dme-mir-977- Best orthologs

dme-mir-977	chrX:19453055-19453153 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 19453120-19453140
   star strand at position 19453079-19453100
   mutations
   read mismatches

Notes: droMoj has A->G SNP

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:19453040-19453168 +		1	GGAATCCCA----------------ACACAACGAATCAA------------------------------------------------------------------------------------------------------------------CAAACAAGGTATGCTTTAGATAACTCGAATATC-AC--ATCTTCA---------GTGTTCGAAATCTGATGAGATA-TTCACGTTGTCTAAATCATGTTTTGTA-----CGAAA----------------------CTACAACTAA
droSim1	chrX:15018618-15018753 +	LASTZ	1	GGAATACCA----------------A----------------------------------------------------CTCCGGA-------------GTGCCG------------------------------A---------AAATGC---ATCCCAAGGTATGGTTTAGATAACTCGAATATC-AC--ATTTTCA---------GTGTTCGATATCTGATGAGATA-TTCACGTTGTCTAAACCATGGTTTGTT-----TTTGA----------------------AAACTACTCA
droSec1	super_8:1735350-1735483 +	LASTZ	1	GGAATACCA----------------A----------------------------------------------------CTCCGGA-------------GTGCCG------------------------------A---------AAATTC---ATCCCAAGGTATGGTTTAGATAACTCGAATATC-AC--ATCTTCA---------GTGTTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGGTTTGTT-----TGAAA------------------------ACTACTCA
droYak2	chrX:11885613-11885797 -	LASTZ	1	TCCTATT-------------------------------------CC--TATTCCGATTCC-GATTCGGAATCAACCAAGTGCGGA-------------CAGCTC------------------------------A---------GAGTTC---ACCCCAAGGTATGGCCTAGATAACACGGGTATC-AC--ATCTTTAT--------GCATTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGTTTTGTA-----AGGAA-ATGCACTCTGCTCATCAGT-TAAACTACTAA
droEre2	scaffold_4690:9689018-9689184 +	LASTZ	1	GGGATCGGG----------------A------------------------------TCCCGGATTCGGAGTCAACAAACT------------------------------------CTTGTCAAACAAACGAGCA---------GAATTC---AACCCAAGGTATGGCCTAGATAACTCGGGTATC-AC--ATCTTTAT--------GCATTCGATATCTGGTGAGATAATTCACGTTGTCTAAACCATGTTTTGTA-----AGAAA----------------------TAACGCCTTA
droEug1	scf7180000409230:879517-879656 -	LASTZ	4	TATATCCAT----------------A-------------------------------------------TCCA-T---GTCCAGTGGAAATCTACAGG-----------------------------------------------CCACC---AACCCAAGGTCTGGTCTCGATCACGCGGGTATCTGC--ATTT-GC---------ATTTTGTATATCTGGTGAGATA-TTCACGTAGTCGAATTCAAGCCTTGGA-----CCGAA----------------------------CTTC
droBia1	scf7180000302069:1150852-1151014 -	LASTZ	4	GGGATCCCCAACGTCGCAGTGGGT--------------------CCTATGTTCCAGTACT-AGTCCAGACCTA-C--------------------------------------------------------------------CCAATTC---ACACCAAGGCCTGGCCTCGATCACGCGGGTATC-GC--ATCT------------GCAACTGATATCTGATGAGATA-TTCACGTCTTCGAAACCAAGCCTTGGC-----CACGA----------------------ATTTGGCTTA
droTak1	scf7180000415169:844680-844813 -	LASTZ	4	TGAGATCTA----------------A---------------------------------------------------------------------TGGGTATCGTATTGTCTAATTATT----------------GAATCTTGCTAGTTA---ACCCCAAGGTCTGGCCTCGATCACGCGGATATC-GC--ATCT------------GCAATTGATATCTGGTGAGATA-TTCACGTCGTCGAAACCATGCCTT---------------------------------------------
droEle1	scf7180000490751:1118890-1119023 +	LASTZ	4	CAGATCGTG----------------A-------------------------------------------TCCA-T--------------------------------------------------------------------CCATTCC---CCTCCAAGGTATGGACTCGATCACGCGAGTATC-GC--ACCTTCCT--------GCAATCGATAATCGGTGAGATA-TTCACGTCGTCGAATCCATGTCTTGGGCAAATCATCA----------------------TTTCATTTAA
droRho1	scf7180000761121:189932-190086 -	LASTZ	4	ATCCCA--A----------------A------------------------------TCTTAGATCCCGACCCA-TCCACTG-----------------------------------CCA----------------GCATCAT-CCATTCC---ACACCAAGGTCTGGCCTCGATCACGCGAGTATC-GC--ACCTTCCT--------GCAATCGATATTCGGTGAGATA-TTCACGTCGTCGAAGCCGTGCCTTGGT-----CAGAG-----------------------TTTGGCTAA
droFic1	scf7180000454073:1734028-1734176 +	LASTZ	4	CTAATTCCC----------------G---------------------------------------------------------------------------------------------------------------------CAAGTCC---AATCCAACATCCGATTTCGACCACGTGGGTATC-ACTCACCTTTCC------GCTCATTTGATATCGGGTGAGATA-TTCACGTCGTTGAATCCGTGTCTTGGA-----AAGGA-GTTTATGTTATATAATAATATACTTTACTTA
droKik1	scf7180000302517:1183794-1183964 +	LASTZ	4	GTAACCAGC--------------------------------------------------TAAACAGCTACCCA-TCTACTCAG------CTCCTCTGGGAGTCG------------------------------AGGCTCT---AGATGCAAACCTCCATGGCACGGTCTGGATTACGAGAATATC-GC--ACCTTTGA------C-GCCTTTGATATCTGGTGAGATA-TTCACGTGGTCGAGTCCGTGTCTAGGA-----CCAAG----------------------TTACAGCTGA
droAna3	scaffold_13417:2467442-2467560 -	LASTZ	1	GGCACACGC----------------G--------------------------------------------------------------------------------------------------------------------------TA---CCGCCGAGGTTCGGCCTCGATCACGAGAACGTC-GC--ATCTTAGT--------TACATTTCCATATGATGAGATA-TTCACGTCGTCGAAACCGTGTCTCGGC-----TTGGC----------------------CACCAATCGC
droBip1	scf7180000395874:39803-39929 -	LASTZ	4	GCTACCCAA----------------A-------------------------------------------------------------------------------------------------------------------------CGCATACCGCTGAGGTCCGGCCTCGATCACGAGAACGTC-GC--ATCTTAGT--------TACGTTTTCATATGATGAGATA-TTCACGTCGTCGAAACCGTGCCTCGGC-GAATCGGAA----------------------ACACACCTAG
dp4	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7956913-7957043 +	LASTZ	1	GATGTGACA----------------CCGTGGACGATCAA-----------------------------------C-----------------------------------------------------------A---------AAATTC---------ATATACAATTTCAATAACGTAGATATC-GC--ATCGTTTTTTTTTACCATATTTGATAAGAGATGAGATA-TTCACGTTGTTGAAGTTGTGAAGGAAT-----TAAA-------------------------------AA
droVir3	scaffold_13042:906546-906707 -	LASTZ	1	GGAACCGGA----------------ACAGAAACAGGAAAAAGAAATTGTGTTCC--------------------------------------------------------------------------------------------CC-----CTGGCCCAGCCCAGTTGCGATTGCGCGGACATC-TC--ATCGTATA------A-ACATTCGATAACCAACGAGATA-TTCACGTTATCGAGACTGAGACGTCGG-----CAAAGAC-------TGCAAGATTGT-GCGACAAGTGA
droMoj3	scaffold_6328:2900856-2900969 -	LASTZ	1	GTTAAACGAAATGAACCAGTTCGTTG------------------------------------------------------------------------------------------------------------------------TT-----CTGGCCCAGCCCGGTTCCGATTGCGCGGACATC-TC--ATCGTCTG------A-CCATTCGATAACCGATGAGATA-TTCACGTTATCGAGACTGCG-------------------------------------------------
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	GGAATCCCA----------------ACACAACGAATCAA------------------------------------------------------------------------------------------------------------------CAAACAAGGTATGCTTTAGATAACTCGAATATC-AC--ATCTTCA---------GTGTTCGAAATCTGATGAGATA-TTCACGTTGTCTAAATCATGTTTTGTA-----CGAAA----------------------CTACAACTAA
droSim1	GGAATACCA----------------A----------------------------------------------------CTCCGGA-------------GTGCCG------------------------------A---------AAATGC---ATCCCAAGGTATGGTTTAGATAACTCGAATATC-AC--ATTTTCA---------GTGTTCGATATCTGATGAGATA-TTCACGTTGTCTAAACCATGGTTTGTT-----TTTGA----------------------AAACTACTCA
droSec1	GGAATACCA----------------A----------------------------------------------------CTCCGGA-------------GTGCCG------------------------------A---------AAATTC---ATCCCAAGGTATGGTTTAGATAACTCGAATATC-AC--ATCTTCA---------GTGTTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGGTTTGTT-----TGAAA------------------------ACTACTCA
droYak2	TCCTATT-------------------------------------CC--TATTCCGATTCC-GATTCGGAATCAACCAAGTGCGGA-------------CAGCTC------------------------------A---------GAGTTC---ACCCCAAGGTATGGCCTAGATAACACGGGTATC-AC--ATCTTTAT--------GCATTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGTTTTGTA-----AGGAA-ATGCACTCTGCTCATCAGT-TAAACTACTAA
droEre2	GGGATCGGG----------------A------------------------------TCCCGGATTCGGAGTCAACAAACT------------------------------------CTTGTCAAACAAACGAGCA---------GAATTC---AACCCAAGGTATGGCCTAGATAACTCGGGTATC-AC--ATCTTTAT--------GCATTCGATATCTGGTGAGATAATTCACGTTGTCTAAACCATGTTTTGTA-----AGAAA----------------------TAACGCCTTA
droEug1	TATATCCAT----------------A-------------------------------------------TCCA-T---GTCCAGTGGAAATCTACAGG-----------------------------------------------CCACC---AACCCAAGGTCTGGTCTCGATCACGCGGGTATCTGC--ATTT-GC---------ATTTTGTATATCTGGTGAGATA-TTCACGTAGTCGAATTCAAGCCTTGGA-----CCGAA----------------------------CTTC
droBia1	GGGATCCCCAACGTCGCAGTGGGT--------------------CCTATGTTCCAGTACT-AGTCCAGACCTA-C--------------------------------------------------------------------CCAATTC---ACACCAAGGCCTGGCCTCGATCACGCGGGTATC-GC--ATCT------------GCAACTGATATCTGATGAGATA-TTCACGTCTTCGAAACCAAGCCTTGGC-----CACGA----------------------ATTTGGCTTA
droTak1	TGAGATCTA----------------A---------------------------------------------------------------------TGGGTATCGTATTGTCTAATTATT----------------GAATCTTGCTAGTTA---ACCCCAAGGTCTGGCCTCGATCACGCGGATATC-GC--ATCT------------GCAATTGATATCTGGTGAGATA-TTCACGTCGTCGAAACCATGCCTT---------------------------------------------
droEle1	CAGATCGTG----------------A-------------------------------------------TCCA-T--------------------------------------------------------------------CCATTCC---CCTCCAAGGTATGGACTCGATCACGCGAGTATC-GC--ACCTTCCT--------GCAATCGATAATCGGTGAGATA-TTCACGTCGTCGAATCCATGTCTTGGGCAAATCATCA----------------------TTTCATTTAA
droRho1	ATCCCA--A----------------A------------------------------TCTTAGATCCCGACCCA-TCCACTG-----------------------------------CCA----------------GCATCAT-CCATTCC---ACACCAAGGTCTGGCCTCGATCACGCGAGTATC-GC--ACCTTCCT--------GCAATCGATATTCGGTGAGATA-TTCACGTCGTCGAAGCCGTGCCTTGGT-----CAGAG-----------------------TTTGGCTAA
droFic1	CTAATTCCC----------------G---------------------------------------------------------------------------------------------------------------------CAAGTCC---AATCCAACATCCGATTTCGACCACGTGGGTATC-ACTCACCTTTCC------GCTCATTTGATATCGGGTGAGATA-TTCACGTCGTTGAATCCGTGTCTTGGA-----AAGGA-GTTTATGTTATATAATAATATACTTTACTTA
droKik1	GTAACCAGC--------------------------------------------------TAAACAGCTACCCA-TCTACTCAG------CTCCTCTGGGAGTCG------------------------------AGGCTCT---AGATGCAAACCTCCATGGCACGGTCTGGATTACGAGAATATC-GC--ACCTTTGA------C-GCCTTTGATATCTGGTGAGATA-TTCACGTGGTCGAGTCCGTGTCTAGGA-----CCAAG----------------------TTACAGCTGA
droAna3	GGCACACGC----------------G--------------------------------------------------------------------------------------------------------------------------TA---CCGCCGAGGTTCGGCCTCGATCACGAGAACGTC-GC--ATCTTAGT--------TACATTTCCATATGATGAGATA-TTCACGTCGTCGAAACCGTGTCTCGGC-----TTGGC----------------------CACCAATCGC
droBip1	GCTACCCAA----------------A-------------------------------------------------------------------------------------------------------------------------CGCATACCGCTGAGGTCCGGCCTCGATCACGAGAACGTC-GC--ATCTTAGT--------TACGTTTTCATATGATGAGATA-TTCACGTCGTCGAAACCGTGCCTCGGC-GAATCGGAA----------------------ACACACCTAG
droWil1	GATGTGACA----------------CCGTGGACGATCAA-----------------------------------C-----------------------------------------------------------A---------AAATTC---------ATATACAATTTCAATAACGTAGATATC-GC--ATCGTTTTTTTTTACCATATTTGATAAGAGATGAGATA-TTCACGTTGTTGAAGTTGTGAAGGAAT-----TAAA-------------------------------AA
droVir3	GGAACCGGA----------------ACAGAAACAGGAAAAAGAAATTGTGTTCC--------------------------------------------------------------------------------------------CC-----CTGGCCCAGCCCAGTTGCGATTGCGCGGACATC-TC--ATCGTATA------A-ACATTCGATAACCAACGAGATA-TTCACGTTATCGAGACTGAGACGTCGG-----CAAAGAC-------TGCAAGATTGT-GCGACAAGTGA
droMoj3	GTTAAACGAAATGAACCAGTTCGTTG------------------------------------------------------------------------------------------------------------------------TT-----CTGGCCCAGCCCGGTTCCGATTGCGCGGACATC-TC--ATCGTCTG------A-CCATTCGATAACCGATGAGATA-TTCACGTTATCGAGACTGCG-------------------------------------------------

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

GGAATACCA----------------A----------------------------------------------------CTCCGGA-------------GTGCCG------------------------------A---------AAATGC---ATCCCAAGGTATGGTTTAGATAACTCGAATATC-AC--ATTTTCA---------GTGTTCGATATCTGATGAGATA-TTCACGTTGTCTAAACCATGGTTTGTT-----TTTGA----------------------AAACTACTCA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.........................................................................................................................................................................TAGATAACTCGAATATC-AC--ATTTT.......................................................................................................	24	1	18.00	0.00	0.00	18.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTTGTCTA........................................................	21	1	18.00	0.00	1.00	17.00	0.00
.........................................................................................................................................................................TAGATAACTCGAATATC-AC--ATT.........................................................................................................	22	1	16.00	0.00	0.00	16.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTTGTCTAA.......................................................	22	1	13.00	0.00	0.00	13.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAAA......................................................	22	1	7.00	0.00	0.00	7.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTTGTCT.........................................................	20	1	7.00	0.00	0.00	7.00	0.00
.........................................................................................................................................................................TAGATAACTCGAATATC-AC--ATTTTC......................................................................................................	25	1	4.00	0.00	0.00	4.00	0.00
.........................................................................................................................................................................TAGATAACTCGAATATC-AC--ATTT........................................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTTGTCC.........................................................	20	1	2.00	0.00	0.00	2.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTTGTCTAAA......................................................	23	1	2.00	0.00	0.00	2.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAA.......................................................	21	1	2.00	0.00	0.00	2.00	0.00
.........................................................................................................................................................................TAGATAACCCGAATATC-AC--ATTTT.......................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAAG......................................................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTTGTCG.........................................................	20	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................................................................GTTCGACATCxGATGAGAT.......................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTTGCCTA........................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTA........................................................	20	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................................................................................CATGGTTTTTG-----TTTGA----------------------AA........	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

GGAATACCA----------------A----------------------------------------------------CTCCGGA-------------GTGCCG------------------------------A---------AAATTC---ATCCCAAGGTATGGTTTAGATAACTCGAATATC-AC--ATCTTCA---------GTGTTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGGTTTGTT-----TGAAA------------------------ACTACTCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAAA......................................................	22	1	104.00	96.00	6.00	2.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCT.........................................................	19	1	80.00	15.00	14.00	51.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTA........................................................	20	1	37.00	36.00	0.00	1.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAA.......................................................	21	1	32.00	30.00	0.00	2.00
..............................................................................................................................................................................................................................TGAGATA-TTCGCGTTGTCT.........................................................	19	1	8.00	0.00	0.00	8.00
.........................................................................................................................................................................TAGATAACTCGAATATC-AC--ATC.........................................................................................................	22	1	7.00	6.00	0.00	1.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAAAA.....................................................	23	1	4.00	3.00	0.00	1.00
.........................................................................................................................................................................TAGATAACTCGAATATC-AC--AT..........................................................................................................	21	1	3.00	2.00	1.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACTTTGTCT.........................................................	19	1	2.00	1.00	0.00	1.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAT.......................................................	21	1	2.00	2.00	0.00	0.00
.........................................................................................................................................................................TAGATAACTCGAATATC-AC--A...........................................................................................................	20	1	2.00	1.00	0.00	1.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCCAAA......................................................	22	1	1.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGGTA-TTCACGTTGTCTA........................................................	20	1	1.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCGA........................................................	20	1	1.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTTT.......................................................	21	1	1.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-ATCACGCTGTCT.........................................................	19	1	1.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................TGGGATA-TTCACGTTGTCTAAA......................................................	22	1	1.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCCA........................................................	20	1	1.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAAT......................................................	22	1	1.00	1.00	0.00	0.00
...............................................................................................................................................................................................................................GAGATA-TTCACGTTGTTGAA.......................................................	20	1	1.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGGGATA-TTCACGTTGTCT.........................................................	19	1	1.00	0.00	0.00	1.00

droYak2

TCCTATT-------------------------------------CC--TATTCCGATTCC-GATTCGGAATCAACCAAGTGCGGA-------------CAGCTC------------------------------A---------GAGTTC---ACCCCAAGGTATGGCCTAGATAACACGGGTATC-AC--ATCTTTAT--------GCATTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGTTTTGTA-----AGGAA-ATGCACTCTGCTCATCAGT-TAAACTACTAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAAA......................................................	22	2	23.00	0.00	0.00	22.00	0.50	0.50
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCT.........................................................	19	2	11.50	0.00	1.00	7.50	3.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTA........................................................	20	2	8.00	0.00	0.00	8.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAA.......................................................	21	2	8.00	0.00	0.00	7.50	0.50	0.00
.........................................................................................................................................................................TAGATAACACGGGTATC-AC--AT..........................................................................................................	21	2	1.50	0.00	0.00	1.50	0.00	0.00
........................................................................................................................................................................CTAGATAACACGGGTATC-AC--A...........................................................................................................	21	2	1.00	0.00	0.00	0.50	0.50	0.00
........................................................................................................................................................................CTAGATAACACGGGTATC-AC--AT..........................................................................................................	22	2	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................TAGATAACACGGGTATC-AC--A...........................................................................................................	20	2	1.00	0.00	0.50	0.50	0.00	0.00
.........................................................................................................................................................................TAGATAACACGGGTATC-AC--ATC.........................................................................................................	22	2	1.00	0.00	0.00	0.50	0.00	0.50
..............................................................................................................................................................................................................................ACAGATA-TTCACGTTGTCT.........................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACATTGTCTAAA......................................................	22	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................TGAxATA-TTCACGTTGTCTAAA......................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAC.......................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
...............................................................................................................................................................................................................................................CCTAAACCxTGTTTTGTA-----A....................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCTAAA......................................................	22	2	0.50	0.00	0.00	0.50	0.00	0.00
..................................................TTCTGATTCC-GAGTCGGA......................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAAAC.....................................................	23	2	0.50	0.00	0.00	0.00	0.00	0.50
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTCTCTA........................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCTAT.......................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCAGGTTGTCTA........................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGA........................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00

droEre2

GGGATCGGG----------------A------------------------------TCCCGGATTCGGAGTCAACAAACT------------------------------------CTTGTCAAACAAACGAGCA---------GAATTC---AACCCAAGGTATGGCCTAGATAACTCGGGTATC-AC--ATCTTTAT--------GCATTCGATATCTGGTGAGATAATTCACGTTGTCTAAACCATGTTTTGTA-----AGAAA----------------------TAACGCCTTA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................................................................................................................................................................TAGATAACTCGGGTATC-AC--AT..........................................................................................................	21	1	3.00	0.00	2.00	0.00	1.00
..............................................................................................................................................................................................................................TGAGATAATTCACGTTGTCT.........................................................	20	1	2.00	0.00	0.00	0.00	2.00
.........................................................................................................................................................................TAGATAACTCGGGTATC-AC--ATC.........................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................TGAGATAATTCACGTTGT...........................................................	18	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................................................................................TAGATAACTCGGGTATC-AC--A...........................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................AACCATGTTTTTTA-----AGAA.................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................TGAGATAATTCACGTTGTCTAAA......................................................	23	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................TGAGATAATTCACGTTGTCTA........................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................TTC---AACCCAAGGTATGGCC..................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................AGCA---------GxATTG---AACCCAAGGT........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................GAGCA---------GxATTG---AACCCAAG..........................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

TATATCCAT----------------A-------------------------------------------TCCA-T---GTCCAGTGGAAATCTACAGG-----------------------------------------------CCACC---AACCCAAGGTCTGGTCTCGATCACGCGGGTATCTGC--ATTT-GC---------ATTTTGTATATCTGGTGAGATA-TTCACGTAGTCGAATTCAAGCCTTGGA-----CCGAA----------------------------CTTC

Size

Hit Count

Total Norm

droBia1

GGGATCCCCAACGTCGCAGTGGGT--------------------CCTATGTTCCAGTACT-AGTCCAGACCTA-C--------------------------------------------------------------------CCAATTC---ACACCAAGGCCTGGCCTCGATCACGCGGGTATC-GC--ATCT------------GCAACTGATATCTGATGAGATA-TTCACGTCTTCGAAACCAAGCCTTGGC-----CACGA----------------------ATTTGGCTTA

Size

Hit Count

Total Norm

droTak1

TGAGATCTA----------------A---------------------------------------------------------------------TGGGTATCGTATTGTCTAATTATT----------------GAATCTTGCTAGTTA---ACCCCAAGGTCTGGCCTCGATCACGCGGATATC-GC--ATCT------------GCAATTGATATCTGGTGAGATA-TTCACGTCGTCGAAACCATGCCTT---------------------------------------------

Size

Hit Count

Total Norm

droEle1

CAGATCGTG----------------A-------------------------------------------TCCA-T--------------------------------------------------------------------CCATTCC---CCTCCAAGGTATGGACTCGATCACGCGAGTATC-GC--ACCTTCCT--------GCAATCGATAATCGGTGAGATA-TTCACGTCGTCGAATCCATGTCTTGGGCAAATCATCA----------------------TTTCATTTAA

Size

Hit Count

Total Norm

droRho1

ATCCCA--A----------------A------------------------------TCTTAGATCCCGACCCA-TCCACTG-----------------------------------CCA----------------GCATCAT-CCATTCC---ACACCAAGGTCTGGCCTCGATCACGCGAGTATC-GC--ACCTTCCT--------GCAATCGATATTCGGTGAGATA-TTCACGTCGTCGAAGCCGTGCCTTGGT-----CAGAG-----------------------TTTGGCTAA

Size

Hit Count

Total Norm

droFic1

CTAATTCCC----------------G---------------------------------------------------------------------------------------------------------------------CAAGTCC---AATCCAACATCCGATTTCGACCACGTGGGTATC-ACTCACCTTTCC------GCTCATTTGATATCGGGTGAGATA-TTCACGTCGTTGAATCCGTGTCTTGGA-----AAGGA-GTTTATGTTATATAATAATATACTTTACTTA

Size

Hit Count

Total Norm

droKik1

GTAACCAGC--------------------------------------------------TAAACAGCTACCCA-TCTACTCAG------CTCCTCTGGGAGTCG------------------------------AGGCTCT---AGATGCAAACCTCCATGGCACGGTCTGGATTACGAGAATATC-GC--ACCTTTGA------C-GCCTTTGATATCTGGTGAGATA-TTCACGTGGTCGAGTCCGTGTCTAGGA-----CCAAG----------------------TTACAGCTGA

Size

Hit Count

Total Norm

droAna3

GGCACACGC----------------G--------------------------------------------------------------------------------------------------------------------------TA---CCGCCGAGGTTCGGCCTCGATCACGAGAACGTC-GC--ATCTTAGT--------TACATTTCCATATGATGAGATA-TTCACGTCGTCGAAACCGTGTCTCGGC-----TTGGC----------------------CACCAATCGC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTCGAA.......................................................	21	1	197.00	173.00	8.00	16.00	0.00
.........................................................................................................................................................................TCGATCACGAGAACGTC-GC--ATCT........................................................................................................	23	1	162.00	144.00	9.00	9.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTCGAAA......................................................	22	1	107.00	102.00	1.00	4.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTCGA........................................................	20	1	103.00	91.00	3.00	9.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTCGTCGAA.......................................................	22	1	47.00	44.00	0.00	3.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTCGTCGA........................................................	21	1	30.00	29.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTCGAAT......................................................	22	1	29.00	25.00	3.00	1.00	0.00
.........................................................................................................................................................................TCGATCACGAGAACGTC-GC--AT..........................................................................................................	21	1	26.00	21.00	0.00	5.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTCGTCGAAA......................................................	23	1	20.00	16.00	2.00	2.00	0.00
.........................................................................................................................................................................TCGATCACGAGAACGTC-GC--ATC.........................................................................................................	22	1	14.00	14.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTCGTCG.........................................................	20	1	10.00	10.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTCG.........................................................	19	1	10.00	8.00	0.00	2.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTCGTCGAAT......................................................	23	1	10.00	7.00	1.00	2.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTCGAATT.....................................................	23	1	8.00	8.00	0.00	0.00	0.00
.........................................................................................................................................................................TCGATCACGAGAACGTC-GC--A...........................................................................................................	20	1	5.00	5.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTCGAAAT.....................................................	23	1	5.00	4.00	1.00	0.00	0.00
.........................................................................................................................................................................TCGATCACGAGAACGTC-GC--ATCTTT......................................................................................................	25	1	3.00	1.00	1.00	1.00	0.00
.........................................................................................................................................................................TAGATCACGAGAACGTC-GC--ATCT........................................................................................................	23	1	3.00	3.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTCGAT.......................................................	21	1	3.00	2.00	0.00	1.00	0.00
.........................................................................................................................................................................TCGATCACGAGAACGTC-TC--ATCT........................................................................................................	23	1	3.00	2.00	0.00	1.00	0.00

droBip1

GCTACCCAA----------------A-------------------------------------------------------------------------------------------------------------------------CGCATACCGCTGAGGTCCGGCCTCGATCACGAGAACGTC-GC--ATCTTAGT--------TACGTTTTCATATGATGAGATA-TTCACGTCGTCGAAACCGTGCCTCGGC-GAATCGGAA----------------------ACACACCTAG

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

GATGTGACA----------------CCGTGGACGATCAA-----------------------------------C-----------------------------------------------------------A---------AAATTC---------ATATACAATTTCAATAACGTAGATATC-GC--ATCGTTTTTTTTTACCATATTTGATAAGAGATGAGATA-TTCACGTTGTTGAAGTTGTGAAGGAAT-----TAAA-------------------------------AA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAAG......................................................	22	1	330.00	286.00	21.00	12.00	11.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGA........................................................	20	1	264.00	257.00	1.00	5.00	1.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAA.......................................................	21	1	128.00	121.00	3.00	4.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAAGT.....................................................	23	1	79.00	64.00	2.00	10.00	3.00
.........................................................................................................................................................................TCAATAACGTAGATATC-GC--ATC.........................................................................................................	22	1	18.00	9.00	2.00	0.00	7.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAAA......................................................	22	1	17.00	17.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAAGA.....................................................	23	1	8.00	7.00	1.00	0.00	0.00
.........................................................................................................................................................................TCAATAACGTAGATATC-GC--AT..........................................................................................................	21	1	6.00	3.00	0.00	0.00	3.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAT.......................................................	21	1	5.00	5.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTG.........................................................	19	1	5.00	4.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAAT......................................................	22	1	4.00	4.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAAGTT....................................................	24	1	3.00	3.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................GAGATA-TTCACGTTGTTGA........................................................	19	1	3.00	3.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................GAGATA-TTCACGTTGTTGAAG......................................................	21	1	2.00	2.00	0.00	0.00	0.00
.................................................................................................................................................................................................................ATTTGATAAAAGATGTGAT.......................................................................	19	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAAAA.....................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAAAT.....................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGACG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAACT.....................................................	23	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTGTTGA........................................................	20	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCGCGTTGTTGA........................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTTGAAG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGxTGTTGA........................................................	19	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATC-TTCACGTTGTTGA........................................................	20	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTCGTCGA........................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCGCGTTGTTGAA.......................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTTA........................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCATGTTGTTGAAG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................................................................................................................GTTGTGATGGAAT-----TAAA-------------------------------C.	18	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCGCGTTGTTGAAG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACTTTGTTGAA.......................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................GGAGATA-TTCACGTTGTTGAAGT.....................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTGTTGAA.......................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTCGA........................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTTACGTTGTTGAAG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAATT.....................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................................GTCGTTTTTTTTTxCCATATTT......................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................................................................................AGTTGTGATGGAAT-----TAAA-------------------------------..	18	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGG........................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCGCGTTGTTGAAG......................................................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCGAAGT.....................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACTTTGTTGAAG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCCCGTTGTTGAAG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGGGATA-TTCACGTTGTTGA........................................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................TCAATAACGTAGATATC-GC--AG..........................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................................................ATATTTGATxAGAGTTGAGA........................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGCGATA-TTCACGTTGTTGAA.......................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTGTTGAAG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGCTGTTG.........................................................	19	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................................................................................................AATAACGTAGATATC-GC--ATC.........................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-CTCACGTTGTTGAA.......................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTCGTTGA........................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTCTTGAAGT.....................................................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................................................AGAGATGAGATA-TTCACGTTGT...........................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGT........................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTTGAAATA....................................................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGCTGTTGAA.......................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATTGAAG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................ATA-TTAAAGTTGTTGAAGT.....................................................	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

GGAACCGGA----------------ACAGAAACAGGAAAAAGAAATTGTGTTCC--------------------------------------------------------------------------------------------CC-----CTGGCCCAGCCCAGTTGCGATTGCGCGGACATC-TC--ATCGTATA------A-ACATTCGATAACCAACGAGATA-TTCACGTTATCGAGACTGAGACGTCGG-----CAAAGAC-------TGCAAGATTGT-GCGACAAGTGA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTATCGAGA......................................................	22	1	71.00	55.00	0.00	1.00	15.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTATCGAG.......................................................	21	1	25.00	23.00	1.00	0.00	1.00	0.00
.........................................................................................................................................................................GCGATTGCGCGGACATC-TC--ATC.........................................................................................................	22	1	14.00	10.00	0.00	0.00	4.00	0.00
.........................................................................................................................................................................GCGATTGCGCGGACATC-TC--ATCG........................................................................................................	23	1	4.00	3.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTATCGAGT......................................................	22	1	4.00	4.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................ATA-TTCACGTTATCGAGACTGA..................................................	22	1	3.00	1.00	0.00	0.00	2.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTATCGAGACC....................................................	24	1	2.00	0.00	0.00	0.00	2.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTATCGAGG......................................................	22	1	2.00	0.00	0.00	0.00	2.00	0.00
...........................AAAAACAGGAAAAAAAAA..............................................................................................................................................................................................................................................................	18	18	0.06	0.00	0.00	0.06	0.00	0.00
.........................................................................................................................................................................GCGATTGCGCGGACATC-AC--ATC.........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................ATA-TTCACGTTCTCGAGACTGA..................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTATCGA........................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................GCGATTGCGCGGACATC-TC--AT..........................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................................TTCGATAACGAACGAGAC.......................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTATCGAGAA.....................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................CGGGATA-TTCACGTTATCGAGA......................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTATCG.........................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCCCGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................................................................................................................................................GCGATTGCGCGGACATC-TC--CTC.........................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................GATAACGAACGAGATC-TT...................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................................................................................................................................................GCGATTGCGCGGCCATC-TC--ATC.........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................................................................................................................................................................CGATAACGAACGAGACA-TT...................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTCATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................CGAGA-TTCACGTTATCGAG.......................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................................................................................................................................................GCGATTGCGCGGACATC-TC--ATCGTA......................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................CGAGATA-TTCACGTTATCGAGAG.....................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

GTTAAACGAAATGAACCAGTTCGTTG------------------------------------------------------------------------------------------------------------------------TT-----CTGGCCCAGCCCGGTTCCGATTGCGCGGACATC-TC--ATCGTCTG------A-CCATTCGATAACCGATGAGATA-TTCACGTTATCGAGACTGCG-------------------------------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGA......................................................	22	1	572.00	561.00	7.00	4.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGAGA......................................................	22	1	406.00	382.00	16.00	7.00	1.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTGTCGAGA......................................................	22	1	205.00	203.00	2.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TC--ATC.........................................................................................................	22	1	83.00	81.00	0.00	2.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TC--AT..........................................................................................................	21	1	38.00	36.00	2.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TC--A...........................................................................................................	20	1	30.00	28.00	0.00	2.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAG.......................................................	21	1	29.00	29.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGAA.....................................................	23	1	22.00	22.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCGAGA......................................................	22	1	16.00	16.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTGTCGAG.......................................................	21	1	13.00	13.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGAAT....................................................	24	1	12.00	12.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGAG.......................................................	21	1	11.00	11.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGAT.....................................................	23	1	11.00	10.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGT......................................................	22	1	8.00	8.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGAGAAT....................................................	24	1	6.00	6.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGAGAA.....................................................	23	1	5.00	4.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGAGT......................................................	22	1	5.00	5.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TC--ATCG........................................................................................................	23	1	5.00	5.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGA........................................................	20	1	4.00	4.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTGTCGA........................................................	20	1	4.00	4.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCGCGTTATCGAGA......................................................	22	1	4.00	4.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TC--ATT.........................................................................................................	22	1	4.00	4.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGAGTCT....................................................	24	1	3.00	2.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGA........................................................	20	1	3.00	3.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGAGAT.....................................................	23	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGATT....................................................	24	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGGGATG-TTCACGTTATCGAGA......................................................	22	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGGTG-TTCACGTTATCGAGA......................................................	22	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCTAGA......................................................	22	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGTCGAG.......................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCATGTTATCGAGA......................................................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTGTCGAGACT....................................................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTTACGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATAGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGATATA-TTCACGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGTCATC-TC--ATC.........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGAGT....................................................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATTGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACTTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTTATCGAGT......................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGAC.....................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGAGG......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCATGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATTGA........................................................	20	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................ATA-TTCATGTGATCGAGA......................................................	18	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATGGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................ATGAGATG-TTCACGTTATCGAGTC.....................................................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TTAGATA-TTCACGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATTGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................ATGAGATG-TTCACGTTGTCGAGA......................................................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TC--ATG.........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGTACATC-TC--ATC.........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCTGACATC-TC--ATC.........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGACT....................................................	24	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................ATGAGATG-TTCACGTTATCGAG.......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGATAAT....................................................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAGTC.....................................................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TC--ATCT........................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTGACGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................GAGATG-TTCACGTTATCGAGA......................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATGGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACATTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TC--AG..........................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTxCGCGGACATC-TC--ATCG........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGCGATG-TTCACGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCGAC.......................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGAACATC-TC--ATC.........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TT--C...........................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCAAGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGACATC-TC--ATCC........................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................CGAGATG-TTCACGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATT-TTCACGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................CTGAGATG-TTCACGTTATCGAGA......................................................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCACGGACATC-TC--AT..........................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATA-TTCACGTTATCGAGATTT...................................................	25	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCA.........................................................	19	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................ATGAGATA-TTCACGTTATCGAGA......................................................	23	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................ATGAGATG-TTCACGTTATCGA........................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACCTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGACATA-TTCACGTTATCGAG.......................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................CCGATTGCGCGGTCATC-TC--ATCG........................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCAAGTTATCGAGA......................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................TGAGATG-TTCACGTTATCCAG.......................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................ATGAGATG-TTCACGTTATCGAGT......................................................	23	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 05:29:18 EDT

dme-mir-977

chrX:19453055-19453153 +

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