dme-mir-312- Best orthologs

dme-mir-312	chr2R:16471561-16471626 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 16471563-16471584
   star strand at position 16471600-16471622
   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	chr2R:16471546-16471641 -		1	AATTAAG----TT-------TGAA-GCGATTTGGTTCGTCACAAG-GGCAATTCTGCATT----TTTTAACTAGTATTGCACTTGAGACGGCCTGATTACTTTAAA-AC-GAATC------------------------------------------
droSim1	chr2R:15132834-15132929 -	LASTZ	1	AATTAAG----TT-------TAAA-GCGTTTTGGTTCGTCACAAG-GGCAATTCTGCATT----TTTAAACTTGTATTGCACTTGAGACGGCCGAATTACTTTAAA-AA-GAATC------------------------------------------
droSec1	super_1:14025748-14025843 -	LASTZ	1	AATTAAG----TT-------TAAA-GCGTTTTGGTTCGTCACAAG-GGCAATTCTGCATT----TTTAAACTTGTATTGCACTTGAGACGGCCGAATTACTTTAAA-AA-GAATC------------------------------------------
droYak2	chr2R:12724685-12724781 +	LASTZ	1	AATTGCG----TT-------TGAA-GCGCTTCGGTTCGTCCCAGG-AGCAATTCTGCACTA---TTAAAGCTAGTATTGCACTTGAGACGGCCGGATTACTTTTAA-AC-GAATC------------------------------------------
droEre2	scaffold_4845:10618147-10618242 -	LASTZ	1	AATTAAG----TT-------TGAA-GCGCTTCGGTTCGTACCAGG-AGCAATTCTGCATT----TTTAAGCTAGTATTGCACTTGAGACGGCCGGATTACTTTTAA-AC-AAAAC------------------------------------------
droEug1	scf7180000409474:1490038-1490133 +	LASTZ	4	AAATAAA---ATT-------TCTA-GTATTTCGGTTCGCCTTTTG-TGCAATTTTAGAGT------CAATAGAAAATTGCACTTCAGACGGCCGGATGACTTGAAATAC-AAAAC------------------------------------------
droBia1	scf7180000302291:2816211-2816324 +	LASTZ	4	ATATAGGCATATT-------TTTG-GCGTTTCGGTCCGTCCCAGG-AGCAATCCTGTATT-----TCCGACTAGAATTGCACTTGAGACGGCCGGAGTGCTTGAAA-AC-AAGGA--------AAGTGCATAG-----AA--------------ACT
droTak1	scf7180000415401:99973-100067 -	LASTZ	4	AACA-TA----TT-------TCTG-GTGTTCCGGTCCGTCTCAGG-CGCAATTCTGAATT-----TTCACCTAGTATTGCACTTGAGACGGCCGGAATACTTTAAATAC-GAAAC------------------------------------------
droEle1	scf7180000491201:736234-736328 -	LASTZ	4	TACTAA-----TT-------TCTG-GTGTTTCGGTACGTCTATGG-GGCAATTCTGCGTT----TTCTGGTTAGCATTGCACTTGAGACGGCCGCAACACTTTGGA-AT-AAAAA------------------------------------------
droRho1	scf7180000780104:82286-82421 -	LASTZ	4	GAACAAA----TT-------TCTG-GTGTTTCGGCTCGTCTCAAA-AGCAATTCTTCGTTT--TTCTTGGCTAGCATTGCACTTGAGACGGCCGCAATACTTTGGATTT-AAAACATTTAAGCAAGTTTATTG-----AAAAAGTTATTTTTGCATT
droFic1	scf7180000454039:1776269-1776366 -	LASTZ	4	AAACCAA----TT-------TCGA-GTGTTTCGGT-CGTCTTGGGTGGCAATACTAAATTAACTTTATGGCTAGCATTGCACTTGAGACGGCCGAAATGCTTTAAA-TT-TA--T------------------------------------------
droKik1	scf7180000302471:941817-941912 -	LASTZ	4	AGCTCCG----GC-------CGTA-AAGGTCTGTGCTGTTTGAGG-TGCAAATCTGTGGT----TAATAGCCAGAATTGCACTTGAAACGGCCAGATCAAGGCGGC-CC-AAAAC------------------------------------------
droAna3	scaffold_13266:4132676-4132765 +	LASTZ	1	TCTAC------------------A-ATTTTCCGGTGCGTCTCTAG-TGCAACTCTTGGTTT---TTTATACAAGTATTGCACTTGAGACGGCCGAAATATAGTGGA-TC-TAAGC------------------------------------------
droBip1	scf7180000396427:2575386-2575498 +	LASTZ	4	ATTTATG----TC-------TACA-ATTTTCGGGGTCATCTCCAG-TGCAAATCTTGGTTT---TTCCAACAAGAATTGCACTCGAGACGGCCAGAATATTGTGGA-TC-TATGC--------AGCTAC----AAGCCGA--------------AAG
dp4	chr3:8679756-8679828 +	LASTZ	1	GG---------------------------------------------GCAATACTGTGTTG--TATTTCACCAGTATTGCACACCCACTGGCCTGAAAGTGCCTACTG-------------------CT----GGGTTCA--------------ACA
droPer1	super_4:2566584-2566654 +	LASTZ	1	ATTAGTG----TACAAGCGGAAGGGTGCATCGAGCTGCTTTGATT----------------------------------------TGTAGGCCGTGGTTCTTGCAA-ATACGAAT------------------------------------------
droWil1	scaffold_180700:3453141-3453235 +	MAF	1	CATAAAC----TC-------GAAAATTTTTTAGGTTCGTTTAGTC-TGCAAATTGTAA-T----ATACGAAAATAATTGCACACTTCACGGCCGGAAAAGTTCAAG-TT-AAACA------------------------------------------
droVir3	scaffold_12875:13669041-13669063 -	MAF	0	AGCTATA----TT-------TTT-------------------------------------------------------------------------------CAGG-CC-GTGTC------------------------------------------
droMoj3	scaffold_6496:9090603-9090622 -	MAF	0	GTCTGCA----AT-------TTAA-GCTTCTT-----------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15245:17564268-17564358 +	LASTZ	1	AAGCAAA----TC-------TTCA-GTTTTTCGGCTGTGGTTAGT-GTCAATTCTTTTT-----ATTTGACAAGCATTGCACTCTTCACGGCCGGATAAATGAGGG------TCT------------------------------------------

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	AATTAAG----TT-------TGAA-GCGATTTGGTTCGTCACAAG-GGCAATTCTGCATT----TTTTAACTAGTATTGCACTTGAGACGGCCTGATTACTTTAAA-AC-GAATC------------------------------------------
droSim1	AATTAAG----TT-------TAAA-GCGTTTTGGTTCGTCACAAG-GGCAATTCTGCATT----TTTAAACTTGTATTGCACTTGAGACGGCCGAATTACTTTAAA-AA-GAATC------------------------------------------
droSec1	AATTAAG----TT-------TAAA-GCGTTTTGGTTCGTCACAAG-GGCAATTCTGCATT----TTTAAACTTGTATTGCACTTGAGACGGCCGAATTACTTTAAA-AA-GAATC------------------------------------------
droYak2	AATTGCG----TT-------TGAA-GCGCTTCGGTTCGTCCCAGG-AGCAATTCTGCACTA---TTAAAGCTAGTATTGCACTTGAGACGGCCGGATTACTTTTAA-AC-GAATC------------------------------------------
droEre2	AATTAAG----TT-------TGAA-GCGCTTCGGTTCGTACCAGG-AGCAATTCTGCATT----TTTAAGCTAGTATTGCACTTGAGACGGCCGGATTACTTTTAA-AC-AAAAC------------------------------------------
droEug1	AAATAAA---ATT-------TCTA-GTATTTCGGTTCGCCTTTTG-TGCAATTTTAGAGT------CAATAGAAAATTGCACTTCAGACGGCCGGATGACTTGAAATAC-AAAAC------------------------------------------
droBia1	ATATAGGCATATT-------TTTG-GCGTTTCGGTCCGTCCCAGG-AGCAATCCTGTATT-----TCCGACTAGAATTGCACTTGAGACGGCCGGAGTGCTTGAAA-AC-AAGGA--------AAGTGCATAG-----AA--------------ACT
droTak1	AACA-TA----TT-------TCTG-GTGTTCCGGTCCGTCTCAGG-CGCAATTCTGAATT-----TTCACCTAGTATTGCACTTGAGACGGCCGGAATACTTTAAATAC-GAAAC------------------------------------------
droEle1	TACTAA-----TT-------TCTG-GTGTTTCGGTACGTCTATGG-GGCAATTCTGCGTT----TTCTGGTTAGCATTGCACTTGAGACGGCCGCAACACTTTGGA-AT-AAAAA------------------------------------------
droRho1	GAACAAA----TT-------TCTG-GTGTTTCGGCTCGTCTCAAA-AGCAATTCTTCGTTT--TTCTTGGCTAGCATTGCACTTGAGACGGCCGCAATACTTTGGATTT-AAAACATTTAAGCAAGTTTATTG-----AAAAAGTTATTTTTGCATT
droFic1	AAACCAA----TT-------TCGA-GTGTTTCGGT-CGTCTTGGGTGGCAATACTAAATTAACTTTATGGCTAGCATTGCACTTGAGACGGCCGAAATGCTTTAAA-TT-TA--T------------------------------------------
droKik1	AGCTCCG----GC-------CGTA-AAGGTCTGTGCTGTTTGAGG-TGCAAATCTGTGGT----TAATAGCCAGAATTGCACTTGAAACGGCCAGATCAAGGCGGC-CC-AAAAC------------------------------------------
droAna3	TCTA------------------CA-ATTTTCCGGTGCGTCTCTAG-TGCAACTCTTGGTTT---TTTATACAAGTATTGCACTTGAGACGGCCGAAATATAGTGGA-TC-TAAGC------------------------------------------
droBip1	ATTTATG----TC-------TACA-ATTTTCGGGGTCATCTCCAG-TGCAAATCTTGGTTT---TTCCAACAAGAATTGCACTCGAGACGGCCAGAATATTGTGGA-TC-TATGC--------AGCTAC----AAGCCGA--------------AAG
dp4	GG---------------------------------------------GCAATACTGTGTTG--TATTTCACCAGTATTGCACACCCACTGGCCTGAAAGTGCCTACTG-------------------CT----GGGTTCA--------------ACA
droPer1	ATTAGTG----TACAAGCGGAAGGGTGCATCGAGCTGCTTTGATT----------------------------------------TGTAGGCCGTGGTTCTTGCAA-ATACGAAT------------------------------------------
droWil1	CATAAAC----TC-------GAAAATTTTTTAGGTTCGTTTAGTC-TGCAAATTGTAA-T----ATACGAAAATAATTGCACACTTCACGGCCGGAAAAGTTCAAG-TT-AAACA------------------------------------------
droGri2	AAGCAAA----TC-------TTCA-GTTTTTCGGCTGTGGTTAGT-GTCAATTCTTTTT-----ATTTGACAAGCATTGCACTCTTCACGGCCGGATAAATGAGGG------TCT------------------------------------------

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image																		None
UNAFold Image																		None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

AATTAAG----TT-------TAAA-GCGTTTTGGTTCGTCACAAG-GGCAATTCTGCATT----TTTAAACTTGTATTGCACTTGAGACGGCCGAATTACTTTAAA-AA-GAATC------------------------------------------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................TATTGCACTTGAGACGGCCG...............................................................	20	2	1124.50	95.00	3.50	279.50	746.50
..........................................................................TATTGCACTTGAGACGGCCGA..............................................................	21	2	1113.00	726.50	0.00	58.00	328.50
..........................................................................TATTGCACTTGAGACGGCCGAAA............................................................	23	2	439.00	283.50	0.00	4.00	151.50
..........................................................................TATTGCACTTGAGACGGCCGAA.............................................................	22	2	425.50	269.50	1.00	17.00	138.00
..........................................................................TATTGCACTTGAGACGGCCGAAAA...........................................................	24	2	105.50	78.50	0.00	0.00	27.00
..........................................................................TATTGCACTTGAGACGGCCGG..............................................................	21	2	72.00	6.00	1.50	7.00	57.50
...............................TGGTTCGTCACAAG-GGCAATTC.......................................................................................................	22	2	39.50	39.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCC................................................................	19	2	29.50	6.00	0.00	8.00	15.50
..........................................................................TATTGCACTTGAGACGGCCGAAT............................................................	23	2	25.50	17.50	0.00	1.50	6.50
...............................TGGTTCGTCACAAG-GGCAATTCT......................................................................................................	23	2	25.00	25.00	0.00	0.00	0.00
...............................TGGTTCGTCACAAG-GGCAATT........................................................................................................	21	2	21.50	19.50	0.00	0.50	1.50
..........................................................................TATTGCACTTGAGACGGCCGAAC............................................................	23	2	21.50	3.50	0.00	1.00	17.00
..........................................................................TATTGCACTTGAGACGGCCGCA.............................................................	22	2	20.50	20.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGCAA............................................................	23	2	15.50	15.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAT.............................................................	22	2	14.50	10.00	0.00	2.50	2.00
..........................................................................TATTGCACTTGAGACGGCCGT..............................................................	21	2	13.00	8.50	0.00	3.50	1.00
..........................................................................TATTGCACTTGAGACGGCCGAAAAA..........................................................	25	2	11.50	11.00	0.00	0.00	0.50
..........................................................................TATTGCACTTGAGACGGCCT...............................................................	20	2	11.50	0.00	0.00	10.50	1.00
..........................................................................TATTGCACTTGAGACGGCCGAC.............................................................	22	2	11.50	2.00	1.50	2.50	5.50
..........................................................................TATTGCACTTGAGACGGCCGC..............................................................	21	2	8.50	8.00	0.00	0.00	0.50
..........................................................................TATTGCACTTGAGACGGCCGGA.............................................................	22	2	7.00	7.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAAG............................................................	23	2	6.50	3.50	0.00	0.00	3.00
..........................................................................TATTTCACTTGAGACGGCCGA..............................................................	21	2	6.50	0.00	0.00	0.50	6.00
..........................................................................TATTGCACTTGAGACGGCCGATA............................................................	23	2	5.50	5.00	0.00	0.50	0.00
..........................................................................TATTGCACTTGAGACGGCCGACA............................................................	23	2	5.50	5.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAAAT...........................................................	24	2	4.50	1.50	0.00	0.00	3.00
...........................................................................ATTGCACTTGAGACGGCCGAA.............................................................	21	2	4.50	3.50	0.00	0.00	1.00
..........................................................................TATTGCACTTGAGACGGC.................................................................	18	2	4.00	0.50	0.00	1.50	2.00
..........................................................................TATTGCACTTGAGACGGCCGAG.............................................................	22	2	4.00	1.50	0.00	0.00	2.50
...........................................................................ATTGCACTTGAGACGGCCGA..............................................................	20	2	4.00	2.00	0.00	0.00	2.00
..........................................................................TATTGCACTTGAGACGGCCC...............................................................	20	2	4.00	0.00	0.00	2.00	2.00
..........................................................................TATTCCACTTGAGACGGCCGA..............................................................	21	2	3.50	0.50	0.00	0.00	3.00
..........................................................................TATTGCACTTGAGTCGGCCGA..............................................................	21	2	3.50	3.50	0.00	0.00	0.00
...............................TGGTTCGTCACAAG-GGCAAT.........................................................................................................	20	2	3.00	2.50	0.00	0.50	0.00
..........................................................................TATTGCACTTGAGACGGCCGGAA............................................................	23	2	3.00	3.00	0.00	0.00	0.00
...............................TGGTTCGTCACAAG-GGCAA..........................................................................................................	19	2	2.50	2.00	0.00	0.50	0.00
..........................................................................TATTGCACTTGAGACGGCCA...............................................................	20	2	2.50	0.50	0.00	0.50	1.50
..........................................................................TATTGCACTTGAGGCGGCCGA..............................................................	21	2	2.50	1.00	0.00	0.00	1.50
..........................................................................TATTGCACTTGCGACGGCCGA..............................................................	21	2	2.50	2.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGCGACGGCCGAAA............................................................	23	2	2.50	2.50	0.00	0.00	0.00
...............................TGGTTCGTCACAAG-GGCAATTCTGC....................................................................................................	25	2	2.50	2.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGTAA............................................................	23	2	2.50	2.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGGCGA..............................................................	21	2	2.50	2.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGACGAAA............................................................	23	2	2.00	2.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGACGAA.............................................................	22	2	2.00	2.00	0.00	0.00	0.00
..........................................................................TATTGCACTTTAGACGGCCGA..............................................................	21	2	2.00	0.50	0.00	0.00	1.50
..........................................................................TATTGCACTTGAGACGGCCGTT.............................................................	22	2	2.00	0.50	0.00	1.00	0.50
..........................................................................TATTGCACTTGAGACGGCCGACT............................................................	23	2	2.00	0.50	0.00	1.50	0.00
...........................................................................ATTGCACTTGAGACGGCCGAAA............................................................	22	2	2.00	2.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGCGACGGCCGAA.............................................................	22	2	2.00	2.00	0.00	0.00	0.00
..................................TTCGTCACAAG-GGCAATTCT......................................................................................................	20	2	2.00	0.00	0.00	0.00	2.00
..........................................................................TATTGCACTTGAGACGGCTG...............................................................	20	2	2.00	0.00	0.00	0.50	1.50
...............................TGGTTCGTCACAAG-GGCAATTA.......................................................................................................	22	2	2.00	2.00	0.00	0.00	0.00
...............................TTGTTCGTCACAAG-GGCAATT........................................................................................................	21	2	2.00	0.00	0.00	1.00	1.00
..........................................................................TATTGCACTTGAGACGGCCGATT............................................................	23	2	2.00	2.00	0.00	0.00	0.00
.........................................................................CTATTGCACTTGAGACGGCCGA..............................................................	22	2	2.00	1.50	0.00	0.50	0.00
..........................................................................TATTGCACTTGAGCCGGCCGAAA............................................................	23	2	2.00	2.00	0.00	0.00	0.00
..........................................................................TAGTGCACTTGAGACGGCCGA..............................................................	21	2	2.00	2.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGGGACGGCCGA..............................................................	21	2	2.00	1.50	0.00	0.00	0.50
..........................................................................TATTGCACTTGAGACGGCCGTA.............................................................	22	2	2.00	2.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCTGA..............................................................	21	2	2.00	2.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGAAGGCCGA..............................................................	21	2	2.00	2.00	0.00	0.00	0.00
..........................................................................TATCGCACTTGAGACGGCCG...............................................................	20	2	2.00	0.00	0.00	0.00	2.00
..........................................................................TATTGAACTTGAGACGGCCGA..............................................................	21	2	2.00	2.00	0.00	0.00	0.00
...........................................................................ATTGCACTTGAGACGGCCG...............................................................	19	2	1.50	0.00	0.00	1.00	0.50
..........................................................................TATTGCACTTGAGACGGCCGAAAC...........................................................	24	2	1.50	0.00	0.00	0.00	1.50
..........................................................................TATTGCACTTGAGGCGGCCG...............................................................	20	2	1.50	0.00	0.00	0.50	1.00
..........................................................................TATTGCACTTGAGACGGCCAA..............................................................	21	2	1.50	1.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACTGCCGAA.............................................................	22	2	1.50	0.50	0.00	0.50	0.50
..........................................................................TACTGCACTTGAGACGGCCGAAA............................................................	23	2	1.50	1.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCAGA..............................................................	21	2	1.50	1.00	0.00	0.00	0.50
..........................................................................TATTGTACTTGAGACGGCCG...............................................................	20	2	1.50	0.00	0.00	0.00	1.50
..........................................................................TATTGCACTTGACACGGCCGA..............................................................	21	2	1.50	0.50	0.00	0.00	1.00
..........................................................................TATTGCACTTGAGCCGGCCTA..............................................................	21	2	1.50	1.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGGGACGGCCG...............................................................	20	2	1.50	0.00	0.00	0.50	1.00
..........................................................................TAGTGCACTTGAGACGGCCGAAA............................................................	23	2	1.50	1.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGCCGGCCGA..............................................................	21	2	1.50	1.50	0.00	0.00	0.00
...............................TGGTTCGTCACAAG-GGCAATTCA......................................................................................................	23	2	1.50	1.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGTCGA..............................................................	21	2	1.50	1.50	0.00	0.00	0.00
..........................................................................TACTGCACTTGAGACGGCCGAA.............................................................	22	2	1.50	1.00	0.00	0.00	0.50
..........................................................................TATTGCACTTGAGACGGACGA..............................................................	21	2	1.50	1.50	0.00	0.00	0.00
..........................................................................TATTGCACTTCAGACGGCCGA..............................................................	21	2	1.50	0.50	0.00	0.00	1.00
..........................................................................TCTTGCACTTGAGACGGCCGAA.............................................................	22	2	1.50	1.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAAACA..........................................................	25	2	1.50	1.00	0.00	0.00	0.50

droSec1

AATTAAG----TT-------TAAA-GCGTTTTGGTTCGTCACAAG-GGCAATTCTGCATT----TTTAAACTTGTATTGCACTTGAGACGGCCGAATTACTTTAAA-AA-GAATC------------------------------------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................................................TATTGCACTTGAGACGGCCGA..............................................................	21	4	622.00	80.25	490.75	51.00
..........................................................................TATTGCACTTGAGACGGCCGAA.............................................................	22	4	326.75	50.00	240.00	36.75
..........................................................................TATTGCACTTGAGACGGCCGAAA............................................................	23	4	295.75	17.25	251.50	27.00
..........................................................................TATTGCACTTGAGACGGCCGAAAA...........................................................	24	4	93.25	5.50	80.25	7.50
..........................................................................TATTGCACTTGAGACGGCCG...............................................................	20	4	70.50	11.00	54.75	4.75
...............................TGGTTCGTCACAAG-GGCAATT........................................................................................................	21	4	49.00	12.75	32.25	4.00
...............................TGGTTCGTCACAAG-GGCAATTCT......................................................................................................	23	4	48.50	12.50	28.50	7.50
...............................TGGTTCGTCACAAG-GGCAATTC.......................................................................................................	22	4	47.25	12.00	30.50	4.75
..........................................................................TATTGCACTTGAGACGGCCGAAT............................................................	23	4	41.75	20.50	20.25	1.00
..........................................................................TATTGCACTTGAGACGGCCGAT.............................................................	22	4	38.25	17.00	18.50	2.75
..........................................................................TATTGCACTTGAGACGGCCGAAAAA..........................................................	25	4	19.50	1.00	16.50	2.00
...............................TGGTTCGTCACAAG-GGCAAT.........................................................................................................	20	4	19.25	6.25	12.50	0.50
..........................................................................TATTGCACTTGAGACGGCCGATA............................................................	23	4	15.50	8.50	5.50	1.50
..........................................................................TATTGCACTTGAGACGGCCGATT............................................................	23	4	8.75	7.75	0.75	0.25
..........................................................................TATTGCACTTGAGACGGCCGT..............................................................	21	4	8.25	3.50	4.00	0.75
..........................................................................TATTGCACTTGAGACGGCCGAAAT...........................................................	24	4	8.25	5.00	2.75	0.50
...............................TGGTTCGTCACAAG-GGCAATTCTGCA...................................................................................................	26	4	5.50	2.25	2.00	1.25
..........................................................................TATTGCACTTGAGACGGC.................................................................	18	4	5.00	0.00	4.00	1.00
...............................TGGTTCGTCACAAG-GGCAA..........................................................................................................	19	4	5.00	2.50	2.25	0.25
..........................................................................TATTGCACTTGAGACGGCCGAAG............................................................	23	4	4.50	0.50	4.00	0.00
...............................TGGTTCGTCACAAG-GGCAATTT.......................................................................................................	22	4	4.50	3.50	1.00	0.00
..........................................................................TATTGCACTTGAGACGGCC................................................................	19	4	4.25	0.75	2.75	0.75
..........................................................................TATTGCACTTGAGACGGCCGATAT...........................................................	24	4	4.25	3.75	0.25	0.25
..........................................................................TATTGCACTTGAGACGGCCGAAC............................................................	23	4	3.75	1.00	2.25	0.50
...............................TGGTTCGTCACAAG-GGCAATTCA......................................................................................................	23	4	3.50	0.25	2.75	0.50
...........................................................................ATTGCACTTGAGACGGCCGA..............................................................	20	4	3.25	0.50	2.25	0.50
...........................................................................ATTGCACTTGAGACGGCCGAAA............................................................	22	4	3.00	0.25	2.00	0.75
..........................................................................TATTGCACTTGAGACGGCCGTT.............................................................	22	4	2.75	1.00	1.25	0.50
..........................................................................TATTGCACTTGAGATGGCCGA..............................................................	21	4	2.75	0.25	2.50	0.00
..........................................................................TATTGCACTTGAGACGGCCGAC.............................................................	22	4	2.75	0.50	2.25	0.00
..........................................................................TATTGCACTTGAGACGGCCGATTT...........................................................	24	4	2.75	2.50	0.25	0.00
...........................................................................ATTGCACTTGAGACGGCCGAA.............................................................	21	4	2.50	0.50	2.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGTTT............................................................	23	4	2.50	2.25	0.00	0.25
..........................................................................TATTGCACTTGAGACGGCCGAATT...........................................................	24	4	2.50	2.25	0.00	0.25
..........................................................................TATTGCACTTGAGATGGCCGAA.............................................................	22	4	2.25	0.00	2.00	0.25
..........................................................................TATTGTACTTGAGACGGCCGA..............................................................	21	4	2.25	0.00	2.25	0.00
..........................................................................TATTGCACTTGAGGCGGCCGA..............................................................	21	4	2.00	0.25	1.75	0.00
..........................................................................TATTGCACTTGAGACGGCCGAG.............................................................	22	4	2.00	0.50	1.25	0.25
............................................................................TTGCACTTGAGACGGCCGA..............................................................	19	4	2.00	0.00	2.00	0.00
..........................................................................TATTGCATTTGAGACGGCCGAA.............................................................	22	4	2.00	0.25	1.75	0.00
...........................................................................ATTGCACTTGAGACGGCCGAAT............................................................	22	4	2.00	1.00	0.75	0.25
..........................................................................TATTGCACTTGAGCCGGCCGA..............................................................	21	4	1.75	0.75	1.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGTA.............................................................	22	4	1.75	1.25	0.50	0.00
..........................................................................TATTGCACTTGAGACGGCCGACA............................................................	23	4	1.75	0.00	1.50	0.25
..........................................................................TATTGCACTTGAGACGGCCTGA.............................................................	22	4	1.75	0.00	1.75	0.00
..........................................................................TATTGCACTTGAGACGGCTGA..............................................................	21	4	1.75	1.00	0.75	0.00
..........................................................................TATTGCACCTGAGACGGCCGA..............................................................	21	4	1.50	0.00	1.50	0.00
..........................................................................TATTGCATTTGAGACGGCCGA..............................................................	21	4	1.50	0.00	1.50	0.00
...............................TGGTTCGTCACAAG-GGCAATTA.......................................................................................................	22	4	1.50	0.75	0.75	0.00
..........................................................................TATTGCACTTGAGACAGCCGAA.............................................................	22	4	1.50	0.00	1.25	0.25
..........................................................................TATTGCACTTGAGAAGGCCGAAA............................................................	23	4	1.50	0.25	1.25	0.00
..........................................................................TATTGCACTTGAGAAGGCCGA..............................................................	21	4	1.50	0.00	1.25	0.25
..........................................................................TCTTGCACTTGAGACGGCCGA..............................................................	21	4	1.25	0.00	1.00	0.25
..........................................................................TATTGCACTTGAGACGGTT................................................................	19	4	1.25	1.25	0.00	0.00
...............................TGGTTTGTCACAAG-GGCAATT........................................................................................................	21	4	1.25	0.00	1.25	0.00
..........................................................................TATTGCACTTGAGACGGCCTAAA............................................................	23	4	1.25	0.00	0.75	0.50
..........................................................................TATTGCACTTGAGACGGCCGAATTT..........................................................	25	4	1.25	1.25	0.00	0.00
..........................................................................TATTGCACTTGAGACGACCGA..............................................................	21	4	1.25	0.00	1.00	0.25
...............................TGGTTCGTCACAAG-GGCAATTCTG.....................................................................................................	24	4	1.25	0.50	0.75	0.00
..........................................................................TATTGCACTTGAGACGGTCGA..............................................................	21	4	1.25	0.25	1.00	0.00
..........................................................................TATTGCATTTGAGACGGCCGAAA............................................................	23	4	1.25	0.00	1.25	0.00
..........................................................................TATTGCACTTGAGACGGTA................................................................	19	4	1.25	1.25	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCTGAAA............................................................	23	4	1.00	0.75	0.25	0.00
..........................................................................TATTGCACTTGAGACGGCCAAAA............................................................	23	4	1.00	0.00	0.75	0.25
..........................................................................TATTGCACTTGAGACAGCCGA..............................................................	21	4	1.00	0.00	1.00	0.00
...............................TGGTTCGTCACAAG-GGCACTT........................................................................................................	21	4	1.00	0.75	0.25	0.00
..........................................................................TATTGCACTTGAGACGGCGGA..............................................................	21	4	1.00	1.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGC..............................................................	21	4	1.00	0.25	0.75	0.00
..........................................................................TATTCCACTTGAGACGGCCGAA.............................................................	22	4	1.00	0.25	0.50	0.25
...............................TGGTTCGTCACAAG-GGCAATTCTGC....................................................................................................	25	4	1.00	0.00	1.00	0.00
..........................................................................TATTGCGCTTGAGACGGCCGAAA............................................................	23	4	1.00	0.00	1.00	0.00
..........................................................................TATTGCACTTGAGACGGCAGA..............................................................	21	4	1.00	0.75	0.25	0.00
...............................TGGTTCGTCACAAG-GGCAATTCC......................................................................................................	23	4	1.00	0.25	0.75	0.00
..........................................................................TATTGCACTTGAGATGGCCGAAA............................................................	23	4	1.00	0.00	0.50	0.50
..........................................................................TATTGCACTTGGGACGGCCGA..............................................................	21	4	1.00	0.00	0.75	0.25
..........................................................................TATTGCACTTGAGACTGCCGA..............................................................	21	4	1.00	0.25	0.50	0.25
...............................TGGTTCGTCACAAG-GGCAATTAA......................................................................................................	23	4	1.00	0.00	1.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAACT...........................................................	24	4	1.00	0.75	0.25	0.00
............................................................................TTGCACTTGAGACGGCCG...............................................................	18	4	0.75	0.00	0.75	0.00
..........................................................................TATTGCACTTGAGACGGCAGAA.............................................................	22	4	0.75	0.50	0.00	0.25
...............................TGGTTCGTCACAAG-GGCAATA........................................................................................................	21	4	0.75	0.50	0.00	0.25
..........................................................................TATTGCACTTGAGACGGCCGATATA..........................................................	25	4	0.75	0.75	0.00	0.00
..........................................................................TATTGCACTAGAGACGGCCGA..............................................................	21	4	0.75	0.00	0.75	0.00
...............................TGGTTCGTCACAAG-GGCA...........................................................................................................	18	4	0.75	0.25	0.50	0.00
..........................................................................TATTGCACTTGAGACGCCCGAA.............................................................	22	4	0.75	0.50	0.25	0.00
..........................................................................TATTGCACTTGAGACGGCCAAA.............................................................	22	4	0.75	0.00	0.50	0.25
..........................................................................TATTGCACTTGAGACGGCCGATTTAT.........................................................	26	4	0.75	0.75	0.00	0.00
..........................................................................TATTGCACTTGAGCCGGCCGAA.............................................................	22	4	0.75	0.00	0.50	0.25
............................................................................TTGCACTTGAGACGGCCGAAA............................................................	21	4	0.75	0.00	0.75	0.00
..........................................................................TATTGCACTTAAGACGGCCGAA.............................................................	22	4	0.75	0.00	0.25	0.50
..........................................................................TATTGCACTTGAGACGGCCGG..............................................................	21	4	0.75	0.00	0.75	0.00
...............................TGGTTCGTCACAAG-GGCAATTTT......................................................................................................	23	4	0.75	0.75	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAATA...........................................................	24	4	0.75	0.75	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAACA...........................................................	24	4	0.75	0.25	0.50	0.00
..........................................................................TATTGCACTTGAGACGGCCGTAT............................................................	23	4	0.75	0.75	0.00	0.00
..........................................................................TATTTCACTTGAGACGGCCGAAA............................................................	23	4	0.75	0.00	0.75	0.00
..........................................................................TATTGCACTTGAGACGGCCGATTA...........................................................	24	4	0.75	0.75	0.00	0.00
..........................................................................TATTGCACTTGAGACGGTCGAAA............................................................	23	4	0.75	0.00	0.75	0.00
..........................................................................TATTGCACTTGAGACGGCCGAATAA..........................................................	25	4	0.75	0.00	0.75	0.00
..........................................................................TATTGCACTTGAGACCGCCGA..............................................................	21	4	0.75	0.00	0.50	0.25
..........................................................................TATTGCACTTGAGTCGGCCGA..............................................................	21	4	0.75	0.00	0.75	0.00

droYak2

AATTGCG----TT-------TGAA-GCGCTTCGGTTCGTCCCAGG-AGCAATTCTGCACTA---TTAAAGCTAGTATTGCACTTGAGACGGCCGGATTACTTTTAA-AC-GAATC------------------------------------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................................TATTGCACTTGAGACGGCCGGA.............................................................	22	2	1156.50	878.00	20.50	205.00	38.50	14.50
..........................................................................TATTGCACTTGAGACGGCCGG..............................................................	21	2	507.00	430.00	5.50	60.50	10.00	1.00
..........................................................................TATTGCACTTGAGACGGCCGGAA............................................................	23	2	306.00	277.00	2.00	18.50	7.50	1.00
..........................................................................TATTGCACTTGAGACGGCCGGAT............................................................	23	2	189.50	88.50	2.00	28.00	3.00	68.00
..........................................................................TATTGCACTTGAGACGGCCG...............................................................	20	2	111.50	91.50	2.00	14.50	1.50	2.00
..........................................................................TATTGCACTTGAGACGGCCGGAAA...........................................................	24	2	106.00	92.00	2.50	8.00	3.00	0.50
..........................................................................TATTGCACTTGAGACGGCCGGT.............................................................	22	2	73.00	43.00	0.50	26.00	3.50	0.00
..........................................................................TATTGCACTTGAGACGGCCGGAC............................................................	23	2	31.00	7.00	0.00	1.00	1.00	22.00
..........................................................................TATTGCACTTGAGACGGCCGGATT...........................................................	24	2	26.50	12.50	0.50	6.00	0.00	7.50
..........................................................................TATTGCACTTGAGACGGCCGGAAT...........................................................	24	2	22.00	17.50	0.00	4.00	0.50	0.00
..........................................................................TATTGCACTTGAGACGGCCGGG.............................................................	22	2	19.00	15.00	0.00	1.50	1.50	1.00
..........................................................................TATTGCACTTGAGACGGCCGGCA............................................................	23	2	17.00	16.00	0.00	0.00	1.00	0.00
..........................................................................TATTGCACTTGAGACGGCCCG..............................................................	21	2	15.50	15.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGC.............................................................	22	2	14.50	9.50	0.50	2.50	1.50	0.50
..........................................................................TATTGCACTTGAGACGGCCGT..............................................................	21	2	11.50	3.00	0.00	8.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGAAAA..........................................................	25	2	11.00	9.50	0.50	1.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGTT............................................................	23	2	7.50	4.00	0.50	3.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGAG............................................................	23	2	7.00	3.50	0.00	1.50	0.00	2.00
..........................................................................TATTGCACTTGAGACGGCCGGATTT..........................................................	25	2	6.50	1.00	0.00	1.50	0.00	4.00
..........................................................................TATTGCACTTGAGACGGCCGGGA............................................................	23	2	5.50	5.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGATA...........................................................	24	2	5.50	5.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGTTT...........................................................	24	2	5.00	0.00	0.00	4.50	0.50	0.00
..........................................................................TATTGCACTTGAGACGGCC................................................................	19	2	5.00	4.00	0.00	0.50	0.50	0.00
..........................................................................TATTGCACTTGAGACGGCCGGATG...........................................................	24	2	5.00	2.00	0.00	0.00	0.00	3.00
..........................................................................TATTGCACTTGAGACGGCCGGACA...........................................................	24	2	4.50	3.00	0.50	0.50	0.00	0.50
..........................................................................TATTGCACTTGAGACGGCCGGCT............................................................	23	2	3.50	3.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCCGA.............................................................	22	2	3.50	3.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACAGCCGGA.............................................................	22	2	3.50	3.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGTA............................................................	23	2	3.00	1.00	0.00	2.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGGCGG..............................................................	21	2	3.00	3.00	0.00	0.00	0.00	0.00
...........................................................................ATTGCACTTGAGACGGCCGGA.............................................................	21	2	3.00	2.00	0.00	1.00	0.00	0.00
..........................................................................TATTGCACTTGCGACGGCCGGA.............................................................	22	2	3.00	2.50	0.00	0.00	0.50	0.00
..........................................................................TATTGCACTTGAGAAGGCCGGA.............................................................	22	2	3.00	3.00	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGGCGGA.............................................................	22	2	3.00	3.00	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGACT...........................................................	24	2	3.00	1.00	0.00	0.50	0.00	1.50
..........................................................................TATCGCACTTGAGACGGCCGGA.............................................................	22	2	2.50	2.00	0.00	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGCCGGCCGGA.............................................................	22	2	2.50	2.00	0.00	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGGT............................................................	23	2	2.50	2.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGTTT............................................................	23	2	2.50	0.00	0.00	2.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGCTT...........................................................	24	2	2.00	1.50	0.00	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCAGA.............................................................	22	2	2.00	2.00	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACCGCCGGA.............................................................	22	2	2.00	2.00	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAA.............................................................	22	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGAAC...........................................................	24	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGACACGGCCGG..............................................................	21	2	1.50	1.00	0.00	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGATGGCCGGA.............................................................	22	2	1.50	1.00	0.00	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGATTAAA........................................................	27	2	1.50	0.00	0.00	0.50	0.00	1.00
..........................................................................TATTGCACTTGCGACGGCCGG..............................................................	21	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGACGG..............................................................	21	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACCTGAGACGGCCGGA.............................................................	22	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGTACTTGAGACGGCCGGA.............................................................	22	2	1.50	1.00	0.00	0.50	0.00	0.00
..........................................................................TAGTGCACTTGAGACGGCCGGG.............................................................	22	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGACGGA.............................................................	22	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGATC...........................................................	24	2	1.50	1.00	0.00	0.00	0.00	0.50
...........................................................................ATTGCACTTGAGACGGCCGGAT............................................................	22	2	1.50	1.00	0.00	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGGC.................................................................	18	2	1.50	0.50	0.50	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGCCCGGA.............................................................	22	2	1.50	1.00	0.00	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCAGGAT............................................................	23	2	1.50	1.00	0.00	0.50	0.00	0.00
..........................................................................TATTACACTTGAGACGGCCGGA.............................................................	22	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGTCGGA.............................................................	22	2	1.50	1.00	0.00	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAAA............................................................	23	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCT...............................................................	20	2	1.50	1.00	0.00	0.00	0.00	0.50
..........................................................................TATTGCACTTTAGACGGCCGGA.............................................................	22	2	1.50	1.50	0.00	0.00	0.00	0.00
...............................CGGTTCGTCCCAGG-AGCAATTC.......................................................................................................	22	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGATGGCCGGAA............................................................	23	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGGCGGCCGGAA............................................................	23	2	1.50	1.00	0.50	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCAGG..............................................................	21	2	1.50	1.50	0.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGTCCGG..............................................................	21	2	1.50	1.00	0.00	0.50	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGA..............................................................	21	2	1.50	1.00	0.00	0.50	0.00	0.00
..........................................................................TATTGCAATTGAGACGGCCGGA.............................................................	22	2	1.50	1.50	0.00	0.00	0.00	0.00

droEre2

AATTAAG----TT-------TGAA-GCGCTTCGGTTCGTACCAGG-AGCAATTCTGCATT----TTTAAGCTAGTATTGCACTTGAGACGGCCGGATTACTTTTAA-AC-AAAAC------------------------------------------	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..........................................................................TATTGCACTTGAGACGGCCGGA.............................................................	22	4	96.00	61.75	4.00	0.00	30.25
..........................................................................TATTGCACTTGAGACGGCCGG..............................................................	21	4	39.25	20.25	2.25	0.00	16.75
..........................................................................TATTGCACTTGAGACGGCCGGAA............................................................	23	4	18.75	17.25	0.00	0.00	1.50
..........................................................................TATTGCACTTGAGACGGCCG...............................................................	20	4	17.25	4.00	2.00	0.00	11.25
..........................................................................TATTGCACTTGAGACGGCCGGT.............................................................	22	4	11.25	1.50	1.75	0.00	8.00
..........................................................................TATTGCACTTGAGACGGCCGGAT............................................................	23	4	9.50	3.75	1.25	0.00	4.50
..........................................................................TATTGCACTTGAGACGGCCGGAAA...........................................................	24	4	7.50	7.25	0.00	0.00	0.25
..........................................................................TATTGCACTTGAGACGGCCGGTT............................................................	23	4	4.25	0.00	0.25	0.00	4.00
..........................................................................TATTGCACTTGAGACGGCCGT..............................................................	21	4	4.00	0.25	0.75	0.00	3.00
..........................................................................TATTGCACTTGAGACGGCCGGTTT...........................................................	24	4	2.50	0.00	0.00	0.00	2.50
..........................................................................TATTGCACTTGAGACGGCC................................................................	19	4	2.25	0.25	0.00	0.00	2.00
..........................................................................TATTGCACTTGAGACGGCCCGA.............................................................	22	4	2.25	2.25	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGTTT............................................................	23	4	2.00	0.00	0.00	0.00	2.00
..........................................................................TATTGCACTTGAGACGGCCCG..............................................................	21	4	1.75	1.75	0.00	0.00	0.00
..........................................................................TATTGCACTTGATACGGCCGGA.............................................................	22	4	1.50	1.00	0.25	0.00	0.25
..........................................................................TATTGCACTTGAGACGGCCT...............................................................	20	4	1.25	0.00	0.25	0.00	1.00
..........................................................................TATTGCACTTGAGACGGCCTGA.............................................................	22	4	1.25	0.75	0.00	0.00	0.50
..........................................................................TATTGCACTTGAGACGGCCGGTA............................................................	23	4	1.00	0.00	0.25	0.00	0.75
..........................................................................TATTGCACTTGAGACGGCCGTT.............................................................	22	4	1.00	0.00	0.25	0.00	0.75
..........................................................................TATTGCCCTTGAGACGGCCGGA.............................................................	22	4	1.00	0.50	0.25	0.00	0.25
..........................................................................TATTGCACTTGAGACGGCCGGG.............................................................	22	4	1.00	1.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGATA...........................................................	24	4	1.00	0.25	0.00	0.00	0.75
..........................................................................TATTGCACTTGAGACGGCCGGGA............................................................	23	4	0.75	0.75	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACTGCCGGA.............................................................	22	4	0.75	0.25	0.00	0.00	0.50
..........................................................................TATTGCACTTGAGACGGCCGGCA............................................................	23	4	0.75	0.75	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGA..............................................................	21	4	0.75	0.75	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGAA.............................................................	22	4	0.75	0.75	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGGATT...........................................................	24	4	0.75	0.25	0.00	0.00	0.50
..........................................................................TATTGCACTTGAGACGGCCGGC.............................................................	22	4	0.75	0.50	0.25	0.00	0.00
..........................................................................TATTGCACTTGATACGGCCGGAA............................................................	23	4	0.75	0.75	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGGCCGTA.............................................................	22	4	0.75	0.50	0.00	0.00	0.25
..........................................................................TATTGCACTTGAGACCGCCGGA.............................................................	22	4	0.75	0.50	0.00	0.00	0.25
..........................................................................TATTGCACTTGAGACTGCCGG..............................................................	21	4	0.75	0.50	0.00	0.00	0.25
..........................................................................TATTGCACTTGAGACGGCCGGTG............................................................	23	4	0.75	0.00	0.00	0.00	0.75
..........................................................................TATTGCACTTGAGACGGCCGGAAT...........................................................	24	4	0.75	0.75	0.00	0.00	0.00

droEug1

AAATAAA---ATT-------TCTA-GTATTTCGGTTCGCCTTTTG-TGCAATTTTAGAGT------CAATAGAAAATTGCACTTCAGACGGCCGGATGACTTGAAATAC-AAAAC------------------------------------------

Size

Hit Count

Total Norm

droBia1

ATATAGGCATATT-------TTTG-GCGTTTCGGTCCGTCCCAGG-AGCAATCCTGTATT-----TCCGACTAGAATTGCACTTGAGACGGCCGGAGTGCTTGAAA-AC-AAGGA--------AAGTGCATAG-----AA--------------ACT

Size

Hit Count

Total Norm

droTak1

AACA-TA----TT-------TCTG-GTGTTCCGGTCCGTCTCAGG-CGCAATTCTGAATT-----TTCACCTAGTATTGCACTTGAGACGGCCGGAATACTTTAAATAC-GAAAC------------------------------------------

Size

Hit Count

Total Norm

droEle1

TACTAA-----TT-------TCTG-GTGTTTCGGTACGTCTATGG-GGCAATTCTGCGTT----TTCTGGTTAGCATTGCACTTGAGACGGCCGCAACACTTTGGA-AT-AAAAA------------------------------------------

Size

Hit Count

Total Norm

droRho1

GAACAAA----TT-------TCTG-GTGTTTCGGCTCGTCTCAAA-AGCAATTCTTCGTTT--TTCTTGGCTAGCATTGCACTTGAGACGGCCGCAATACTTTGGATTT-AAAACATTTAAGCAAGTTTATTG-----AAAAAGTTATTTTTGCATT

Size

Hit Count

Total Norm

droFic1

AAACCAA----TT-------TCGA-GTGTTTCGGT-CGTCTTGGGTGGCAATACTAAATTAACTTTATGGCTAGCATTGCACTTGAGACGGCCGAAATGCTTTAAA-TT-TA--T------------------------------------------

Size

Hit Count

Total Norm

droKik1

AGCTCCG----GC-------CGTA-AAGGTCTGTGCTGTTTGAGG-TGCAAATCTGTGGT----TAATAGCCAGAATTGCACTTGAAACGGCCAGATCAAGGCGGC-CC-AAAAC------------------------------------------

Size

Hit Count

Total Norm

droAna3

TCTAC------------------A-ATTTTCCGGTGCGTCTCTAG-TGCAACTCTTGGTTT---TTTATACAAGTATTGCACTTGAGACGGCCGAAATATAGTGGA-TC-TAAGC------------------------------------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..........................................................................TATTGCACTTGAGACGGCCGA..............................................................	21	2	1519.50	194.00	10.00	24.00	1291.50
..........................................................................TATTGCACTTGAGACGGCCGAAA............................................................	23	2	687.50	53.00	4.00	6.50	624.00
...............................CGGTGCGTCTCTAG-TGCAACT........................................................................................................	21	2	570.00	3.50	1.00	0.50	565.00
..........................................................................TATTGCACTTGAGACGGCCGAA.............................................................	22	2	507.00	131.00	3.00	13.00	360.00
..........................................................................TATTGCACTTGAGACGGCCGAAAA...........................................................	24	2	380.50	10.50	0.00	3.00	367.00
..........................................................................TATTGCACTTGAGACGGCCG...............................................................	20	2	330.50	72.50	4.50	7.50	246.00
..........................................................................TATTGCACTTGAGACGGCCGAAAAA..........................................................	25	2	69.00	1.50	0.50	0.00	67.00
..........................................................................TATTGCACTTGAGACGGCCGAAT............................................................	23	2	51.00	21.00	0.00	2.50	27.50
..........................................................................TATTGCACTTGAGACGGCCCA..............................................................	21	2	34.00	0.00	0.00	0.00	34.00
..........................................................................TATTGCACTTGAGACGGCCGAT.............................................................	22	2	32.50	15.00	1.00	1.50	15.00
..........................................................................TATTGCACTTGAGACGGCCGCAA............................................................	23	2	29.00	0.00	0.00	0.00	29.00
..........................................................................TATTGCACTTGAGACGGCCGCA.............................................................	22	2	28.50	0.50	0.00	0.50	27.50
..........................................................................TATTGCACTTGAGACGGCCGT..............................................................	21	2	24.50	9.50	1.50	1.00	12.50
..........................................................................TATTGCACTTGAGACGGCCGC..............................................................	21	2	23.50	0.00	0.00	0.50	23.00
..........................................................................TATTGCACTTGAGACGGCCGAAAAAA.........................................................	26	2	22.00	0.50	0.00	0.00	21.50
..........................................................................TATTGCACTTTAGACGGCCGA..............................................................	21	2	21.50	1.50	0.00	0.00	20.00
.......................................CTCTAG-TGCAGATCTTGGT..................................................................................................	19	2	21.00	10.00	4.00	6.00	1.00
...............................CGGTGCGTCTCTAG-TGCAACTCT......................................................................................................	23	2	18.00	12.50	3.50	2.00	0.00
..........................................................................TATTGCACTTGATACGGCCGA..............................................................	21	2	17.00	2.00	0.00	0.00	15.00
..........................................................................TATTGCACTTGAGACGTCCGA..............................................................	21	2	17.00	1.50	0.00	0.50	15.00
..........................................................................TATTGCACTTGAGACGGCCGG..............................................................	21	2	16.50	0.50	0.00	0.50	15.50
..........................................................................TATTGCACTTGAGACGGCC................................................................	19	2	16.00	2.00	0.00	0.50	13.50
..........................................................................TATTGCACTTGAGACGGCCGATA............................................................	23	2	15.50	4.50	0.50	0.00	10.50
...............................CGGTGCGTCTCTAG-TGCAAC.........................................................................................................	20	2	15.50	0.00	0.00	0.00	15.50
..........................................................................TATTGCACTTGAGACGGCCGACA............................................................	23	2	15.00	0.00	0.00	0.00	15.00
..........................................................................TATTGCACTTGAGACGGCCGGA.............................................................	22	2	14.50	0.00	0.00	0.50	14.00
..........................................................................TATTGCACTTGAGACGGCCGGAA............................................................	23	2	13.00	0.00	0.00	0.00	13.00
..........................................................................TATTGCACTTGAGACGGCCCAA.............................................................	22	2	12.00	0.00	0.00	0.00	12.00
..........................................................................TATTGCACTTGAGACGGCCGCAAA...........................................................	24	2	12.00	0.00	0.00	0.00	12.00
...............................CGGTGCGTCTCTAG-TGCAACTC.......................................................................................................	22	2	11.50	2.50	0.00	1.50	7.50
..........................................................................TATTGCACTTGAGACGGCCCAAA............................................................	23	2	11.00	0.00	0.00	0.00	11.00
...............................CGGTGCGTCTCTAG-TGCCACT........................................................................................................	21	2	11.00	0.00	0.00	0.00	11.00
..........................................................................TATTGCACTTGAGACGGCCGACAA...........................................................	24	2	10.50	0.00	0.00	0.00	10.50
..........................................................................TATTGCACTTGAGACTGCCGA..............................................................	21	2	10.00	1.00	0.00	0.50	8.50
..........................................................................TATTGCACTTGAGACGGCCGATT............................................................	23	2	10.00	8.00	0.50	0.50	1.00
..........................................................................TATTGCACTTGAGACGGCCGAAAT...........................................................	24	2	9.50	2.00	0.00	0.50	7.00
...............................CGGTGCGTCTCTAG-TTCAACT........................................................................................................	21	2	9.00	0.00	0.00	0.00	9.00
..........................................................................TATTGCACTTGAGACGGCCGAAG............................................................	23	2	9.00	0.50	0.00	0.50	8.00
..........................................................................TATTGCACTTGAGACGGCCGAAC............................................................	23	2	9.00	1.00	0.00	0.00	8.00
..........................................................................TATTGCACTTGAGACGGCCTA..............................................................	21	2	8.00	0.50	0.00	0.00	7.50
..........................................................................TATTGCACTTGAGACGGCCGAG.............................................................	22	2	7.50	2.00	0.50	0.50	4.50
..........................................................................TATTGCACTTGCGACGGCCGA..............................................................	21	2	7.50	1.00	0.00	0.00	6.50
..........................................................................TATTGCACTTGAGACTGCCGAAA............................................................	23	2	7.00	0.00	0.00	0.00	7.00
..........................................................................TATTGCACTTGAGACGGCCGGAAA...........................................................	24	2	7.00	0.00	0.00	0.00	7.00
..........................................................................TATTGCACTTGAGACCGCCGA..............................................................	21	2	7.00	0.50	0.00	0.00	6.50
..........................................................................TATTGCACTTGAGACGGCCGAAAC...........................................................	24	2	7.00	0.50	0.50	0.00	6.00
...........................................................................ATTGCACTTGAGACGGCCGA..............................................................	20	2	6.50	1.50	0.00	0.50	4.50
..........................................................................TATTGCACTTGAGACGGCCGAAAAAAA........................................................	27	2	6.50	0.00	0.50	0.00	6.00
..........................................................................TATTGCACTTGATACGGCCGAAA............................................................	23	2	6.50	0.00	0.00	0.00	6.50
...............................CGGTGCGTCTCTAC-TGCAACT........................................................................................................	21	2	6.00	0.00	0.00	0.00	6.00
..........................................................................TATTGCACTTGAGACGTCCGAAA............................................................	23	2	6.00	0.00	0.00	0.00	6.00
...............................CGGGGCGTCTCTAG-TGCAACT........................................................................................................	21	2	6.00	0.00	0.00	0.50	5.50
..........................................................................TATTGCACTTGAGACTGCCGAA.............................................................	22	2	6.00	1.00	0.00	0.00	5.00
........................................TCTAG-TGCAGATCTTGGT..................................................................................................	18	2	6.00	1.50	3.00	1.50	0.00
..........................................................................TATTGCACTTTAGACGGCCGAAAA...........................................................	24	2	6.00	0.00	0.00	0.00	6.00
..........................................................................TATTGCACTTGAGACGGCCGAC.............................................................	22	2	5.50	0.00	0.00	0.00	5.50
...............................CGGTGCGTCTCTAT-TGCAACT........................................................................................................	21	2	5.50	0.00	0.00	0.00	5.50
..........................................................................TATTGCACTTGAGACGGCCT...............................................................	20	2	5.50	2.00	0.50	0.00	3.00
..........................................................................TATTGCACTTCAGACGGCCGA..............................................................	21	2	5.50	0.00	0.00	0.00	5.50
...............................CGGTGCGTCTCTAG-CGCAACT........................................................................................................	21	2	5.50	0.00	0.00	0.00	5.50
..........................................................................TATTGCACTTGCGACGGCCGAAA............................................................	23	2	5.00	0.50	0.00	0.00	4.50
..........................................................................TATTGCACTTGAGACGGCCGTAA............................................................	23	2	5.00	1.00	0.00	0.00	4.00
..........................................................................TATTTCACTTGAGACGGCCGA..............................................................	21	2	5.00	1.00	0.00	0.00	4.00
..........................................................................TATTGCACTTGAGACGGGCGA..............................................................	21	2	4.50	0.00	0.00	0.00	4.50
..........................................................................TATTGCACTTGAGACGGACGA..............................................................	21	2	4.50	2.00	0.00	0.00	2.50
..........................................................................TATTGCACTTGATACGGCCGAA.............................................................	22	2	4.50	0.00	0.00	0.00	4.50
..........................................................................TATTGCACTTTAGACGGCCGAAA............................................................	23	2	4.50	0.00	0.00	0.00	4.50
..........................................................................TATTGCACTTGACACGGCCGA..............................................................	21	2	4.50	1.00	0.00	0.00	3.50
..........................................................................TATTGCACTTGAGACGGCCCAAAA...........................................................	24	2	4.50	0.00	0.00	0.00	4.50
..........................................................................TATTGCACTTGAGACGTCCG...............................................................	20	2	4.50	0.50	0.00	0.00	4.00
..........................................................................TATTGCACTTGAGACAGCCGA..............................................................	21	2	4.00	0.00	0.00	0.00	4.00
..........................................................................TAGTGCACTTGAGACGGCCGA..............................................................	21	2	4.00	0.00	0.00	0.50	3.50
..........................................................................TATTGCACTTGATACGGCCG...............................................................	20	2	4.00	0.50	0.00	0.00	3.50
...............................CGGTGCGTCTCTCG-TGCAACT........................................................................................................	21	2	4.00	0.00	0.00	0.00	4.00
..........................................................................TATTGCACTTGAGCCGGCCGA..............................................................	21	2	4.00	0.00	0.00	0.00	4.00
..........................................................................TATTGCACTTGAGACGACCGA..............................................................	21	2	4.00	0.00	0.00	0.00	4.00
..........................................................................TATTGCACTTGAGACGGCCGAAACA..........................................................	25	2	4.00	0.00	0.00	0.00	4.00
..........................................................................TATTGCACTTGAGACGGCCTAAA............................................................	23	2	4.00	0.00	0.00	0.00	4.00
..........................................................................CATTGCACTTGAGACGGCCGA..............................................................	21	2	4.00	1.00	0.00	0.00	3.00
..........................................................................TATTGCACTTGATACGGCCGAAAA...........................................................	24	2	4.00	0.00	0.00	0.00	4.00
..........................................................................TATTGCGCTTGAGACGGCCGA..............................................................	21	2	3.50	0.50	0.00	0.00	3.00
..........................................................................TATTGCACTTGCGACGGCCGAA.............................................................	22	2	3.50	1.00	0.00	0.00	2.50
..........................................................................TATTGCACTTGAGACTGCCG...............................................................	20	2	3.50	0.00	0.00	0.00	3.50
..........................................................................TATTGCACTTGAGACGTCCGAA.............................................................	22	2	3.50	0.50	0.00	0.00	3.00
..........................................................................TATTGCACTTGATACGTCCGAAA............................................................	23	2	3.50	0.00	0.00	0.00	3.50
..........................................................................TATTGCACTTGAGACGGCCGTAAA...........................................................	24	2	3.50	0.00	0.00	0.00	3.50
..........................................................................TATTGCACTTGAGACGGCCTAA.............................................................	22	2	3.50	0.00	0.00	0.00	3.50
..........................................................................TATTGCACTTGAGACGGCCGAACA...........................................................	24	2	3.50	0.00	0.00	0.00	3.50
..........................................................................TATTGCACTTTAGACGGCCGAA.............................................................	22	2	3.50	0.50	0.00	0.00	3.00
...............................CGGCGCGTCTCTAG-TGCAACT........................................................................................................	21	2	3.50	0.00	0.00	0.00	3.50
...............................CGGTGCGTCTCTAG-TGCAACTCTA.....................................................................................................	24	2	3.50	3.00	0.00	0.50	0.00
..........................................................................TATTGCACTTGAGACGCCCGA..............................................................	21	2	3.50	0.00	0.00	0.00	3.50
..........................................................................TATTGCACTTGAGACGGCCGCAT............................................................	23	2	3.00	0.00	0.00	0.00	3.00
..........................................................................TATTGCACTTGAGACCGCCGAAA............................................................	23	2	3.00	0.50	0.00	0.00	2.50
..........................................................................TATTGCACTTGAGACGGCCGAAAAT..........................................................	25	2	3.00	0.50	0.00	0.00	2.50
..........................................................................TATTGCACTTGAGACGGACGAA.............................................................	22	2	3.00	3.00	0.00	0.00	0.00
..........................................................................TATTGCACTTGAGACGTCCGAAAA...........................................................	24	2	3.00	0.00	0.00	0.00	3.00
..........................................................................TATTGCACTTGAGACGCCCGAAA............................................................	23	2	3.00	0.00	0.00	0.00	3.00
..........................................................................TATTGCACTTGACACGGCCGAAA............................................................	23	2	3.00	0.00	0.00	0.00	3.00
..........................................................................TATTGCACTTGAGACGGCCGTA.............................................................	22	2	3.00	0.00	0.00	0.50	2.50
..........................................................................TATTGCACTCGAGACGGCCGA..............................................................	21	2	3.00	0.50	0.00	0.00	2.50

droBip1

ATTTATG----TC-------TACA-ATTTTCGGGGTCATCTCCAG-TGCAAATCTTGGTTT---TTCCAACAAGAATTGCACTCGAGACGGCCAGAATATTGTGGA-TC-TATGC--------AGCTAC----AAGCCGA--------------AAG

Size

Hit Count

Total Norm

dp4

GG---------------------------------------------GCAATACTGTGTTG--TATTTCACCAGTATTGCACACCCACTGGCCTGAAAGTGCCTACTG-------------------CT----GGGTTCA--------------ACA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..........................................................................TATTGCACACCCACTGGCCTGA.............................................................	22	3	346.33	69.00	247.33	26.67	3.33
..........................................................................TATTGCACACCCACTGGCCTG..............................................................	21	3	183.33	36.67	33.33	19.67	93.67
..........................................................................TATTGCACACCCACTGGCCTGT.............................................................	22	3	25.00	16.00	3.67	4.00	1.33
..........................................................................TATTGCACACCCACTGGCCTGAA............................................................	23	3	19.67	2.00	16.67	1.00	0.00
..........................................................................TATTGCACACCCACTGGCCT...............................................................	20	3	10.00	4.00	3.33	1.67	1.00
..........................................................................TATTGCACACCCACTGGCCTGTC............................................................	23	3	5.00	4.00	0.00	0.67	0.33
..........................................................................TATTGCACACCCACTGGCCTGTT............................................................	23	3	2.67	1.33	0.00	1.00	0.33
..........................................................................TATTGCACACCCACTGGCCTGC.............................................................	22	3	2.33	0.33	1.67	0.00	0.33
..........................................................................TATTGCACACCCACTGGCCTGAAA...........................................................	24	3	2.33	0.00	2.33	0.00	0.00
..........................................................................TATTGCACACCCCCTGGCCTGA.............................................................	22	3	1.67	0.00	1.67	0.00	0.00
..........................................................................TATTGCACACCCTCTGGCCTGA.............................................................	22	3	1.67	0.00	1.67	0.00	0.00
..........................................................................TATTGCACACCCACTGGCC................................................................	19	3	1.67	0.00	0.33	0.33	1.00
..........................................................................TATTGCACACCCACTGGCCTT..............................................................	21	3	1.67	0.67	0.33	0.00	0.67
..........................................................................TATTGCACACCCAATGGCCTGA.............................................................	22	3	1.33	0.00	1.33	0.00	0.00
..........................................................................TATTGCACACCCACTAGCCTGA.............................................................	22	3	1.33	0.00	1.33	0.00	0.00
..........................................................................TATTGCACACCCACTGGCCTGAT............................................................	23	3	1.33	0.67	0.00	0.67	0.00
..........................................................................TATTGCACACCCACTTGCCTGA.............................................................	22	3	1.33	1.00	0.33	0.00	0.00
..........................................................................TATTGCACACCCACTGGCCTAA.............................................................	22	3	1.00	0.00	0.33	0.67	0.00
..........................................................................TACTGCACACCCACTGGCCTGA.............................................................	22	3	1.00	0.00	0.67	0.33	0.00
..........................................................................TATTGCACACCCACTGGCCCGA.............................................................	22	3	1.00	0.33	0.67	0.00	0.00
..........................................................................TATTGCACACCCACTGGCCTGAG............................................................	23	3	1.00	0.67	0.33	0.00	0.00
.........................................................................GTATTGCACACCCACTGGCC................................................................	20	3	1.00	0.67	0.00	0.33	0.00
..........................................................................TATTGCACACCCACTGGCATGA.............................................................	22	3	1.00	0.67	0.33	0.00	0.00
..........................................................................TATTGCACACTCACTGGCCTGA.............................................................	22	3	1.00	0.00	1.00	0.00	0.00

droPer1

ATTAGTG----TACAAGCGGAAGGGTGCATCGAGCTGCTTTGATT----------------------------------------TGTAGGCCGTGGTTCTTGCAA-ATACGAAT------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................................................................AGGCCGTGGTTCTTGCAA-ATA...............................................	21	3	1.00	0.67	0.33	0.00	0.00	0.00
........................................................................................AGGCCGTGGTTCTTGCAA-AT................................................	20	3	1.00	0.67	0.33	0.00	0.00	0.00
........................................................................................AGGCCGTGGTTCTTGCAA-ATACG.............................................	23	3	0.33	0.00	0.33	0.00	0.00	0.00
........................................................................................AGGCCGTGGTTCTTGCAA-ATACGT............................................	24	3	0.33	0.33	0.00	0.00	0.00	0.00

droWil1

CATAAAC----TC-------GAAAATTTTTTAGGTTCGTTTAGTC-TGCAAATTGTAA-T----ATACGAAAATAATTGCACACTTCACGGCCGGAAAAGTTCAAG-TT-AAACA------------------------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................................AATTGCACACTTCACGGCCGGA.............................................................	22	2	8130.00	263.00	7833.00	29.50	4.50
..........................................................................AATTGCACACTTCACGGCCGG..............................................................	21	2	4235.00	304.00	3893.50	37.50	0.00
..........................................................................AATTGCACACTTCACGGCCGGAA............................................................	23	2	3225.50	92.50	3112.00	21.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGAAA...........................................................	24	2	1702.50	21.50	1679.50	1.50	0.00
...........................................................................ATTGCACACTTCACGGCCGGAA............................................................	22	2	809.00	25.50	777.50	6.00	0.00
...........................................................................ATTGCACACTTCACGGCCGGA.............................................................	21	2	638.50	38.00	595.50	4.50	0.50
..........................................................................AATTGCACACTTCACGGCCG...............................................................	20	2	610.00	74.00	514.00	6.50	15.50
...........................................................................ATTGCACACTTCACGGCCGGAAA...........................................................	23	2	429.50	5.00	423.50	0.50	0.50
..........................................................................AATTGCACACTTCACGGCCGGT.............................................................	22	2	351.50	25.00	324.50	1.00	1.00
...............................AGGTTCGTTTAGTC-TGCAAATTG......................................................................................................	23	2	343.00	19.00	316.50	1.00	6.50
..........................................................................AATTGCACACTTCACGGCCGGAAAA..........................................................	25	2	184.50	1.50	182.00	1.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGAT............................................................	23	2	162.50	9.50	150.50	1.00	1.50
...............................AGGTTCGTTTAGTC-TGCAAATTGT.....................................................................................................	24	2	131.50	9.00	122.50	0.00	0.00
...............................AGGTTCGTTTAGTC-TGCAAATTGTAA-..................................................................................................	26	2	93.50	0.00	93.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGAAT...........................................................	24	2	82.00	7.00	75.00	0.00	0.00
...............................AGGTTCGTTTAGTC-TGCAAATTGTAA-A----.............................................................................................	27	2	71.00	0.00	71.00	0.00	0.00
...............................AGGTTCGTTTAGTC-TGCAAATTGA.....................................................................................................	24	2	68.00	0.50	67.50	0.00	0.00
...........................................................................ATTGCACACTTCACGGCCGG..............................................................	20	2	67.00	11.50	55.00	0.50	0.00
..........................................................................AATTGCACACTTCACGGCCGGAG............................................................	23	2	54.00	7.50	45.50	1.00	0.00
...............................AGGTTCGTTTAGTC-TGCAAATT.......................................................................................................	22	2	52.50	5.50	40.50	1.50	5.00
...........................................................................ATTGCACACTTCACGGCCGGAAAA..........................................................	24	2	45.00	1.50	43.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGAAG...........................................................	24	2	34.00	3.50	29.50	1.00	0.00
...............................AGGTTCGTTTAGTC-TGCAAATTGTA....................................................................................................	25	2	33.00	0.50	31.50	0.00	1.00
............................................................................TTGCACACTTCACGGCCGGAAA...........................................................	22	2	29.00	1.00	28.00	0.00	0.00
..........................................................................AATTGCACACTTCACGTCCGGA.............................................................	22	2	26.50	0.50	26.00	0.00	0.00
..............................TAGGTTCGTTTAGTC-TGCAAATTG......................................................................................................	24	2	26.00	1.00	25.00	0.00	0.00
...........................................................................ATTGCACACTTCACGGCCGGAAT...........................................................	23	2	24.50	3.00	21.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGAAAAA.........................................................	26	2	23.50	0.00	23.50	0.00	0.00
............................................................................TTGCACACTTCACGGCCGGAA............................................................	21	2	23.50	1.00	22.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGT..............................................................	21	2	22.50	9.50	13.00	0.00	0.00
..........................................................................AATTGCACACTTCACTGCCGGA.............................................................	22	2	22.50	0.00	22.00	0.50	0.00
..........................................................................AATTGCACACTTCACGGCCGGAC............................................................	23	2	20.00	0.50	18.50	0.50	0.50
..........................................................................AATTGCACACTTCACGGCCGGTA............................................................	23	2	19.00	2.50	16.00	0.50	0.00
...............................AGGTTCGTTTAGTC-TGCAAATTGAA....................................................................................................	25	2	18.00	0.00	17.00	0.00	1.00
..........................................................................AATTGCACACTTCACGGCCTGA.............................................................	22	2	17.50	0.00	17.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGC.............................................................	22	2	17.00	0.00	17.00	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGAAAT..........................................................	25	2	17.00	0.50	16.50	0.00	0.00
..........................................................................AATTGCACACTTCCCGGCCGG..............................................................	21	2	16.50	0.00	16.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGTA.............................................................	22	2	16.00	0.00	16.00	0.00	0.00
..........................................................................AATTTCACACTTCACGGCCGGA.............................................................	22	2	15.00	0.50	14.50	0.00	0.00
..........................................................................AATTGCACACTTCACGTCCGG..............................................................	21	2	14.50	0.50	14.00	0.00	0.00
..........................................................................AATTGCACACTTCACGGACGGA.............................................................	22	2	14.00	0.00	14.00	0.00	0.00
..........................................................................AATTGCACACTTCACGCCCGG..............................................................	21	2	14.00	2.00	12.00	0.00	0.00
............................................................................TTGCACACTTCACGGCCGGA.............................................................	20	2	14.00	2.00	11.50	0.50	0.00
..........................................................................AATTGCACACTTCACGGCCGGATA...........................................................	24	2	13.50	0.50	13.00	0.00	0.00
...........................................................................ATTGCACACTTCACGGCCGGAT............................................................	22	2	13.50	1.50	11.50	0.00	0.50
..........................................................................AATTGCACACTTCACGGCCGGTT............................................................	23	2	13.00	1.00	11.50	0.00	0.50
..........................................................................AATTGCACACTTCACGCCCGGA.............................................................	22	2	13.00	0.50	12.50	0.00	0.00
..........................................................................AATTGCACACTTCACTGCCGG..............................................................	21	2	12.50	0.00	12.00	0.50	0.00
..........................................................................AATTGCACACTTCACGGCC................................................................	19	2	12.00	0.00	10.50	0.00	1.50
..............................TAGGTTCGTTTAGTC-TGCAAATT.......................................................................................................	23	2	12.00	1.50	10.00	0.50	0.00
..............................TAGGTTCGTTTAGTC-TGCAAATTGA.....................................................................................................	25	2	12.00	0.50	11.50	0.00	0.00
..........................................................................AATTGCACACTTCACAGCCGGA.............................................................	22	2	11.50	0.50	11.00	0.00	0.00
..........................................................................AATTGCACACTTCCCGGCCGGA.............................................................	22	2	11.50	0.00	11.50	0.00	0.00
...........................................................................ATTGCACACTTCACGGCCGGAC............................................................	22	2	11.00	0.00	11.00	0.00	0.00
..........................................................................AATTGCACACCTCACGGCCGGA.............................................................	22	2	11.00	0.00	11.00	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGAAAAAA........................................................	27	2	11.00	0.00	11.00	0.00	0.00
..........................................................................AATTGCGCACTTCACGGCCGGA.............................................................	22	2	10.50	0.00	10.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCTG..............................................................	21	2	10.50	0.00	10.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGC.................................................................	18	2	10.50	1.00	9.50	0.00	0.00
..........................................................................AATTGCACACTTCACGTCCGGAA............................................................	23	2	10.00	0.00	10.00	0.00	0.00
..........................................................................AATTGCACACTTCACGGCAGGA.............................................................	22	2	9.50	0.00	9.50	0.00	0.00
..........................................................................AATCGCACACTTCACGGCCGGA.............................................................	22	2	9.50	0.00	9.50	0.00	0.00
...............................AGGTTCGTTTAGTC-TGCAAAT........................................................................................................	21	2	9.50	1.00	8.50	0.00	0.00
..........................................................................AATTTCACACTTCACGGCCGG..............................................................	21	2	9.50	0.00	9.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGACGG..............................................................	21	2	9.50	0.00	9.50	0.00	0.00
..........................................................................AATTGCACACTTCCCGGCCGGAA............................................................	23	2	9.00	0.00	9.00	0.00	0.00
..........................................................................GATTGCACACTTCACGGCCGGA.............................................................	22	2	9.00	0.00	9.00	0.00	0.00
..........................................................................AATTGCACACTTCGCGGCCGGA.............................................................	22	2	9.00	1.00	8.00	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGACA...........................................................	24	2	8.00	0.50	6.50	0.00	1.00
..........................................................................AATTTCACACTTCACGGCCGGAA............................................................	23	2	8.00	0.00	8.00	0.00	0.00
...............................AGGTTCGTTTAGTC-TGCAAATTGAAA-..................................................................................................	26	2	8.00	0.00	7.50	0.00	0.50
..........................................................................AATTGCACACTTCACGGCTGGA.............................................................	22	2	8.00	0.50	7.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCCG..............................................................	21	2	8.00	0.50	7.50	0.00	0.00
...........................................................................ATTGCACACTTCACGGCCGGAAG...........................................................	23	2	8.00	0.50	7.50	0.00	0.00
..........................................................................AATTGCACACTTCACTGCCGGAA............................................................	23	2	8.00	0.00	8.00	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCAGA.............................................................	22	2	8.00	1.00	6.50	0.50	0.00
..........................................................................AACTGCACACTTCACGGCCGGAA............................................................	23	2	7.50	0.50	7.00	0.00	0.00
...........................................................................ATTGCACACTTCACGGCCG...............................................................	19	2	7.50	0.50	7.00	0.00	0.00
..........................................................................AATTGCACACTCCACGGCCGGA.............................................................	22	2	7.50	0.00	7.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCTGAA............................................................	23	2	7.50	0.00	7.50	0.00	0.00
..........................................................................AATTGCACACTTCACGACCGGA.............................................................	22	2	7.50	0.00	7.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGG.............................................................	22	2	7.00	0.00	6.00	0.00	1.00
..........................................................................AATTGCACACTTCACGGTCGGA.............................................................	22	2	7.00	0.00	6.50	0.50	0.00
..........................................................................AATTGCACACTTCACAGCCGG..............................................................	21	2	7.00	0.50	6.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGTAA...........................................................	24	2	6.50	0.50	6.00	0.00	0.00
..........................................................................AATTGCACACCTCACGGCCGG..............................................................	21	2	6.50	0.50	6.00	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGA..............................................................	21	2	6.50	0.00	6.50	0.00	0.00
...........................................................................ATTGCACACTTCACGGCCGGAAAAA.........................................................	25	2	6.50	0.00	6.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGACGGAA............................................................	23	2	6.50	0.00	6.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCTGGAA............................................................	23	2	6.50	0.00	6.50	0.00	0.00
..........................................................................AATTGCACCCTTCACGGCCGGA.............................................................	22	2	6.50	0.00	6.50	0.00	0.00
..........................................................................AATTCCACACTTCACGGCCGGA.............................................................	22	2	6.50	0.00	6.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCAGG..............................................................	21	2	6.50	0.50	6.00	0.00	0.00
..........................................................................AATTGCCCACTTCACGGCCGGA.............................................................	22	2	6.50	0.00	6.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCGGAAC...........................................................	24	2	6.50	0.00	6.50	0.00	0.00
..........................................................................AATTGCACACTTCACGGCAGGAA............................................................	23	2	6.50	0.00	6.50	0.00	0.00
..........................................................................AATTGCACACTCCACGGCCGG..............................................................	21	2	6.00	0.50	5.50	0.00	0.00
..........................................................................AATTGAACACTTCACGGCCGG..............................................................	21	2	6.00	0.00	6.00	0.00	0.00
..........................................................................AATTGCACACTTCACGGCCCGA.............................................................	22	2	6.00	0.00	6.00	0.00	0.00
..........................................................................AATTGTACACTTCACGGCCGGA.............................................................	22	2	6.00	0.00	6.00	0.00	0.00

droVir3

AGCTATA----TT-------TTT-------------------------------------------------------------------------------CAGG-CC-GTGTC------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GTCTGCA----AT-------TTAA-GCTTCTT-----------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

AAGCAAA----TC-------TTCA-GTTTTTCGGCTGTGGTTAGT-GTCAATTCTTTTT-----ATTTGACAAGCATTGCACTCTTCACGGCCGGATAAATGAGGG------TCT------------------------------------------	Size	Hit Count	Total Norm	V109 Male body
..........................................................................CATTGCACTCTTCACGGCCGGA.............................................................	22	2	5.00	5.00
..........................................................................CATTGCACTCTTCACGGCCGG..............................................................	21	2	2.00	2.00
..........................................................................CATTGCACTCTTCACGGCCGGAA............................................................	23	2	1.00	1.00
..........................................................................CATTGCACTCTTCACGGCCG...............................................................	20	2	1.00	1.00
..........................................................................CATTGCACTCTTCACGGCCGGATTC..........................................................	25	2	0.50	0.50
..........................................................................CATTGCACTCTTCACGGCCGGAT............................................................	23	2	0.50	0.50

Generated: 04/20/2012 at 05:21:40 EDT

dme-mir-312

chr2R:16471561-16471626 -

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