dme-mir-994- Best orthologs

dme-mir-994	chr3R:6233859-6233949 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 6233870-6233891
   star strand at position 6233916-6233938
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3R:6233844-6233964 +		1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAACAG-----CCTAGATC---C
droSim1	chr3R:15159284-15159404 -	LASTZ	1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GCATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C
droSec1	super_0:15709450-15709570 -	LASTZ	1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GATTTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C
droYak2	chr3R:10262359-10262479 +	LASTZ	1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTC---C
droEre2	scaffold_4770:15384035-15384155 -	LASTZ	1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GAATTGTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTC---C
droEug1	scf7180000409692:710064-710184 +	LASTZ	4	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CTTA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTTGATC---C
droBia1	scf7180000302402:8322793-8322912 +	LASTZ	4	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GCATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC----
droTak1	scf7180000415380:1406182-1406305 -	LASTZ	4	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CTTAGATCATCC
droEle1	scf7180000490995:508571-508691 -	LASTZ	4	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C
droRho1	scf7180000777158:16475-16595 -	LASTZ	4	C--------------GC------GCTCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CTTAGATT---C
droFic1	scf7180000453800:2313511-2313631 +	LASTZ	4	C--------------GC------GTCCTGTATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GATTATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---C
droKik1	scf7180000302475:1425726-1425847 +	LASTZ	4	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCTC-AGAATCTTTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---T
droAna3	scaffold_13340:867356-867469 -	LASTZ	1	-----------------------------GATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCTC-GAAGTCATTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---T
droBip1	scf7180000394085:131779-131890 +	LASTZ	4	------------------------------ATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAG--AAGTCTTTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---C
dp4	chr2:7233487-7233613 -	LASTZ	1	T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAAC--ATAC--AAATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---G
droPer1	super_0:1094175-1094302 -	LASTZ	1	T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAAC--ATAA-CAAATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---G
droWil1	scaffold_181108:495-611 +	LASTZ	1	C--------------G--------ACATGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAATTATTC--AAATCTTTGACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTA--------
droVir3	scaffold_13047:1194160-1194276 +	LASTZ	1	C------------CAGC------GATTTTGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTA--GAAGCTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCT---------
droMoj3	scaffold_6540:5225156-5225284 +	LASTZ	1	AGGTCTAACGTTGAAGC------GATATCAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTT--CAACCTATTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCT---------
droGri2	scaffold_14906:5077444-5077577 -	LASTZ	1	G--------------ATGACAATGATTTACATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTTGAAACTCTCTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAACAAACCCTAACTC---C

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	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAACAG-----CCTAGATC---C
droSim1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GCATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C
droSec1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GATTTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C
droYak2	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTC---C
droEre2	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GAATTGTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTC---C
droEug1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CTTA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTTGATC---C
droBia1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GCATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC----
droTak1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CTTAGATCATCC
droEle1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C
droRho1	C--------------GC------GCTCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CTTAGATT---C
droFic1	C--------------GC------GTCCTGTATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GATTATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---C
droKik1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCTC-AGAATCTTTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---T
droAna3	-----------------------------GATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCTC-GAAGTCATTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---T
droBip1	------------------------------ATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAG--AAGTCTTTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---C
dp4	T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAAC--ATAC--AAATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---G
droPer1	T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAAC--ATAA-CAAATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---G
droWil1	C--------------G--------ACATGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAATTATTC--AAATCTTTGACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTA--------
droVir3	C------------CAGC------GATTTTGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTA--GAAGCTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCT---------
droMoj3	AGGTCTAACGTTGAAGC------GATATCAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTT--CAACCTATTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCT---------
droGri2	G--------------ATGACAATGATTTACATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTTGAAACTCTCTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAACAAACCCTAACTC---C

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

C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GCATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................................................................................TATCACAGTGGCTGTTTTTTT.......................................	21	4	4.75	0.00	0.00	0.00	4.75
.............................................................................................TATCACAGTGGCTGTTTTTTTT......................................	22	4	3.25	0.00	0.00	0.00	3.25
.............................................................................................TATCACAGTGGCTGTTTTTT........................................	20	4	2.00	0.00	0.00	0.00	2.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	4	1.25	0.25	0.00	0.00	1.00
.............................................................................................TATCACAGTTGCTGTTCTTTT.......................................	21	4	0.75	0.25	0.00	0.00	0.50
.............................................................................................TATCACAGTGGCTGGTTCTTTT......................................	22	1	2.00	0.00	0.00	0.00	2.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	1	2.00	0.00	0.00	0.00	2.00
.............................................................................................TATCACAGTTGCTGTTCGT.........................................	19	4	0.25	0.25	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGG......................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
..............................................CTAACGAAATAGTAGCCGTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TATCACAGTGGCTGTTCCTTTT......................................	22	4	0.25	0.00	0.00	0.00	0.25
.............................................................................................TATCACAGTAGCTGTTTTTTTT......................................	22	4	0.25	0.00	0.00	0.00	0.25
..............................................CTAAGGAAATAGTAGCCGTGATT....................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................ATCACAGTGGCTGTTTTTTT.......................................	20	4	0.25	0.00	0.00	0.00	0.25
.............................................................................................TATCACAGTTGCxATTTCTT........................................	19	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTCTTTTT.....................................	23	2	0.50	0.00	0.00	0.00	0.50
.............................................................................................TATCACAGTGGCTGTTTGTTT.......................................	21	4	0.25	0.25	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GATTTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	530.00	187.00	0.00	343.00
.............................................................................................TATCACAGTGGCTGTTCCTTTT......................................	22	5	62.20	0.00	61.40	0.80
.............................................................................................TATCACAGTGGCTGTTTTTTTT......................................	22	5	45.60	0.00	44.40	1.20
...............................................TAAGGAAATAGTAGCCGTGAT.....................................................................................	21	1	211.00	80.00	1.00	130.00
................................................................................................CACAGTTGCTGTTTCTTTTAGAT..................................	23	1	167.00	28.00	0.00	139.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	137.00	63.00	0.00	74.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	5	18.40	0.00	18.20	0.20
.............................................................................................TATCACAGTGGCTGTTCCTTT.......................................	21	5	14.20	0.00	14.20	0.00
.............................................................................................TATCACAGTGGCTGTTTTTTT.......................................	21	5	13.00	0.00	12.80	0.20
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	1	61.00	25.00	0.00	36.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	1	48.00	21.00	0.00	27.00
.............................................TCTAAGGAAATAGTAGCCGTGA......................................................................................	22	1	31.00	8.00	0.00	23.00
.............................................................................................TATCACAGTTGCTGTTTCTTTT......................................	22	1	21.00	3.00	0.00	18.00
.............................................................................................TATCACAGTGGCTGTTTTT.........................................	19	5	4.00	0.00	4.00	0.00
.............................................................................................TATCACAGTGGCTGTTTTTT........................................	20	5	3.80	0.00	3.80	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTT.......................................	21	5	3.40	0.00	3.40	0.00
...............................................................................................TCACAGTTGCTGTTTCTTTTAG....................................	22	1	13.00	1.00	0.00	12.00
..............................................................................................ATCACAGTTGCTGTTTCTTTTAG....................................	23	1	10.00	1.00	0.00	9.00
..............................................CTAAGGAAATAGTAGCCGTG.......................................................................................	20	1	9.00	0.00	0.00	9.00
..............................................CTAAGGAAATAGTAGCCGTGATT....................................................................................	23	1	9.00	4.00	0.00	5.00
................................................................................................CACAGTTGCTGTTTCTTTTAG....................................	21	1	8.00	1.00	0.00	7.00
...............................................................................................TCACAGTTGCTGTTTCTTTTAGA...................................	23	1	7.00	0.00	0.00	7.00
.............................................................................................TATCACAGTGGCTGTTCCTT........................................	20	5	1.40	0.00	1.40	0.00
.................................................................................................ACAGTTGCTGTTTCTTTTAGATT.................................	23	1	5.00	2.00	0.00	3.00
.............................................................................................TATCACAGTTGCTGTTCTTT........................................	20	5	1.00	0.00	1.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTT.......................................	21	1	4.00	1.00	0.00	3.00
..............................................CTAAGGAAATAGTAGCCGTGATA....................................................................................	23	1	4.00	2.00	0.00	2.00
.............................................................................................TATCACAGTGGCTGTTTT..........................................	18	5	0.80	0.00	0.80	0.00
...............................................TAAGGAAATAGTAGCCTTGATT....................................................................................	22	1	3.00	0.00	0.00	3.00
.................................................................................................ACAGTGGCTGTTCCTTTT......................................	18	5	0.60	0.00	0.60	0.00
................................................................................................CACAGTTGCTGTTTCTTTTAGA...................................	22	1	3.00	0.00	0.00	3.00
................................................................................................CACAGTTGCTGTTTCTTTTAGATT.................................	24	1	3.00	0.00	0.00	3.00
..............................................CTAAGGAAATAGTAGCCGAGAT.....................................................................................	22	1	3.00	1.00	0.00	2.00

droYak2

C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTC---C	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	168.00	0.00	16.00	83.00	55.00	14.00
...............................................TAAGGAAATAGTAGCCGTGAT.....................................................................................	21	1	120.00	0.00	15.00	63.00	30.00	12.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	76.00	0.00	4.00	50.00	16.00	6.00
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	1	20.00	0.00	2.00	9.00	7.00	2.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	1	20.00	0.00	0.00	15.00	4.00	1.00
................................................................................................CACAGTTGCTGTTTCTTTTAGAT..................................	23	1	12.00	0.00	0.00	10.00	2.00	0.00
.............................................TCTAAGGAAATAGTAGCCGTGA......................................................................................	22	1	11.00	0.00	1.00	6.00	4.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATT....................................................................................	23	1	6.00	0.00	0.00	4.00	2.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGCT.....................................................................................	22	1	3.00	0.00	0.00	0.00	2.00	1.00
.............................................................................................TATCACAGTTGCTGTTTCTTTT......................................	22	1	3.00	0.00	0.00	2.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATA....................................................................................	23	1	3.00	0.00	1.00	2.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGTT.....................................................................................	22	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................TCTAAGGAAATAGTAGCCGTG.......................................................................................	21	1	2.00	0.00	1.00	0.00	0.00	1.00
...............................................TAAGGAAATGGTAGCCGTGATT....................................................................................	22	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	8	0.25	0.25	0.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGG......................................................................................	20	1	2.00	0.00	0.00	0.00	0.00	2.00
..............................................CTAAGGAAATAGTAGCCGTGGT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATATTAGCCGTGATT....................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................TAAGGAAATAGTAGCAGTGAT.....................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTGCTT....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATTTA..................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................ATCACAGTTGCTGTTTCTTTTAG....................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATGGTAGCCGTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGCAATAGTAGCCGGGAT.....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................TAAGGAGATAGTAGCCGTGAT.....................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGGAGCCGTGTTT....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGxAATAGTAGCCGTGATT....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................................ACAGTTGCTGTTTCTTTTAGATT.................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTTTT........................................	20	8	0.13	0.13	0.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGAC.....................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................TATCACAGTTGCTGTTTTTTTT......................................	22	8	0.13	0.13	0.00	0.00	0.00	0.00
...............................................TAATGAAATAGTAGCCGTGA......................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................ATAAGGAAATACTAGCCGTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTGGGT....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAACTAGCAGCCGTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATTT...................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTT.......................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGGAGCCGTGATT....................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................TAGCACAGATGCTGTTTCT.........................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................TAAGGAAATATTAGCCGTGA......................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGAG.....................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................TAAGGAAATAGTAGCCGTGATA....................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCG.........................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.................................................................................................ACAGTTGCTGTTTCTTTTTGAT..................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TATCACAGTAGCTGTTTTTTT.......................................	21	8	0.13	0.13	0.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGCAGCCGCGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................TCTAAGGAAATAGTAGCCGTGAT.....................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTGTTT....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTTAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGGAGCCGTGAT.....................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTTTA.....................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCCTGGT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGCAATAGTAGCCGAGATT....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TATCACAGTTGTTGTTTCTTTT......................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................TATCACAGTGGCGGTTTCTTTT......................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTATCCGTGATT....................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCCTGAT.....................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTGCT.....................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATAA...................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................AGTTGCTGTTTxTTTTACA...................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGATATAGTAGCCGCGAT.....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAACCGTGAT.....................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGATATAGTAGCCGTGAG.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGGAATAGTAGCCGTGAT.....................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................CTAATGAAATAGTAGCCGTGAT.....................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................TACGGAAATAGTAGCCGTGATT....................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................TAAGGAAATAATAGCCGTGATT....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................CTAAGGGAATAGTAGCCGTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGCAAATAGTAGCCGTTA......................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGAAGCCGTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAACTAGTAGCCGTGA......................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATC....................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................CTAAGGAAATAGTAGCCTTGAC.....................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................................CACAGTTGCTGTTTCTTTTA.....................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGAGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAATTAGTAGCCGTGATT....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAACTAGTAGCCTTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCCTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGG......................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................TAAGGAAATAGCAGCCGTGAT.....................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAAGAGTAGCCGTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATCGTAGCCGTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GAATTGTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTC---C	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.............................................................................................TATCACAGTGGCTGTTTTTTTT......................................	22	5	0.80	0.80	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGAT.....................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	5	0.20	0.20	0.00	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTTTTT.......................................	21	5	0.20	0.20	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TATCACAGTGGCTGGTTCTTT.......................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTCCTTTT......................................	22	5	0.20	0.20	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
..................................................................ATTTTAC--CTAT--GATTTGTT................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TATCACAGTTTCTGTTGCTTTT......................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTCTTT.......................................	21	5	0.20	0.20	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	1	1.00	0.00	0.00	0.00	1.00

droEug1

C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CTTA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTTGATC---C

Size

Hit Count

Total Norm

droBia1

C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT--GCATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC----

Size

Hit Count

Total Norm

droTak1

C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CTTAGATCATCC

Size

Hit Count

Total Norm

droEle1

C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C

Size

Hit Count

Total Norm

droRho1

C--------------GC------GCTCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GAATATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CTTAGATT---C

Size

Hit Count

Total Norm

droFic1

C--------------GC------GTCCTGTATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA--GATTATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---C

Size

Hit Count

Total Norm

droKik1

C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCTC-AGAATCTTTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---T

Size

Hit Count

Total Norm

droAna3

-----------------------------GATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCTC-GAAGTCATTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---T	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	1	5.00	5.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGAT.....................................................................................	21	1	5.00	4.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	4.00	3.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTG.......................................................................................	20	1	3.00	3.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	1	2.00	2.00	0.00	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTTTTTT......................................	22	8	0.25	0.00	0.00	0.00	0.25
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	2.00	2.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATT....................................................................................	23	1	2.00	2.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGTT.....................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	8	0.13	0.00	0.13	0.00	0.00
................................................................................................................................................ATATT---T	18	3	0.33	0.00	0.00	0.00	0.33
.............................................TCTAAGGAAATAGTAGCCGTGA......................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGT......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................TCTAAGGAAATAGTAGCCGTAA......................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...................................................GATATGGTAGCCGTGAT.....................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATTTT..................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
................................................................................................CACAGTTGCTGTTTCTTTTAGAT..................................	23	1	1.00	0.00	1.00	0.00	0.00

droBip1

------------------------------ATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAG--AAGTCTTTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---C

Size

Hit Count

Total Norm

dp4

T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAAC--ATAC--AAATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---G	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	9.00	9.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	1	8.00	5.00	0.00	0.00	3.00
...............................................TAAGGAAATAGTAGCCGTGAT.....................................................................................	21	1	5.00	5.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	5.00	4.00	0.00	0.00	1.00
.............................................TCTAAGGAAATAGTAGCCGTGA......................................................................................	22	1	2.00	2.00	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTT.......................................	21	9	0.22	0.00	0.22	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	9	0.22	0.00	0.22	0.00	0.00
.............................................................................................TATCACAGATGCTGGTTCT.........................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................................CACAGTTGCTGTTTCTTTTAGAT..................................	23	1	1.00	0.00	1.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGT......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTTTTT.......................................	21	9	0.11	0.00	0.11	0.00	0.00
...............................................TAAGGAAATAGTAGCCGAGA......................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................TCTAAGGAAATGGTAGCCGTG.......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TATCACAGTAGCTGTTTTTT........................................	20	9	0.11	0.00	0.11	0.00	0.00
.............................................................................................TATCACAGTGGCTGTGTCTTTT......................................	22	1	1.00	0.00	1.00	0.00	0.00
.............................................TCTAAGGAAATAGTAGCCGTG.......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................................................CACAGTTGCTGGTTCTTTTAGAT..................................	23	1	1.00	0.00	1.00	0.00	0.00

droPer1

T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAAC--ATAA-CAAATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---G	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	10.00	7.00	0.00	2.00	0.00	1.00
.............................................................................................TATCACAGTGGCTGTTTTTTTT......................................	22	8	0.63	0.25	0.00	0.00	0.00	0.38
...............................................TAAGGAAATAGTAGCCGTGAT.....................................................................................	21	1	3.00	2.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	1	2.00	1.00	0.00	1.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	2.00	1.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	1	2.00	1.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGT......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATT....................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................TCTAAGGAAATACTAGCCGTG.......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGAC.....................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................TCTAAGGAAATAGTAGCCGTGA......................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTG.......................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGTT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	8	0.13	0.00	0.13	0.00	0.00	0.00
.............................................TCTAAGGGAATAGTAGCCGTGA......................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................AGTTATCTAAGGAAATGGG..............................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

C--------------G--------ACATGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAATTATTC--AAATCTTTGACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTA--------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.............................................................................................TATCACAGTGGCTGTTTTTTTT......................................	22	10	21.50	0.00	21.40	0.10	0.00
.............................................................................................TATCACAGTGGCTGTTCCTTTT......................................	22	10	21.30	0.00	21.30	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	2	102.00	42.50	5.50	1.00	53.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	10	19.40	0.00	19.40	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGAT.....................................................................................	21	2	59.00	23.50	1.00	0.00	34.50
.............................................................................................TATCACAGTGGCTGTTCCTTT.......................................	21	10	6.50	0.00	6.40	0.10	0.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	2	30.00	10.50	0.00	0.00	19.50
.............................................................................................TATCACAGTTGCTGTTCTTTT.......................................	21	10	5.40	0.00	5.40	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGAC.....................................................................................	22	2	19.50	3.50	0.00	0.00	16.00
.............................................................................................TATCACAGTGGCTGTTTTTTT.......................................	21	10	2.40	0.00	2.40	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	2	8.50	7.50	0.00	0.00	1.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	2	6.00	5.00	1.00	0.00	0.00
.............................................TCTAAGGAAATAGTAGCCGTGA......................................................................................	22	2	6.00	3.50	0.00	0.00	2.50
.............................................................................................TATCACAGTGGCTGTTTTT.........................................	19	10	1.10	0.00	1.10	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTTTT........................................	20	10	0.90	0.00	0.90	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTT........................................	20	10	0.90	0.00	0.90	0.00	0.00
................................................................................................CACAGTTGCTGTTTCTTTTAGAC..................................	23	2	4.00	0.00	0.00	0.00	4.00
................................................................................................CACAGTTGCTGTTTCTTTTAGAT..................................	23	2	3.50	1.00	1.50	1.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTTTA.....................................	23	10	0.60	0.00	0.60	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTCCTTTTA.....................................	23	10	0.50	0.00	0.50	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATT....................................................................................	23	2	2.50	1.00	0.50	0.00	1.00
.............................................................................................TATCACAGTGGCTGTTTTTTTTA.....................................	23	10	0.50	0.00	0.50	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGACT....................................................................................	23	2	2.00	0.00	0.00	0.00	2.00
...............................................TAAGGAAATAGTAGCCGTGAC.....................................................................................	21	2	2.00	0.00	0.00	0.00	2.00
.............................................TCTAAGGAAATAGTAGCCGTGG......................................................................................	22	2	1.50	0.00	0.00	0.00	1.50
..............................................CTAAGGAAATAGTAGCCGTGG......................................................................................	21	2	1.50	0.00	0.00	0.00	1.50
..............................................CTAAGGAAATAGTAGCCGTG.......................................................................................	20	2	1.50	1.00	0.00	0.50	0.00
.............................................................................................TATCACAGTGGCTGTTCCTT........................................	20	10	0.30	0.00	0.30	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGACC....................................................................................	23	2	1.00	0.00	0.00	0.00	1.00
...............................................TAAGGAAATAGTAGCCGTGATC....................................................................................	22	2	1.00	0.00	0.00	0.00	1.00
..............................................CTAAGGAAATAGTAGCCTTGAT.....................................................................................	22	2	1.00	0.50	0.00	0.00	0.50
...............................................TAAGGAAATAGTAGCCGTGG......................................................................................	20	2	1.00	0.00	0.00	0.00	1.00
..............................................CTAATGAAATAGTAGCCGTGAC.....................................................................................	22	2	1.00	0.00	0.00	0.00	1.00
.............................................................................................TATCACAGTTGCTGTTCT..........................................	18	10	0.20	0.00	0.20	0.00	0.00
.................................................................................................ACAGTGGCTGTTTTTTTT......................................	18	10	0.20	0.00	0.20	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTCTTT.......................................	21	10	0.20	0.00	0.20	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTCCT.........................................	19	10	0.20	0.00	0.20	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTT..........................................	18	10	0.20	0.00	0.20	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTCCTTT.......................................	21	10	0.10	0.00	0.10	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTCC..........................................	18	10	0.10	0.00	0.10	0.00	0.00
..............................................................................................ATCACAGTTGCTGTTTCTTTT......................................	21	2	0.50	0.50	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCCTGAC.....................................................................................	22	2	0.50	0.00	0.00	0.00	0.50
...............................................TAAGGAAATAGTAGCCGTG.......................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATC....................................................................................	23	2	0.50	0.00	0.00	0.00	0.50
..............................................CTAAGGAAATAGTAGCCGTGAG.....................................................................................	22	2	0.50	0.00	0.00	0.00	0.50
..............................................CTAAGGAAATAGTAGCCG.........................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
...............................................................................................TCACAGTTGCTGTTTCTTTTAG....................................	22	2	0.50	0.50	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTT.......................................	21	2	0.50	0.50	0.00	0.00	0.00
...............................................TAGGGAAATAGTAGCCGTGAT.....................................................................................	21	2	0.50	0.00	0.00	0.00	0.50
.............................................TCTAAGGAAATAGTAGCCGTGAT.....................................................................................	23	2	0.50	0.00	0.00	0.00	0.50
..............................................CTAAGGAAATAGTAGCCGGGAT.....................................................................................	22	2	0.50	0.00	0.00	0.00	0.50
...............................................TAAGGAAATAGGAGCCGTGAT.....................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATTTTAAT...............................................................................	27	2	0.50	0.50	0.00	0.00	0.00
................................................................................................CACAGATGCTGTTTCTTTTAGAT..................................	23	2	0.50	0.00	0.00	0.50	0.00
.............................................................................................TATCACAGTGGCTGGTTCTTT.......................................	21	2	0.50	0.00	0.50	0.00	0.00
..............................................TTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTTTA.....................................	23	2	0.50	0.50	0.00	0.00	0.00
..............................................................................................ATCACAGTGGCTGTTTTTTTT......................................	21	10	0.10	0.00	0.10	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATTG...................................................................................	23	2	0.50	0.50	0.00	0.00	0.00
...............................................TAACGAAATAGTAGCCGTGATT....................................................................................	22	2	0.50	0.00	0.00	0.00	0.50
..............................................CTAAGGAAATAGTAGCCGTGGT.....................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
..............................................CTAAGGAAATATTAGCCGTGAT.....................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCTTGATT....................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
..............................................CTAAGGAAATATTAGCCGTGAC.....................................................................................	22	2	0.50	0.00	0.00	0.00	0.50
..............................................CTAAGGAAATAGTAGCTGTGAT.....................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGxTTCTTTTAA....................................	23	2	0.50	0.00	0.50	0.00	0.00
...............................................TAAGGAAATAATAGCCGTGATT....................................................................................	22	2	0.50	0.00	0.00	0.00	0.50
.............................................TCTAAGGACATAGTAGCCGTGA......................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTTT......................................	22	2	0.50	0.50	0.00	0.00	0.00
................................................AAGGAAATAGTAGCCGTGATTT...................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
.............................................TCTAAGGAAATAGCAGCCGTGA......................................................................................	22	2	0.50	0.50	0.00	0.00	0.00

droVir3

C------------CAGC------GATTTTGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTA--GAAGCTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCT---------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	40.00	3.00	21.00	1.00	1.00	14.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	13.00	0.00	6.00	0.00	1.00	6.00
...............................................TAAGGAAATAGTAGCCGTGAT.....................................................................................	21	1	11.00	0.00	7.00	0.00	0.00	4.00
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	1	10.00	0.00	7.00	1.00	0.00	2.00
.............................................TCTAAGGAAATAGTAGCCGTGA......................................................................................	22	1	3.00	0.00	2.00	0.00	0.00	1.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	1	2.00	0.00	2.00	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTTT......................................	22	1	2.00	0.00	2.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGGAGCCGTGAT.....................................................................................	22	1	2.00	0.00	2.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCG.........................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................CTAAGGAAATAGTAGCCGTG.......................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGAAT....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................TCTAAGGAAATAGTAGCCGTG.......................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGG......................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................CACAGTTGCTGTTTCTTTTAG....................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGACC....................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCGGTGCTT....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................................TCACAGTTGCTGTTTCTTTTAG....................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	8	0.13	0.00	0.00	0.13	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTT.......................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................TATCACAGAGGCTGTTTCT.........................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................TATCACAGTGGCTGTTTTTTTT......................................	22	8	0.13	0.00	0.00	0.13	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATAA...................................................................................	24	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

AGGTCTAACGTTGAAGC------GATATCAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTT--CAACCTATTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCT---------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	331.00	324.00	2.00	3.00	2.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	128.00	123.00	4.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTGAT.....................................................................................	21	1	90.00	88.00	1.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGA......................................................................................	21	1	61.00	59.00	2.00	0.00	0.00
.............................................TCTAAGGAAATAGTAGCCGTGA......................................................................................	22	1	60.00	58.00	2.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGA......................................................................................	20	1	46.00	44.00	1.00	0.00	1.00
..............................................CTAAGGAAATAGTAGCCGTGATT....................................................................................	23	1	19.00	19.00	0.00	0.00	0.00
................................................................................................CACAGTTGCTGTTTCTTTTAGAT..................................	23	1	13.00	11.00	0.00	0.00	2.00
.............................................TCTAAGGAAATAGTAGCCGTG.......................................................................................	21	1	4.00	4.00	0.00	0.00	0.00
...............................................................................................TCACAGTTGCTGTTTCTTTTAG....................................	22	1	4.00	4.00	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTTT......................................	22	1	3.00	3.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATTT...................................................................................	24	1	3.00	3.00	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTTT.......................................	21	1	3.00	3.00	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTTCTT........................................	20	1	2.00	2.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATC....................................................................................	23	1	2.00	2.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATTT...................................................................................	23	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................ATCACAGTTGCTGTTTCTTTTAG....................................	23	1	2.00	1.00	0.00	0.00	1.00
..............................................CTAAGGAAATAGTAGCCGTGAC.....................................................................................	22	1	2.00	2.00	0.00	0.00	0.00
................................................................................................CACAGTTGCTGTTTCTTTTAG....................................	21	1	2.00	1.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTG.......................................................................................	19	1	2.00	1.00	0.00	1.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATC....................................................................................	22	1	2.00	1.00	1.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATTC...................................................................................	24	1	2.00	2.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTG.......................................................................................	20	1	2.00	2.00	0.00	0.00	0.00
...............................................CAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAATAGCCGTGAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGxAATAGTAGCCGTGAT.....................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................TCTAAGGAAATAGTAGCCGT........................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................TGAGGAAATAGTAGCCGTGATT....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................TCTAAGGAAATAGTAGCCGTGAA.....................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................TCACAGTTGCTGTTTCTTTTAGA...................................	23	1	1.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGACT....................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTATCCGTGAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................TCTAAGGAAGTAGTAGCCGTG.......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGAAGCCGTGA......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................ACAGTTGCTGTTTCTTTTAGATT.................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATA....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGCAGCCGTGAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGCTTTTTT.......................................	21	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................TCACAGTTGCTGTTTCTTTT......................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTTTA.....................................	23	4	0.25	0.00	0.00	0.00	0.25
...............................................TAAGGACATAGTAGCCGTGAT.....................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................AAAGGAAATAGTAGCCGTGAT.....................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................................CACAGTTGCTGTATCTTTTAGATT.................................	24	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTCCTTCT......................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................TAAGGAAATAGTAGCCGCGAT.....................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTAAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTTGCCGTGAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................TAAGGAAATATTAGCCGTGAT.....................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAACCGTGAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAGTAGTAGCCGTGATA....................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGCAAATAGTAGCCATGAT.....................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................TAAGAAAATAGTAGCCGTGATT....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGCT.....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGGGAT.....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TATCACTGTTGCTGTCTCTTTT......................................	22	1	1.00	0.00	0.00	0.00	1.00
.GTTCGAACGTTGAAGC------GA................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..............................................CTAAGGAAGTAGTAGCCGTGA......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCTTGAT.....................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATGGTAGCCGTGAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................TATCACAGTTGCTGTTCTTTTT......................................	22	4	0.25	0.00	0.00	0.00	0.25
.............................................................................................TATCACAGTTGCTGxCTCTTTTA.....................................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................CTAAGGAAATAGTAGCCGTGT......................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................TTTAAGGAAATAGTAGCCGTGA......................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTACCCGTGAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCGTGATG....................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCCTGA......................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................CAAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................CTAAGGAAATAGTAGCCTTGAT.....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................TCACAGTTGCTGTTTCTTTTCG....................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................TAATGAAATAGTAGCCGTGATT....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................ATCACAGTTGCTGTTTCTTTT......................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................TAAGGAAATAGTAGCCGTGATTTC..................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
.GTTCGAACGTTGAAGC------GAT...............................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................ATCACAGTTGCTGTTTCTTTTA.....................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................TAAGGAAGTAGTAGCCGTGATT....................................................................................	22	1	1.00	1.00	0.00	0.00	0.00

droGri2

G--------------ATGACAATGATTTACATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTTGAAACTCTCTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAACAAACCCTAACTC---C	Size	Hit Count	Total Norm	V109 Male body
..............................................CTAAGGAAATAGTAGCCGTGAT.....................................................................................	22	1	1.00	1.00
...............................................TAAGGAAATAGTAGCCGTGATT....................................................................................	22	1	1.00	1.00

Generated: 04/20/2012 at 05:19:43 EDT

dme-mir-994

chr3R:6233859-6233949 +

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