dme-mir-955- Best orthologs

dme-mir-955	chr3L:3299055-3299151 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 3299072-3299094
   star strand at position 3299113-3299134
   mutations
   read mismatches

Notes: This is similar to the cluster miRNA in 972-977 that has the obscura lineage missing.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3L:3299040-3299166 +		1	TAAGGAA--CAC--TT-----TTTGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAA------------------------------------------------------CAATT
droSim1	chr3L:2834561-2834687 +	LASTZ	1	TAAAGAA--CTC--TT-----TTTGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAA-TCGCATTCAATTTCTGCACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAG------------------------------------------------------AAATT
droSec1	super_2:3291343-3291466 +	LASTZ	1	TAATAAA--CAC--TT-----TTTGGTCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAA-TCGCATTCAATTTCTGCAG---AGAGATGGTA-CGCTTAGAAACAACCTACAA------------------------------------------------------AAATT
droYak2	chr3L:3844747-3844864 +	LASTZ	1	TAAAGT------------------AAACAGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGTG----TGTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAA------------------------------------------------------TGAGT
droEre2	scaffold_4784:5981989-5982116 +	LASTZ	1	AAGGAAT--ACA--CT-----TTTGTCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGTG----TGTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAG------------------------------------------------------CAAGT
droEug1	scf7180000409466:1024712-1024826 +	LASTZ	4	T--------------------TTTTGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----ACTTGCCAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTC-AGCTTAAAAGCAACCTAAAG--------------------------------------------------------ACT
droBia1	scf7180000302428:2658402-2658538 +	LASTZ	4	CAGGATT--TGC--TTTTCG-TTTGGTCAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCCTGTA----TCTTGCCAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTC-TGCTTCAAAGCAACATAAAACATT------------------------------AA------------------AAACA
droTak1	scf7180000415378:64765-64932 -	LASTZ	4	TACAGGG--TAT--TTTTTGTTTCGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TCTCGACAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTA-TGCTCAAAAGCAACATAAATAA-ATTC-----------------CTAATTCCTAAAAATTCCTAAAAAAAATTGCAATT
droEle1	scf7180000491249:1960492-1960621 -	LASTZ	4	TGTGGAAGGTAT--TT-----GTCGGCCAGCTTTTCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TCTTGCCAAT-TCGCATTCAATCTCTGAACGATAGAGATGGTC-AGCTTAAAAGCAACATAAGAT-----------------------------------------------------CAAAA
droRho1	scf7180000769770:13927-14066 -	LASTZ	4	ATATGAA--GAC--TT-----TCTGGCTAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TCTTGCCAAT-CCGCATTCAATCTTTGAACGATAGATATGGTC-AGCTTAAATGCAACCTAAACAT-C------------------------TATTCGAAAT----------------TCAGA
droFic1	scf7180000454105:1620302-1620432 +	LASTZ	4	TGAAGCA--ACC--TT-----TTCAGCTAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TCTTGTCAAATTCGCATTCAATCTCTGAACGGTAGAGATGGTGGAGCTATAGATCAGCCTAAATAT-A---------------------------------------------------TACA
droKik1	scf7180000302391:414346-414467 +	LASTZ	4	TTCGA---------CA-----TTTGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGTG----TATTGCCAAA-TCGCATTCAACCTCTGAACGGTAGAGATGGTG-AGCTTTAGAGCAACCTAAAT------------------------------------------------------TTATA
droAna3	scaffold_13337:7606422-7606539 +	LASTZ	1	TGAAGGA--TGT--TT-----TTTGAGAAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAATT----T-TTAACCAT-TCGCATTCAACCTTTGGACGGTAGAGATGGTC-AGTGAGAAAGCAACCTA--------------------------------------------------------------
droBip1	scf7180000395543:273565-273688 +	LASTZ	4	GAAGGCT--GTT--TT-----TTTGAGAAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTC-TATT----TTTTAACCTT-TCGCATTCAACCTTTGGACGGTAGAGATGGTC-AGTGAAAAAGCAACCTAAAA--------------------------------------------------------AAG
dp4	chrXR_group8:3252997-3253027 -	MAF	0	-------------------------------------------TCCTGCAGGGGTTTGAGGGTCCTGTG----TCTTG----------------------------------------------------------------------------------------------------------------------
droPer1	super_65:53567-53597 -	MAF	0	-------------------------------------------TCCTGCAGGAGTTCGAGGATCCTGGG----TCTTG----------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180698:10215726-10215851 +	LASTZ	1	ATTCAAA--TACTTTT-GC--GTT--AAGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTTC-GTTTGTTTTCTCTAA-TGGCATTCAACCTTGGAGCGATAGAGACGGCC-AATCGAGAAACAGCCTAAA------------------------------------------------------------
droVir3	scaffold_12758:855562-855687 -	LASTZ	1	TATGTAT--GGA--TC-----TCTCATCAGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGAG----TTTTTCCTAG-TGGCATTCAACCTTTGAACGGTAGAGATGGCC-AACTGAAAAGCGACCTAAAC------------------------------------------------------TAATA
droMoj3	scaffold_6680:1909563-1909732 -	LASTZ	1	TCAGGTA--TCC--AA-----TATG---GGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGTG----TTT-GGCTAG-TCGCATTCAGCCTTTGAACGGTAGAGATGGCC-AACTGAAAAGCGACCTAACTGA-AAGCGAATCAAGGGAACTAGGCCAATAGGCGAGAAT-CATATAG-AAA---TAGTT
droGri2	scaffold_15110:657067-657177 +	LASTZ	1	TAAAG------------------------GTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGAG----T-TTGCCAAG-TGGCATTCAGCCCCTGGACGCTAGAGATGGCC-AACTGAAAAGCAACCTAAAAA-----------------------------------------------------CAATC

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	TAAGGAA--CACTTT-----T-TGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAA------------------------------------------------------CAATT
droSim1	TAAAGAA--CTCTTT-----T-TGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAA-TCGCATTCAATTTCTGCACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAG------------------------------------------------------AAATT
droSec1	TAATAAA--CACTTT-----T-TGGTCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAA-TCGCATTCAATTTCTGCAG---AGAGATGGTA-CGCTTAGAAACAACCTACAA------------------------------------------------------AAATT
droYak2	TAAAGT-----------------AAACAGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGT---GTGTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAA------------------------------------------------------TGAGT
droEre2	AAGGAAT--ACACTT-----T-TGTCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGT---GTGTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAG------------------------------------------------------CAAGT
droEug1	T-------------T-----T-TTGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GACTTGCCAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTC-AGCTTAAAAGCAACCTAAAG--------------------------------------------------------ACT
droBia1	CAGGATT--TGCTTT-TCGTT-TGGTCAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCCTGT---ATCTTGCCAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTC-TGCTTCAAAGCAACATAAAACATT------------------------------AA------------------AAACA
droTak1	TACAGGG--TATTTT-TTGTTTCGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTCTCGACAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTA-TGCTCAAAAGCAACATAAATAA-ATTC-----------------CTAATTCCTAAAAATTCCTAAAAAAAATTGCAATT
droEle1	TGTGGAAGGTATTTG-----T-CGGCCAGCTTTTCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTCTTGCCAAT-TCGCATTCAATCTCTGAACGATAGAGATGGTC-AGCTTAAAAGCAACATAAGAT-----------------------------------------------------CAAAA
droRho1	ATATGAA--GACTTT-----C-TGGCTAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTCTTGCCAAT-CCGCATTCAATCTTTGAACGATAGATATGGTC-AGCTTAAATGCAACCTAAACAT-C------------------------TATTCGAAAT----------------TCAGA
droFic1	TGAAGCA--ACCTTT-----T-CAGCTAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTCTTGTCAAATTCGCATTCAATCTCTGAACGGTAGAGATGGTGGAGCTATAGATCAGCCTAAATAT-A---------------------------------------------------TACA
droKik1	TTCGA-------CAT-----T-TGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGT---GTATTGCCAAA-TCGCATTCAACCTCTGAACGGTAGAGATGGTG-AGCTTTAGAGCAACCTAAAT------------------------------------------------------TTATA
droAna3	TGAAGGA--TGTTTT-----T-TGAGAAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAAT---TT-TTAACCAT-TCGCATTCAACCTTTGGACGGTAGAGATGGTC-AGTGAGAAAGCAACCTA--------------------------------------------------------------
droBip1	GAAGGCT--GTTTTT-----T-TGAGAAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTC-TAT---TTTTTAACCTT-TCGCATTCAACCTTTGGACGGTAGAGATGGTC-AGTGAAAAAGCAACCTAAAA--------------------------------------------------------AAG
droWil1	ATTCAAA--TACTTTTGCGTT----AAGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTTCGTTTGTTTTCTCTAA-TGGCATTCAACCTTGGAGCGATAGAGACGGCC-AATCGAGAAACAGCCTAAA------------------------------------------------------------
droVir3	TATGTAT--GGATCT-----C-TCATCAGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGA---GTTTTTCCTAG-TGGCATTCAACCTTTGAACGGTAGAGATGGCC-AACTGAAAAGCGACCTAAAC------------------------------------------------------TAATA
droMoj3	TCAGGTA--TCCAAT-----A-TG---GGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGT---GTT-TGGCTAG-TCGCATTCAGCCTTTGAACGGTAGAGATGGCC-AACTGAAAAGCGACCTAACTGA-AAGCGAATCAAGGGAACTAGGCCAATAGGCGAGAAT-CATATAG-AAA---TAGTT
droGri2	TAAAG-----------------------GTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGA---GT-TTGCCAAG-TGGCATTCAGCCCCTGGACGCTAGAGATGGCC-AACTGAAAAGCAACCTAAAAA-----------------------------------------------------CAATC

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

Small RNA-seq read pileup

Species

Alignment

droSim1

TAAAGAA--CTC--TT-----TTTGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAA-TCGCATTCAATTTCTGCACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAG------------------------------------------------------AAATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.........................................CATCGTGCAGAGGTTTGAGTGTC....................................................................................................................................	23	1	836.00	395.00	5.00	0.00	436.00
..........................................ATCGTGCAGAGGTTTGAGTGTC....................................................................................................................................	22	1	154.00	29.00	1.00	0.00	124.00
.........................................CATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	127.00	84.00	2.00	0.00	41.00
.......................................................................................CATTCAATTTCTGCACGGTAGT.......................................................................................	22	1	95.00	4.00	5.00	1.00	85.00
.........................................CATCGTGCAGAGGTTTGAGTG......................................................................................................................................	21	1	76.00	60.00	3.00	0.00	13.00
.......................TGGCCAGCTAATCAACTC...........................................................................................................................................................	18	1	64.00	0.00	0.00	0.00	64.00
.......................................................................................CATTCAATTTCTGCACGG...........................................................................................	18	1	50.00	0.00	0.00	0.00	50.00
......................TTGGCCAGCTAATCAACTC...........................................................................................................................................................	19	1	33.00	1.00	0.00	0.00	32.00
.......................................................................................CATTCAATTTCTGCACGGTAGA.......................................................................................	22	1	31.00	17.00	0.00	0.00	14.00
.......................TGGCCAGCTAATCAACTCC..........................................................................................................................................................	19	1	16.00	8.00	0.00	0.00	8.00
..........................................ATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	21	1	14.00	4.00	2.00	0.00	8.00
.......................................................................................CATTCAATTTCTGCACGGTAG........................................................................................	21	1	14.00	0.00	0.00	0.00	14.00
.........................................CATCGTGCAGAGGTTTGAGTGG.....................................................................................................................................	22	1	13.00	0.00	2.00	0.00	11.00
..........................................ATCGTGCAGAGGTTTGAGTGTCC...................................................................................................................................	23	1	12.00	6.00	1.00	0.00	5.00
.....................TTTGGCCAGCTAATCAACTC...........................................................................................................................................................	20	1	12.00	0.00	0.00	0.00	12.00
.........................................CATCGTGCAGAGGTTTGAG........................................................................................................................................	19	1	8.00	0.00	2.00	0.00	6.00
.......................................................................................CATTCAATTTCTGCACGGTAGG.......................................................................................	22	1	8.00	1.00	1.00	0.00	6.00
.........................................CATCGTGCAGCGGTTTGAGTGTC....................................................................................................................................	23	1	6.00	6.00	0.00	0.00	0.00
...............T-----TTTGGCCAGCTAATCAACTC...........................................................................................................................................................	21	1	6.00	0.00	0.00	0.00	6.00
..........................................ATCGTGCAGAGGTTTGAGTGTCCTG.................................................................................................................................	25	1	6.00	2.00	0.00	0.00	4.00
.........................................CATCGTGCAGAGGTTTGAGGGTC....................................................................................................................................	23	1	5.00	1.00	0.00	0.00	4.00
.........................................CATCGTGCAGATGTTTGAGTGTC....................................................................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
.........................................CATCGTGCAGAGGTTTGAGTGTCT...................................................................................................................................	24	1	5.00	2.00	0.00	0.00	3.00
.........................................CATCGTGCAGAGGTTTGAGCGTC....................................................................................................................................	23	1	5.00	1.00	0.00	0.00	4.00
......................TTGGCCAGCTAATCAACTCC..........................................................................................................................................................	20	1	5.00	0.00	0.00	0.00	5.00
..........................................ATCGTGCAGAGGTTTGAGTGTCT...................................................................................................................................	23	1	5.00	1.00	0.00	0.00	4.00
.........................................CATCTTGCAGAGGTTTGAGTGTC....................................................................................................................................	23	1	4.00	0.00	0.00	0.00	4.00
.......................................................................................CATTCAATTTCTGCACGGTAGC.......................................................................................	22	1	4.00	0.00	0.00	0.00	4.00
.........................................CATCGTGCATAGGTTTGAGTGTC....................................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
..........................................ATCGTGCAGAGGTTTGAGTGTCCT..................................................................................................................................	24	1	3.00	1.00	0.00	0.00	2.00
.........................................CATCGTGCAGAGGTTTGAGT.......................................................................................................................................	20	1	3.00	3.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTGC.....................................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
.........................................CATCGTGCAGAGGTTTGAGTGAC....................................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00

droSec1

TAATAAA--CAC--TT-----TTTGGTCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAA-TCGCATTCAATTTCTGCAG---AGAGATGGTA-CGCTTAGAAACAACCTACAA------------------------------------------------------AAATT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.............................................................................................CTTTCxGCAG---AGAGATGGT.................................................................................	18	1	4.00	0.00	3.00	1.00
.............................................................................................CTTTCxGCAG---AGAGATGGTA-...............................................................................	19	1	2.00	0.00	2.00	0.00
..............................................CGCAGCGGTTTGAGTGTC....................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TAAAGT------------------AAACAGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGTG----TGTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAA------------------------------------------------------TGAGT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................CATCGTGCAGAAGTTTGAGTGTC....................................................................................................................................	23	1	293.00	206.00	0.00	15.00	4.00	68.00
.........................................CATCGTGCAGAAGTTTGAGTGT.....................................................................................................................................	22	1	96.00	16.00	8.00	33.00	12.00	27.00
.........................................CATCGTGCAGAAGTTTGAGTGTCT...................................................................................................................................	24	1	16.00	0.00	0.00	3.00	1.00	12.00
.........................................CATCGTGCAGAAGTTTGAGTG......................................................................................................................................	21	1	7.00	1.00	0.00	5.00	1.00	0.00
.........................................CATCGTGCAGAAGTTTGAGTGC.....................................................................................................................................	22	1	6.00	0.00	0.00	2.00	0.00	4.00
..........................................ATCGTGCAGAAGTTTGAGTGTC....................................................................................................................................	22	1	5.00	4.00	0.00	0.00	0.00	1.00
..........................................ATCGTGCAGAAGTTTGAGTGTCT...................................................................................................................................	23	1	3.00	0.00	0.00	0.00	0.00	3.00
.........................................CATCGTGCAGCAGTTTGAGTGTC....................................................................................................................................	23	1	3.00	3.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTGAGTGTCC...................................................................................................................................	24	1	2.00	0.00	0.00	1.00	0.00	1.00
.....T------------------AAACAGCTAAGCGACTCCAT........................................................................................................................................................	21	1	2.00	0.00	0.00	2.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTGAGTGTT....................................................................................................................................	23	1	2.00	0.00	0.00	2.00	0.00	0.00
.......................................................................................CATTCAATTTCTGAACGGTAGA.......................................................................................	22	1	2.00	2.00	0.00	0.00	0.00	0.00
.........................................CATCGCGCAGAAGTTTGAGTGTC....................................................................................................................................	23	1	2.00	2.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTGAGT.......................................................................................................................................	20	1	2.00	0.00	0.00	2.00	0.00	0.00
.........................................CATCGTGTAGAAGTTTGAGTGTC....................................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................CATCGTGCAGAAGTTTGAGTGAC....................................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................CATCGTGCAGACGTTTGAGTGT.....................................................................................................................................	22	1	2.00	0.00	0.00	0.00	1.00	1.00
........................................................................................ATTCAATTTCTGAACGGTAGAGT.....................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................CATCGTGCAGAAGTTTGAGTGG.....................................................................................................................................	22	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................CATCGGGCAGAAGTTTGAGTGTC....................................................................................................................................	23	1	2.00	2.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCCGAAGTTTGAGTGTC....................................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................CATCGTGCAGAAGTTTGAGTGTG....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAATTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCAGAAGTTTGAGAGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAAGCTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................CATCGGGCAGAAGTTTGAGCG......................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAAGTTTAAGTGTA....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.....T------------------AAACAGCTAATCAACTCC..........................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTGTGTGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CAACGTGCAGAAGTTTCAGTGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAATTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCAGAAGTTTCAGTGAC....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................ATCGTGCAGAAGTTTGAGTGTCC...................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
........................AAACAGCTAAGCGACTCCATC.......................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCCGACGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAAGTTTGAGTGTCA...................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
........................AAACAGCTAAACGACTCCATC.......................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................CCATCGTGCAGAAGTTTGAGTGT.....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTCAG........................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTGAGTGTCTT..................................................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAAGTTTGAGTT......................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTGAGA.......................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAATCTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGAGCAGACGTTTGAGTGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAAGGTTGAGTGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................TCGTGCAGAAGTTTGAGTGTCCTG.................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................ATCGTGCAGAAGTTTGAGTGTCCTG.................................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGTAGTTTGAGTGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTGAGTGA.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTGGGTG......................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGCTGTTTGAGTGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAAGTTTGAGTATC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCTTGCAGAAGTTTGAGTGAC....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................ATTGTGCAGAAGxTTGAGTGT.....................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
........................AAACAGCTAAGCGACTCCAT........................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAAGCTTGAGTGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00

droEre2

AAGGAAT--ACA--CT-----TTTGTCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGTG----TGTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTAAAG------------------------------------------------------CAAGT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................................CATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	289.00	57.00	18.00	0.00	214.00
.........................................CATCGTGCAGAGGTTTGAGTGTC....................................................................................................................................	23	1	260.00	228.00	1.00	0.00	31.00
.........................................CATCGTGCAGAGGTTTGAGTG......................................................................................................................................	21	1	201.00	41.00	9.00	0.00	151.00
.........................................CATCGTGCAGAGGTTTGAGTGTCT...................................................................................................................................	24	1	27.00	6.00	1.00	0.00	20.00
.........................................CATCGTGCAGAGGTTTGAGT.......................................................................................................................................	20	1	16.00	2.00	1.00	0.00	13.00
.........................................CATCGTGCAGAGGTTTTAGTGTC....................................................................................................................................	23	1	9.00	9.00	0.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGAGTGTT....................................................................................................................................	23	1	5.00	5.00	0.00	0.00	0.00
..........................................ATCGTGCAGAGGTTTGAGTGTCT...................................................................................................................................	23	1	5.00	2.00	0.00	0.00	3.00
.........................................CATCGTGCATAGGTTTGAGTGTC....................................................................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
.........................................CATCGTGCAGCGGTTTGAGTGTC....................................................................................................................................	23	1	4.00	3.00	0.00	0.00	1.00
.........................................AATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	4.00	0.00	0.00	0.00	4.00
.........................................CATCGTGCAGATGTTTGAGTGT.....................................................................................................................................	22	1	4.00	0.00	0.00	0.00	4.00
..........................................ATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	21	1	3.00	0.00	0.00	0.00	3.00
.........................................CATCGTGCAGAGGTTTGATTGT.....................................................................................................................................	22	1	3.00	1.00	0.00	0.00	2.00
.........................................CATCGTTCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00

droEug1

T--------------------TTTTGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----ACTTGCCAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTC-AGCTTAAAAGCAACCTAAAG--------------------------------------------------------ACT

Size

Hit Count

Total Norm

droBia1

CAGGATT--TGC--TTTTCG-TTTGGTCAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCCTGTA----TCTTGCCAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTC-TGCTTCAAAGCAACATAAAACATT------------------------------AA------------------AAACA

Size

Hit Count

Total Norm

droTak1

TACAGGG--TAT--TTTTTGTTTCGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TCTCGACAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTA-TGCTCAAAAGCAACATAAATAA-ATTC-----------------CTAATTCCTAAAAATTCCTAAAAAAAATTGCAATT

Size

Hit Count

Total Norm

droEle1

TGTGGAAGGTAT--TT-----GTCGGCCAGCTTTTCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TCTTGCCAAT-TCGCATTCAATCTCTGAACGATAGAGATGGTC-AGCTTAAAAGCAACATAAGAT-----------------------------------------------------CAAAA

Size

Hit Count

Total Norm

droRho1

ATATGAA--GAC--TT-----TCTGGCTAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TCTTGCCAAT-CCGCATTCAATCTTTGAACGATAGATATGGTC-AGCTTAAATGCAACCTAAACAT-C------------------------TATTCGAAAT----------------TCAGA

Size

Hit Count

Total Norm

droFic1

TGAAGCA--ACC--TT-----TTCAGCTAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TCTTGTCAAATTCGCATTCAATCTCTGAACGGTAGAGATGGTGGAGCTATAGATCAGCCTAAATAT-A---------------------------------------------------TACA

Size

Hit Count

Total Norm

droKik1

TTCGA---------CA-----TTTGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGTG----TATTGCCAAA-TCGCATTCAACCTCTGAACGGTAGAGATGGTG-AGCTTTAGAGCAACCTAAAT------------------------------------------------------TTATA

Size

Hit Count

Total Norm

droAna3

TGAAGGA--TGT--TT-----TTTGAGAAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAATT----T-TTAACCAT-TCGCATTCAACCTTTGGACGGTAGAGATGGTC-AGTGAGAAAGCAACCTA--------------------------------------------------------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.........................................CATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	124.00	62.00	40.00	19.00	3.00
.........................................CATCGTGCAGAGGTTTGAGTGTC....................................................................................................................................	23	1	60.00	21.00	18.00	8.00	13.00
.........................................CATCGTGCAGAGGTTTGAGTG......................................................................................................................................	21	1	41.00	21.00	16.00	2.00	2.00
.........................................CATCGTGCAGAGGTTTGAGTGTCT...................................................................................................................................	24	1	37.00	16.00	13.00	2.00	6.00
.........................................CATCGTGCAGAGGTTTGAGT.......................................................................................................................................	20	1	9.00	5.00	1.00	3.00	0.00
.......................................................................................CATTCAACCTTTGGACGGTAGA.......................................................................................	22	1	7.00	4.00	1.00	1.00	1.00
.........................................CATCGTGCAGAGGTTTGAGTGTT....................................................................................................................................	23	1	6.00	3.00	2.00	1.00	0.00
.........................................................................................TTCAACCTTTGGACGGTAGAG......................................................................................	21	1	4.00	4.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTTAGTGTC....................................................................................................................................	23	1	4.00	0.00	2.00	0.00	2.00
.........................................CATCGTGCAGAGGTTTGAGTTTC....................................................................................................................................	23	1	3.00	0.00	1.00	0.00	2.00
..........................................ATCGTGCAGAGGTTTGAGTGTCT...................................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTT......................................................................................................................................	21	1	2.00	1.00	0.00	0.00	1.00
.........................................CATCGTGCAGAGGTTAGAGTGT.....................................................................................................................................	22	1	2.00	2.00	0.00	0.00	0.00
........................................CCATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	23	1	2.00	1.00	1.00	0.00	0.00
.........................................................................................TTCAACCTTTGGACGGTAGAGT.....................................................................................	22	1	2.00	1.00	0.00	1.00	0.00
.........................................CATCGGGCAGAGGTTTGAGTGTC....................................................................................................................................	23	1	2.00	0.00	0.00	1.00	1.00
.........................................AATGGTGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAGGTTTGAGCGT.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................AATCGTGCAGAGGTTTGAGTG......................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................TTCAACCTTTGGACGATAGAGA.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................CCTCGTGCAGAGGTTTGAGT.......................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCACGGGTTTGAGTG......................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCTTGCATAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................TTCAACCTTTGGACGGTAGA.......................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCATAGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGCGGTTTGAGTATC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTTGGT.......................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................GATCGTGCAGAGGTTTGAG........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................CATTCAACCTTTGTACGATAGA.......................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................CATAGTGCAGAGGTTTGAGTGTCT...................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................CGCATTCAACCTTTGGACGGTAG........................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTTCAGAGGTTTGCGTG......................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAAGTTTGAGTGTCT...................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTAAGTGTC....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGCGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAGGCTTGAGTGTCT...................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
...........................................TCGTGCAGAGGTTTGAGTGTCT...................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAGCTTTGAGTG......................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................CATTGTGCAGAGGTTTGAGTT......................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTA......................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGTGGTTTGTGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................TGGTA-AGTGAGAAAGCAAGC................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAGGTTTGAT........................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTGG.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTTAGT.......................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTGTCTA..................................................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................TTCAACCTTTGGAAGGTAGAG......................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................CATTCAACCTTTGGACGGTGGA.......................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGGGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTGTTT...................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGCTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCAGCGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................TTCAACCTTTGAACGGTAGAGT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTATC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................AATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAGCTTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGATTTGAGTGTCT...................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
..........................................ATCGTGCAGAGGTTTGAGTGTCA...................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...........................................TCGTGCGGAGGTTTGAGTGTCT...................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTTCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGTGTGTC....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCAGAGGTTTGAGTGC.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................CATTCAACCTTTGGACGGTAG........................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAGGTTGGAGTGT.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................CAACGTGCAGAGGTTTGAGCGT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCATAGGTTTTAGTGTC....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...........................................TCGTGCAGAGGTTTGAGTGTC....................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGCGCAGAGGTTTGAGTG......................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTTTCT...................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTCTC....................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..........................................ATCGTGCAGAGGTTTGAGTG......................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCATAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGTTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................TTCAACCTTTGGACGGTAGAGA.....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAAGGTC....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCAGAGGTTTGAG........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droBip1

GAAGGCT--GTT--TT-----TTTGAGAAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTC-TATT----TTTTAACCTT-TCGCATTCAACCTTTGGACGGTAGAGATGGTC-AGTGAAAAAGCAACCTAAAA--------------------------------------------------------AAG

Size

Hit Count

Total Norm

dp4

-------------------------------------------TCCTGCAGGGGTTTGAGGGTCCTGTG----TCTTG----------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

-------------------------------------------TCCTGCAGGAGTTCGAGGATCCTGGG----TCTTG----------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.............................................CTGCAGGAGATCCAGGATC....................................................................................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00

droWil1

ATTCAAA--TACTTTT-GC--GTT--AAGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTTC-GTTTGTTTTCTCTAA-TGGCATTCAACCTTGGAGCGATAGAGACGGCC-AATCGAGAAACAGCCTAAA------------------------------------------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........................................CATCGTGCTTAGGTTTGAGTGTC....................................................................................................................................	23	1	673.00	2.00	653.00	11.00	7.00
.........................................CATCGTGCTTAGGTTTGAGTGT.....................................................................................................................................	22	1	116.00	2.00	68.00	14.00	32.00
.........................................CATCGTGCTTAGGTTTGAGTG......................................................................................................................................	21	1	41.00	1.00	28.00	2.00	10.00
.........................................CATCGTGCTTAGGTTTGAGTGTCT...................................................................................................................................	24	1	29.00	0.00	10.00	4.00	15.00
.......................................................................................CATTCAACCTTGGAGCGATAGA.......................................................................................	22	1	9.00	0.00	9.00	0.00	0.00
..........................................ATCGTGCTTAGGTTTGAGTGTC....................................................................................................................................	22	1	5.00	0.00	5.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGTGTCC...................................................................................................................................	24	1	4.00	0.00	2.00	0.00	2.00
.........................................CATCGTGCTTAGGTTTGATTGTC....................................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
.........................................CATCTTGCTTAGGTTTGAGTGTC....................................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
.........................................CATCGTGCTTAGGCTTGAGTGTC....................................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGTGTCA...................................................................................................................................	24	1	3.00	0.00	2.00	1.00	0.00
.........................................CATCGTGCTTAGGTTTGAGTGC.....................................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
.........................................CATCGTGCTTATGTTTGAGTGTC....................................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTTAGTGTC....................................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
.........................................CATCGTTCTTAGGTTTGAGTGTC....................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGCGTCT...................................................................................................................................	24	1	2.00	0.00	1.00	0.00	1.00
.........................................CATCGCGCTTAGGTTTGAGTGTC....................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGTGG.....................................................................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
..........................................ATCGTGCTTAGGTTTGAGTGTCT...................................................................................................................................	23	1	2.00	0.00	1.00	1.00	0.00
.........................................CATCGTGCTTAGATTTGAGTGTC....................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
..........................................ATCGTGCTTAGGTTTGAGTGT.....................................................................................................................................	21	1	2.00	0.00	1.00	1.00	0.00
.........................................CATCGTGCTTAGGTTTGAGTGTCAA..................................................................................................................................	25	1	2.00	0.00	2.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGT.......................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
.............................................GTGCTTAGGTTTGAGTGTC....................................................................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGTGCC....................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGAGTC....................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
.........................................CATTGTGCTTAGGTTTGAGTGTC....................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGTGTCG...................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTxCTTAGGTTTGAGTGTC....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCCTGCTTAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................CATAGTGCTTAGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
......A--TACTTTT-GC--GxT--CAGGTTG...................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAATGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................CACCGTGCTTAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTGGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................CCATCGTGCTTAGGGTTGAGTG......................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTAGGCTTGAGTG......................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGCGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................TATCGTGCTTAGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
........................................CCATCGTGCTTAGGTTTGAGTGTC....................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAGTGTT....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................CATGGTGCTTAGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAG........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................................................................TGGCATTCAACCTTGGAGCGATA.........................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTTCTTAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTTAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTACGTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCTTAGGTTTGAGTCTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGAATGT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCTTAGGCTTGAGTGTCA...................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCCTAGGTTTGAATGTC....................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
..................................................................................A-TGGCATTCAACCTTGGAGCGATAGAA......................................................................................	27	1	1.00	0.00	1.00	0.00	0.00
.........................................CATTGTGCTTAGGTTTGAGTG......................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................................AATCGTGCTTAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CGTCGTGCTTAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................CCATCGTGCTTAGGTTTGAGTG......................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTAGGxTTGAGTGTC....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGATTAGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................CGTCGTGCTTAGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................AATCGTGCTTAGGTTTGAGTG......................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................GCGATAGAxACGGCA-AATCG..........................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCCTAGGTTTGAGTGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCTTAGGTTTGACTGTC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.............................................GTGCTTAGGTTTGAGTGT.....................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................CATTCAACCTTGGAGCGATAG........................................................................................	21	1	1.00	0.00	1.00	0.00	0.00

droVir3

TATGTAT--GGA--TC-----TCTCATCAGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGAG----TTTTTCCTAG-TGGCATTCAACCTTTGAACGGTAGAGATGGCC-AACTGAAAAGCGACCTAAAC------------------------------------------------------TAATA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.........................................CATCGTGCACAGGTTTGAGTGTT-...................................................................................................................................	23	1	46.00	1.00	0.00	44.00	1.00	0.00
.........................................CATCGTGCACAGGTTTGAGTGT.....................................................................................................................................	22	1	23.00	5.00	5.00	13.00	0.00	0.00
.......................................................................................CATTCAACCTTTGAACGGTAGA.......................................................................................	22	1	2.00	0.00	1.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTTTTAGTGT.....................................................................................................................................	22	1	2.00	0.00	0.00	2.00	0.00	0.00
.......................................................................................CATTCAACCTCTGAACGGTAGA.......................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CGTCGTGCACAGGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGAGTATT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGATTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTTTTAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGAGTGTT-A..................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGGGCACAGGTTTGAGGGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGGGCTCAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGAGCGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................................AGTGGCC-AACTGAAAAGCG...................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCACAGGTTTGAGTGTT-T..................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGAACAGGTTTGAGTGTT-T..................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGA.........................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................ATCGTGCAGAGGTTTGAGTGTC-...................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................CATGGTGCACAGGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................GTGCAGAGGTTTGAGTGTC-T..................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................CAGCGTGCACAGGTTTTAGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACCGGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGAGTTTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGAGTG......................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................CATCGTGCCCAGGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTCTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

TCAGGTA--TCC--AA-----TATG---GGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGTG----TTT-GGCTAG-TCGCATTCAGCCTTTGAACGGTAGAGATGGCC-AACTGAAAAGCGACCTAACTGA-AAGCGAATCAAGGGAACTAGGCCAATAGGCGAGAAT-CATATAG-AAA---TAGTT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........................................CATCGTGCACAGGTTTGAGTGTT-...................................................................................................................................	23	1	200.00	22.00	2.00	0.00	176.00
.........................................CATCGTGCACAGGTTTGAGTGT.....................................................................................................................................	22	1	65.00	37.00	12.00	5.00	11.00
.......................................................................................CATTCAGCCTTTGAACGGTAGA.......................................................................................	22	1	18.00	4.00	0.00	0.00	14.00
.........................................CATCGTGCACAGGTTTGAGTGTT-T..................................................................................................................................	24	1	12.00	6.00	3.00	1.00	2.00
.........................................CATCGTGCACAGGTTTGAGT.......................................................................................................................................	20	1	2.00	1.00	0.00	0.00	1.00
.........................................CATCGTGCAGAGGTTTGAGTGT.....................................................................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
.....................................................GTTTGAATGTG-TGTG----TTT-GG.....................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCACAGGTTTTAGTG......................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGGGCACAGGTTTGGGTGTT-T..................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGAGTG......................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCACAGGTTTGCGTGT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................CATCGTGCACAGGTTTGAGTGTT-TGTT----...........................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCACAGGTTTGAGTGGT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGGGCACAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................CATCGTGCACAGGTTTGTGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCACAGGTTTGCGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGCGCACAGGTTTGAGGGTT-T..................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
.............................................GTGCACAGGTTTGAGTGTT-...................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCACAGGTTTGAATGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCACAGGTTTGAG........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...........C--AA-----TATG---GGTTAGCGAGCTC...........................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.........................................CAGCGTGCACAGGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCACAAGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
..............AA-----TATG---GGTTAGCGAGCTC...........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGGGAACAGGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGGGCACAGGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGCGCACAGGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCACAGGTTTGAGTGTT-TGTG----...........................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGCGCACAGGTTTGAGTGGT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGCGCACAGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................CATCGTGCACAGGGTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................CATTCAGCCTTCGAACGGTAGA.......................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCACAGGTTTGAGTTTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTGCACAGGTTTGAGTGTT-C..................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
.........................................CATCGTCCACAGGTTTGAGTGTT-...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00

droGri2

TAAAG------------------------GTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGAG----T-TTGCCAAG-TGGCATTCAGCCCCTGGACGCTAGAGATGGCC-AACTGAAAAGCAACCTAAAAA-----------------------------------------------------CAATC	Size	Hit Count	Total Norm	V109 Male body
.........................................CATCGTGCACGGGTTTGAGTG......................................................................................................................................	21	1	44.00	44.00
.........................................CATCGTGCACGGGTTTGAGTGT.....................................................................................................................................	22	1	41.00	41.00
.........................................CATCGTGCACGGGTTTGAGT.......................................................................................................................................	20	1	16.00	16.00
.........................................CATCGTGCACGGGTTTGAGTGTC-...................................................................................................................................	23	1	5.00	5.00
.........................................CATCGTGCACGGGTTTGAGTGA.....................................................................................................................................	22	1	2.00	2.00
.........................................CAACGTGCACGGGTTTGAGT.......................................................................................................................................	20	1	2.00	2.00
.........................................CATCGTGCACGGGTTTGGGTG......................................................................................................................................	21	1	1.00	1.00
.........................................CATCGTGCATGGGTTTGAGTG......................................................................................................................................	21	1	1.00	1.00
.........................................CATCGTGCACGGGTTTGAGTGTC-A..................................................................................................................................	24	1	1.00	1.00
.........................................TATCGTGCACGGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00
..........................................ATGGTGCACGGGTTTGAGT.......................................................................................................................................	19	1	1.00	1.00
.........................................CATCGTGCACGGGTTTGAGTGTC-T..................................................................................................................................	24	1	1.00	1.00
.........................................CATCGTGCGCGGGTTTGAGTG......................................................................................................................................	21	1	1.00	1.00
.........................................CATCGTGCCCGGGTTTGAGTG......................................................................................................................................	21	1	1.00	1.00
.........................................CACCGTGCACGGGTTTGAGTG......................................................................................................................................	21	1	1.00	1.00
.........................................CATCGTGCACCGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00
.........................................CATCGCGCACGGGTTTGAGTG......................................................................................................................................	21	1	1.00	1.00
..........................................ATCGTGCACGGGTTTGAGTG......................................................................................................................................	20	1	1.00	1.00
..........................................ATCGTGCACAGGxTTGAGTGTC-...................................................................................................................................	21	1	1.00	1.00
.........................................CATCGTGCACGGGTTTGCGTGT.....................................................................................................................................	22	1	1.00	1.00
.........................................CATCGTGCACGGGTTTGAATG......................................................................................................................................	21	1	1.00	1.00
.........................................CATCGAGCACGGGTTTGAGT.......................................................................................................................................	20	1	1.00	1.00
.........................................CATCGTACACGGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00
.........................................CATAGTGCACGGGTTTGAGTGT.....................................................................................................................................	22	1	1.00	1.00
..........................................ATCGTGCACGGGTTTGAGTGTC-...................................................................................................................................	22	1	1.00	1.00

Generated: 04/20/2012 at 05:32:52 EDT

dme-mir-955

chr3L:3299055-3299151 +

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