCAATGG....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGA....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................ATTGGATTAGTTCTCATCGATGT....................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCGTCGATGG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCACATCGATGG....................................................................	22	1	1.00	0.00	0.00	1.00	0.00

droVir3

ATCGTTATCGTTATCGTTATCGTTATCAGAATTAATTATCGTTGAAGTGCGTTC------TTTGGTGCAGCCCCTCGCGATTGATGATAG-CATCTCCAATGA-G-CA------------TATCACATTGGATTAGTTCTCATCGATGCCGATGCGCTGTACC--AGCAACAACAAC---------------AGG------AATAGCAACGGAAACA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...............................................................................................................................TTGGATTAGTTCTCATCGATGCC...................................................................	23	1	144.00	4.00	0.00	0.00	138.00	2.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGC....................................................................	22	1	104.00	56.00	0.00	1.00	44.00	3.00
...............................................................................................................................TTGGATTAGTTCTCATCGATG.....................................................................	21	1	97.00	77.00	0.00	0.00	20.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGCCG..................................................................	23	1	27.00	24.00	1.00	0.00	2.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGCCC..................................................................	24	1	19.00	1.00	0.00	0.00	18.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATC.....................................................................	21	1	13.00	1.00	0.00	0.00	12.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGAT......................................................................	20	1	12.00	11.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGCCT..................................................................	24	1	9.00	0.00	0.00	0.00	9.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGA.......................................................................	19	1	8.00	1.00	0.00	0.00	7.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGCT...................................................................	23	1	5.00	1.00	0.00	0.00	4.00	0.00
.............................................................................CGATTGATGATAG-CATCTC........................................................................................................................	19	1	4.00	0.00	0.00	0.00	4.00	0.00
.............................................................................CGATTGATGATAG-CATCTCCAAT....................................................................................................................	23	1	3.00	1.00	0.00	1.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGCA...................................................................	23	1	2.00	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTC...................................................................	23	1	2.00	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTCC..................................................................	24	1	2.00	0.00	0.00	0.00	2.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGAC...................................................................	23	1	2.00	0.00	0.00	0.00	2.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGT....................................................................	22	1	2.00	2.00	0.00	0.00	0.00	0.00
..AGCTATCGTTATCGTTATC....................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
..................................................................................................................................TATTAGTTCTCATCGATGCCG..................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGG....................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGCTCTCATCGATGC....................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGCCG..................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................CGATTGATGATAG-CATCTCCA......................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCGTCGATGC....................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGCTCTCATCGATGCC...................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCACCGATGC....................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTATTTCTCATCGATC.....................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
ATTGTTATCGTTATCGTTATC....................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50	0.00
...............................................................................................................................TTGGATTAGTTCTCATAGATC.....................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGAC......................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
........AGCTATCGTTATCGTTATC..............................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
...GCTATCGTTATCGTTATCGTTAT...............................................................................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGCCC..................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................................................................................CTTGGATTAGTTCTCATCGATGC....................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGC....................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGATCTCATCGATGC....................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCTATGCCC..................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGGTCTCATCGATGCC...................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATTC....................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................CGATTGATGATAG-CATCTCCAC.....................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................................................................................ATTGGATTAGxTCTCATCC........................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGCTT..................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
......ATTGTTATCGTTATCGTTATC..............................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50	0.00
..AGCTATCGTTATCGTTATCGTTA................................................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................................................................TGTATTAGTTCTCATCGATGCCG..................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...................................................................................................................................ATTAGTTCTCATCGATGCCG..................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATAGATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCxATGCC...................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCCATGC....................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCCCATCGATGCC...................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................CGATTGATGATAG-CATCTCCAA.....................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCCATGCT...................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGCCGTC................................................................	25	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGATCTCATCGAT......................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTATTTCTCATCGATG.....................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGCC...................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCCATG.....................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

TATCG-----TTATCGCTAG---------CGACG-----------------CTT------C-GGGTGCAGCCCCTCGCGATTGATGAAAG-CATCTCCAATGA-G-TA------------TTTCGCATTGGATTAGTTCTCATCGATGTCGATGCGCTGTATC--AGCAACAACAAC---------------AAC------------------ATGA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
................................................................................................................................TGGATTAGTTCTCATCGATGTCG..................................................................	23	1	298.00	297.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGT....................................................................	22	1	185.00	180.00	2.00	2.00	1.00
...............................................................................ATTGATGAAAG-CATCTCCAATG...................................................................................................................	22	1	92.00	91.00	0.00	1.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATG.....................................................................	21	1	59.00	59.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTC...................................................................	23	1	39.00	38.00	1.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGTC...................................................................	22	1	14.00	14.00	0.00	0.00	0.00
...............................................................................ATTGATGAAAG-CATCTCCAATGT-.................................................................................................................	23	1	10.00	9.00	1.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTT...................................................................	23	1	10.00	10.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGT....................................................................	21	1	10.00	9.00	0.00	1.00	0.00
.................................................................................................................................GGATTAGTTCTCATCGATGTCGTC................................................................	24	1	9.00	9.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTCT..................................................................	24	1	7.00	7.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGAT......................................................................	20	1	6.00	6.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTTC..................................................................	24	1	5.00	5.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGTCGTC................................................................	25	1	4.00	4.00	0.00	0.00	0.00
.............................................................................CGATTGATGAAAG-CATCTCCAAT....................................................................................................................	23	1	3.00	3.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATTGATGG....................................................................	22	1	3.00	0.00	0.00	3.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTCG..................................................................	24	1	2.00	2.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATG.....................................................................	20	1	2.00	2.00	0.00	0.00	0.00
...............................................................................ATTGATGAAAG-CATCTCCAATGA-.................................................................................................................	23	1	2.00	2.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGTCGT.................................................................	24	1	2.00	2.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGC....................................................................	22	1	2.00	2.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTTT..................................................................	24	1	2.00	2.00	0.00	0.00	0.00
................................................................................................................................TGAATTAGTTCTCATCGATGTCG..................................................................	23	1	2.00	2.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGTCGC.................................................................	24	1	2.00	2.00	0.00	0.00	0.00
................................................................................................................................TGGATTATTTCTCATCGATGTCG..................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGGTGT....................................................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................TGGATTAGTTCTCATCAATGTCG..................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTA...................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTCTC.................................................................	25	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCTATGTCG..................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ATTGATGAAAG-CATCTCCACTG...................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................ATTGATGxAAG-CATCTCCAATGT-.................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ATTGATGAAAG-CATCTCCAATGT-C-...............................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................TGGCTTAGTTCTCATCGATGTCG..................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGCTCTCATCGATGT....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTTTCATCGATGT....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCxTCGATGTCG..................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................................C--AGCAACAACAAC---------------ATC------------------ATCA	22	4	0.25	0.00	0.00	0.00	0.25
...............................................................................................................................TTGGATTAGTCCTCATCGATGT....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ATTTATGAAAG-CATCTCCAATG...................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTAATCGATGTC...................................................................	23	1	1.00	1.00	0.00	0.00	0.00
................................................................................TTGATGAAAG-CATCTCCAATG...................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................TGGATTxxTTCTCATCGATGTCG..................................................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTCCTCATCGATGTCG..................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................................................GGATTAGTTCTCATCGATGTCG..................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTxGTTCTCATCGATGT....................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ATTGATGAGAG-CATCTCCAATG...................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ATTGATGxAAG-CATCTCCAATG...................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATAGATGT....................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ATTGATGAAAG-CATCTCCAATT...................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................CGATTGATGAACG-CATCTCCAAT....................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................ATTGATGAAAG-CAxCTCCAATG...................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TTGGATTAGTTCTCATCGATGTCC..................................................................	24	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................TGGATTAGTTCTCATCGATGTCT..................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.............................................................................CGATTGATGAAAG-CATCTCC.......................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...................G---------GGACG-----------------CxT------C-GGGTGCA....................................................................................................................................................	16	1	1.00	0.00	1.00	0.00	0.00
...............................................................................ATTGATGAAAG-CACCTCCAATG...................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:28:14 EDT

dme-mir-976

chrX:19452928-19453024 +

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