dme-mir-1013- Best orthologs

dme-mir-1013	chr3R:26617358-26617418 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 26617358-26617380
   star strand at position 26617398-26617418
   mutations
   read mismatches

Notes: droEug has a small deletion that causes the hairpin structure to disappear. LASTZ correctly inferred the coordinates of the droVir3 - droGri2 orthologs. The inferred regions are introns within the Flybase reported ortholog for wts/dmel gene

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3R:26617343-26617433 -		1	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droSim1	chr3R:26257486-26257576 -	LASTZ	1	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droSec1	super_4:5435200-5435290 -	LASTZ	1	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTTTGCCGAACTCG-------CAGGCGACGGATGCGCGA
droYak2	chr3R:27538983-27539073 -	LASTZ	1	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATT---GGGA---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droEre2	scaffold_4820:1381504-1381594 +	LASTZ	1	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATT---GGAG---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droEug1	scf7180000409679:78776-78859 -	LASTZ	5	CACAGTGCTGGAAAGGTGAGTT-----CATAGACTA----AATCAGTA---TGAA---AAGT-----------G---ACTA-----------AT------ATACCGAATTCG-------CAGGAGACGGATGCGCGA
droBia1	scf7180000302113:733286-733375 +	LASTZ	4	CACCGTGCTGGAGCGGTGAGTTT----CGTACACTT----AGTTAATT---CG-G---AGGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGGCGGATGCGCGA
droTak1	scf7180000415367:120661-120751 +	LASTZ	4	CACTGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---TGGA---AAGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droEle1	scf7180000491280:2970971-2971061 -	LASTZ	4	CACAGTGCTGGAGAGGTGAGTTT----CGTACGCTT----AATTAATA---AATG---AAGC-----------A---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droRho1	scf7180000774800:25017-25107 -	LASTZ	4	CACAGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---AAGG---AAGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droFic1	scf7180000453782:677613-677706 +	LASTZ	4	CACGGTTCTGGAGCGGTGAGTTT----CGTACACTT----AATTAATA---CAAGAAGCGGG-----------G---ATTA-----------ATAAAAGTATGTCGAACTCG-------CAGGCGGCGGATGCGCGA
droKik1	scf7180000302390:601160-601259 -	LASTZ	4	CACGGTGCTGGAAAGGCGAGTTT----TGTATATTT----AATTAATT---TTCA---AAGT-----ATCGTTCATAATTA-----------ATAAAAGTATGCTGAACTCG-------CAGGCGGCGAATGCGCGA
droAna3	scaffold_12911:4366271-4366356 +	LASTZ	5	CACTGTGCTGGAGAGGTAATCTT----TGAATAATT----ATCTGTGA---GTTG---TGGC-----------A---TCTA-----------ATGATTGT-----TATCTTC-------CAGACGTCGCATGCGTGA
droBip1	scf7180000396640:1207116-1207199 +	LASTZ	5	CACAGTGCTGGAGCGGTAAGTTG----GA-G-GAAT----GCCTATGAGTCACG-------------------------TC-----------ATGTACTGATCTTTATCTTC-------CAGACGACGGATGCGCGA
dp4	chr2:577090-577184 +	LASTZ	5	CACTGTGCTGGAGCGGTAAGTC-----CATG-------------AATT---GCAT---CCCCCTTTGATTATTCTTT-------AATCTGGA----AATCCCTGTGATCCCA-------TAGACGACGGATGCGCGA
droPer1	super_7:3361274-3361368 +	LASTZ	5	CACTGTGCTGGAGCGGTAAGTC-----CATG-------------AATT---GCAT---CCCCCTTTGATTATTCTTT-------AATCTGGA----AATCCCTGTGATCCCA-------TAGACGACGGATGCGCGA
droWil1	scaffold_181130:10168431-10168520 -	LASTZ	5	AACTGTATTAGAAAGGTATAATG----AATAAACCA----ATTTGAAT---AG-C---AAAC-----------C---ATTA-----------AATCAATTTCCTTTTTTGTC-------TAGACGACGTATGCGTGA
droVir3	scaffold_13047:11434928-11435028 -	LASTZ	5	CACAGTGCTGGAGAGGTGGGTG-----CATCCACAT----CAGCTGCT---TG-A---TAAC-----------C---ATTTGTAAA--TGTA---AATCCTCCTTTAACTCG-TTTGAACAGGCGACGCATGCGCGA
droMoj3	scaffold_6540:30312688-30312787 +	LASTZ	5	CACAGTGCTGGAGAGGTGGGAG-----CATTGATTTCACCACCCATAAGACACA-------------------------TTCTCAC--AGTT---TTTCTTGC-TTAATTCC-TTTGTACAGGCGGCGCATGCGCGA
droGri2	scaffold_14624:1473562-1473665 -	LASTZ	5	CACAGTGCTGGAAAGGTGATTCAAATCCATA----------------AGCCACAA---TCTTCTT-AAATATTATTT-------TCGCT------AATGCTATTTGTACTCGCTTTGATTAGGCGTCGCATGCGGGA

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	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droSim1	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droSec1	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTTTGCCGAACTCG-------CAGGCGACGGATGCGCGA
droYak2	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATT---GGGA---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droEre2	CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATT---GGAG---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droEug1	CACAGTGCTGGAAAGGTGAGTT-----CATAGACTA----AATCAGTA---TGAA---AAGT-----------G---ACTA-----------AT------ATACCGAATTCG-------CAGGAGACGGATGCGCGA
droBia1	CACCGTGCTGGAGCGGTGAGTTT----CGTACACTT----AGTTAATT---CG-G---AGGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGGCGGATGCGCGA
droTak1	CACTGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---TGGA---AAGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droEle1	CACAGTGCTGGAGAGGTGAGTTT----CGTACGCTT----AATTAATA---AATG---AAGC-----------A---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droRho1	CACAGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---AAGG---AAGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA
droFic1	CACGGTTCTGGAGCGGTGAGTTT----CGTACACTT----AATTAATA---CAAGAAGCGGG-----------G---ATTA-----------ATAAAAGTATGTCGAACTCG-------CAGGCGGCGGATGCGCGA
droKik1	CACGGTGCTGGAAAGGCGAGTTT----TGTATATTT----AATTAATT---TTCA---AAGT-----ATCGTTCATAATTA-----------ATAAAAGTATGCTGAACTCG-------CAGGCGGCGAATGCGCGA
droAna3	CACTGTGCTGGAGAGGTAATCTT----TGAATAATT----ATCTGTGA---GTTG---TGGC-----------A---TCTA-----------ATGATTGT-----TATCTTC-------CAGACGTCGCATGCGTGA
droBip1	CACAGTGCTGGAGCGGTAAGTTG----GA-G-GAAT----GCCTATGAGTCACG-------------------------TC-----------ATGTACTGATCTTTATCTTC-------CAGACGACGGATGCGCGA
dp4	CACTGTGCTGGAGCGGTAAGTC-----CATG-------------AATT---GCAT---CCCCCTTTGATTATTCTTT-------AATCTGGA----AATCCCTGTGATCCCA-------TAGACGACGGATGCGCGA
droPer1	CACTGTGCTGGAGCGGTAAGTC-----CATG-------------AATT---GCAT---CCCCCTTTGATTATTCTTT-------AATCTGGA----AATCCCTGTGATCCCA-------TAGACGACGGATGCGCGA
droWil1	AACTGTATTAGAAAGGTATAATG----AATAAACCA----ATTTGAAT---AG-C---AAAC-----------C---ATTA-----------AATCAATTTCCTTTTTTGTC-------TAGACGACGTATGCGTGA
droVir3	CACAGTGCTGGAGAGGTGGGTG-----CATCCACAT----CAGCTGCT---TG-A---TAAC-----------C---ATTTGTAAA--TGTA---AATCCTCCTTTAACTCG-TTTGAACAGGCGACGCATGCGCGA
droMoj3	CACAGTGCTGGAGAGGTGGGAG-----CATTGATTTCACCACCCATAAGACACA-------------------------TTCTCAC--AGTT---TTTCTTGC-TTAATTCC-TTTGTACAGGCGGCGCATGCGCGA
droGri2	CACAGTGCTGGAAAGGTGATTCAAATCCATA----------------AGCCACAA---TCTTCTT-AAATATTATTT-------TCGCT------AATGCTATTTGTACTCGCTTTGATTAGGCGTCGCATGCGGGA

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
............................................................................................ATAAAAGTATGCCGAACTCG-------..................	20	1	275.00	2.00	211.00	41.00	21.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CA................	22	1	206.00	11.00	126.00	26.00	43.00
............................................................................................ATAAAAGTATGCCGAACTCG-------C.................	21	1	104.00	4.00	78.00	12.00	10.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGT..............	23	1	100.00	4.00	18.00	10.00	68.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAG...............	23	1	78.00	48.00	12.00	2.00	16.00
............................................................................................ATAAAAGTATGCCGAACTC..........................	19	1	24.00	0.00	21.00	2.00	1.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CA................	21	1	22.00	1.00	14.00	4.00	3.00
..............................................................................................AAAAGTATGCCGAACTCG-------CAGT..............	22	1	20.00	0.00	5.00	1.00	14.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAG...............	22	1	14.00	8.00	2.00	3.00	1.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGC..............	23	1	13.00	0.00	3.00	2.00	8.00
.............................................................................................TAAAAGTATGCCGAACTCG-------C.................	20	1	12.00	0.00	8.00	3.00	1.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGG..............	23	1	12.00	0.00	4.00	1.00	7.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CG................	22	1	11.00	0.00	4.00	4.00	3.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAGT..............	24	1	8.00	1.00	0.00	4.00	3.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CT................	22	1	6.00	0.00	6.00	0.00	0.00
..................................TT----AATTAATA---GGAT---CGGC-----------C---............................................................	19	1	5.00	0.00	5.00	0.00	0.00
............................................................................................ATAAAAGGATGCCGAACTCG-------CA................	22	1	4.00	1.00	2.00	0.00	1.00
............................................................................................ATAAAAGTATGCCGAACT...........................	18	1	4.00	0.00	4.00	0.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAGC..............	24	1	4.00	0.00	1.00	0.00	3.00
............................GTACACTT----AATTAATA---GGAT---CGGC-----------C---............................................................	25	1	3.00	0.00	3.00	0.00	0.00
.................................CTT----AATTAATA---GGAT---CGGC-----------C---............................................................	20	1	3.00	0.00	3.00	0.00	0.00
............................................AATA---GGAT---CGGC-----------C---GTTA-----------ATAA.........................................	21	1	3.00	0.00	3.00	0.00	0.00
..............................................................................................AAAAGTATGCCGAACTCG-------CAGG..............	22	1	2.00	0.00	0.00	0.00	2.00
............................................................................................ATAAAATTATGCCGAACTCG-------..................	20	1	2.00	0.00	1.00	0.00	1.00
.............................................................................................TAAAATTATGCCGAACTCG-------C.................	20	1	2.00	0.00	2.00	0.00	0.00
.............................................ATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGT.....................................	24	1	2.00	0.00	2.00	0.00	0.00
................................ACTT----AATTAATA---GGAT---CGGC-----------C---............................................................	21	1	2.00	0.00	2.00	0.00	0.00
.............................................................................................TAAAAGTATCCCGAACTCG-------CAGT..............	23	1	2.00	0.00	2.00	0.00	0.00
............................................................................................ATAAAAGTATGCCGAACTGG-------..................	20	1	2.00	0.00	0.00	2.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAGG..............	24	1	2.00	0.00	1.00	0.00	1.00
.....................TT----CGTACACTT----AATTAATA---GGAT---C..............................................................................	24	1	2.00	0.00	2.00	0.00	0.00
...........................................TAATA---GGAT---CGGC-----------C---GTTA-----------ATAA.........................................	22	1	1.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAACTATGCCGAACTCG-------CA................	22	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TAAAAGTATGCCGAACTCG-------AC................	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TAAAAGTATGTCGAACTCG-------CAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................AGTATGCCGAACTCG-------CAGT..............	19	1	1.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATACCGATCTCG-------CAG...............	23	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATAAAAGTATGCTGAACTCG-------..................	20	1	1.00	0.00	1.00	0.00	0.00
...................................T----AATTAATA---GGAT---CGGC-----------C---GTTA-----------A............................................	23	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TAAAAGTATGCCGAACTC..........................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TAAAAGCATGCCGAACTCG-------CAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
............................................AATA---GGAT---CGGC-----------C---GTTA-----------ATAAAA.......................................	23	1	1.00	0.00	1.00	0.00	0.00
............................................................................................ATAAAAGAATGCCGAACTCG-------CAGT..............	24	1	1.00	0.00	0.00	1.00	0.00
................................................................................A-----------ATAAAAGTATGCCGAACTC..........................	20	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................TAAAAGTATGCCGAACTCG-------..................	19	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TAAAAGTATGCCAAACTCG-------CAG...............	22	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATAAAAGTTTGCAGAACTCG-------CAG...............	23	1	1.00	1.00	0.00	0.00	0.00
...................................T----AATTAATA---GGAT---CGGC-----------C---............................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAC...............	23	1	1.00	0.00	1.00	0.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCT-------..................	20	1	1.00	0.00	1.00	0.00	0.00
.........................................ATTAATA---GGAT---TGGC-----------C---GTTA-----------A............................................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................................................ATAAAAGTAAGCCGAACTCG-------C.................	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGTT.............	24	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................AAAAGTATGCCGAACTCG-------CAGC..............	22	1	1.00	0.00	0.00	0.00	1.00
.........................................ATTAATA---GGAT---CGGC-----------C---GTTA-----------AT...........................................	22	1	1.00	0.00	1.00	0.00	0.00
............................................................................................ATAACAGTATGCCGAACTCG-------CAG...............	23	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATCAAAGTATGCCGAACTCG-------..................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................A-----------ATAAAAGxATGCCGTACTCG-------CAG...............	23	1	1.00	1.00	0.00	0.00	0.00
.............................................ATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAG......................................	23	1	1.00	0.00	1.00	0.00	0.00
...........................................TAATA---GGAT---CGGC-----------C---GTTA-----------AT...........................................	20	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................GTATGCCGAACTCG-------CAGT..............	18	1	1.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CC................	22	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TAAAAGTATGCCGTACTCG-------CA................	21	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATAAAAGAATGCCGAACTCG-------..................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................ATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTAT...................................	26	1	1.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------T.................	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CT................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCC-------..................	20	1	1.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAT...............	23	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATAAAAGTATACCGAACTCG-------CAGT..............	24	1	1.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGAATGCCGAACTCG-------CAG...............	23	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATAAAAGGATGCCGAACTCG-------C.................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................................................ATAAAAGTCTGCCGCACTCG-------CAG...............	23	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATAAAAGTATGGCGAACTCG-------..................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TAAAAATATACCGAACTCG-------CA................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................A-----------ATAAAAGTATGCCGAACTCG-------CAGC..............	25	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................TAAAAGTATGCCGGACTCG-------CAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
............................................AATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAG......................................	24	1	1.00	0.00	1.00	0.00	0.00
.............................................ATA---GGAT---CGGC-----------C---GTTA-----------ATAAAA.......................................	22	1	1.00	0.00	1.00	0.00	0.00
............................................................................................ATAAAAGTATGCCGAAATCG-------CAG...............	23	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATAAAAGGATGCCGAACTCG-------..................	20	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................AAAAGTATGCCGAACTCG-------CAG...............	21	1	1.00	1.00	0.00	0.00	0.00
............................................................................................ATAAAAGTATGTCGAACTCG-------CA................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................TA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTATGC.................................	27	1	1.00	0.00	0.00	0.00	1.00

droSec1

CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTTTGCCGAACTCG-------CAGGCGACGGATGCGCGA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
............................................................................................ATAAAAGTTTGCCGAACTCG-------C.................	21	1	172.00	7.00	142.00	23.00
............................................................................................ATAAAAGTTTGCCGAACTCG-------CAG...............	23	1	88.00	1.00	74.00	13.00
............................................................................................ATAAAAGTTTGCCGAACTCG-------..................	20	1	32.00	3.00	18.00	11.00
.............................................................................................TAAAAGTTTGCCGAACTCG-------CAGT..............	23	1	27.00	0.00	25.00	2.00
.............................................................................................TAAAAGTTTGCCGAACTCG-------CAG...............	22	1	25.00	2.00	21.00	2.00
..............................................................................................AAAAGTTTGCCGAACTCG-------CAGT..............	22	1	20.00	2.00	16.00	2.00
............................................................................................ATAAAAGTTTGCCGAACTCG-------CA................	22	1	17.00	0.00	12.00	5.00
............................................................................................ATAAAAGTTTGCCGAACTCG-------CAGT..............	24	1	12.00	1.00	11.00	0.00
.............................................................................................TAAAAGTTTGCCGAACTCG-------CA................	21	1	7.00	1.00	4.00	2.00
............................................................................................ATAAAAGTTTGCCGAATTCG-------C.................	21	1	3.00	0.00	3.00	0.00
..............................................................................................AAAAGTTTGCCGAACTCG-------CAG...............	21	1	3.00	0.00	2.00	1.00
............................................................................................ATAAAAGTTTGCCGAACTCG-------T.................	21	1	2.00	0.00	0.00	2.00
.............................................................................................TAAAAGTTTGCCGAACTCG-------C.................	20	1	2.00	0.00	1.00	1.00
............................................................................................ATAAAAGTTTGCCGAACTC..........................	19	1	2.00	0.00	0.00	2.00
.............................................................................................TAAAAGTTTGCCGAACTCG-------CAGA..............	23	1	1.00	0.00	1.00	0.00
............................................................................................ATAAAAGTTTGCCAAACTCG-------C.................	21	1	1.00	0.00	0.00	1.00
..............................................................................................AAAAGTTTGCCGAACTCG-------TAGT..............	22	1	1.00	0.00	1.00	0.00
............................................................................................ATGAAAGTTTGCCGAACTCG-------..................	20	1	1.00	0.00	1.00	0.00
............................................................................................ATTAAAGTTTGCCGAACTCG-------..................	20	1	1.00	0.00	1.00	0.00
.............................................................................................TAAAAGTTTGCCGAACTCG-------CAGTT.............	24	1	1.00	0.00	0.00	1.00
............................................................................................ATAAAAGxTTGCCGAACTCG-------CGG...............	22	1	1.00	0.00	1.00	0.00
............................................................................................ATAAAAGTTTGCCGATCTCG-------C.................	21	1	1.00	0.00	1.00	0.00
............................................................................................ATAAAAGTTTGCCGAAGTCG-------CAG...............	23	1	1.00	0.00	1.00	0.00
............................................................................................ATATAAGTTTGCCGAACTCG-------..................	20	1	1.00	0.00	1.00	0.00
............................................................................................ATAAAAGTTTGCCGAACCCG-------C.................	21	1	1.00	0.00	1.00	0.00
............................................................................................ATAAAAGTTTGCCGAACTCG-------GAG...............	23	1	1.00	0.00	1.00	0.00
.............................................................................................TAAAAGxTTGCCGAACTCG-------CAGT..............	22	1	1.00	0.00	1.00	0.00
................................................................................................AAGTTTGCCGAACTCG-------CAG...............	19	1	1.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAG...............	23	1	1.00	0.00	1.00	0.00
...............GTGAGTTT----CGTACACTT----AATT.............................................................................................	21	1	1.00	0.00	0.00	1.00
............................................................................................ATAAAAGxTTGCCGAACTCG-------C.................	20	1	1.00	0.00	1.00	0.00
..............................................................................................AAAAGTTTGCCGAACTCG-------CGGT..............	22	1	1.00	0.00	1.00	0.00
............................................................................................ATAAAAGTTTGCCGAACTCA-------C.................	21	1	1.00	0.00	1.00	0.00
............................................................................................ATAAAAGTTTGCCGACCTCG-------CAG...............	23	1	1.00	0.00	0.00	1.00
.............................................................................................TAAAACTTTGCCGAACTCG-------CAG...............	22	1	1.00	0.00	1.00	0.00
.............................................ATA---GGAT---CGGC-----------C---GTTA-----------ATAAAAGTTTG..................................	27	1	1.00	1.00	0.00	0.00
............................................................................................ATAAAAGTTTGCCGAACTCG-------CT................	22	1	1.00	1.00	0.00	0.00
.............................................................................................ATAAAGTTTGCCGAACTCG-------CAG...............	22	1	1.00	0.00	1.00	0.00
............................................AATA---GGAT---CGGC-----------C---GTTA-----------A............................................	18	1	1.00	0.00	0.00	1.00

droYak2

CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATT---GGGA---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............................................................................................ATAAAAGTATGCCGAACTCG-------CA................	22	1	232.00	19.00	10.00	6.00	41.00	156.00
............................................................................................ATAAAAGTATGCCGAACTCG-------..................	20	1	139.00	2.00	0.00	14.00	21.00	102.00
............................................................................................ATAAAAGTATGCCGAACTCG-------C.................	21	1	130.00	14.00	6.00	14.00	35.00	61.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAG...............	23	1	60.00	18.00	11.00	1.00	23.00	7.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGT..............	23	1	33.00	9.00	1.00	2.00	4.00	17.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CA................	21	1	29.00	5.00	0.00	5.00	7.00	12.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAG...............	22	1	20.00	4.00	1.00	1.00	10.00	4.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CT................	22	1	18.00	0.00	1.00	0.00	1.00	16.00
.............................................................................................TAAAAGTATGCCGAACTCG-------C.................	20	1	17.00	0.00	1.00	2.00	0.00	14.00
..............................................................................................AAAAGTATGCCGAACTCG-------CAGT..............	22	1	14.00	5.00	3.00	2.00	1.00	3.00
............................................................................................ATAAAAGTATGCCGAACTC..........................	19	1	13.00	1.00	0.00	0.00	0.00	12.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CC................	22	1	11.00	0.00	0.00	0.00	0.00	11.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAGT..............	24	1	5.00	2.00	0.00	2.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CG................	22	1	4.00	0.00	0.00	0.00	0.00	4.00
.............................................................................................TAAAAGTATGCCGAACTCG-------..................	19	1	4.00	0.00	0.00	0.00	0.00	4.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGC..............	23	1	4.00	0.00	0.00	0.00	1.00	3.00
..............................................................................................AAAAGTATGCCGAACTCG-------CAG...............	21	1	3.00	1.00	0.00	1.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAA...............	23	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAA...............	22	1	2.00	1.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATGCCGAACTCG-------T.................	21	1	2.00	0.00	0.00	1.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAT...............	23	1	2.00	0.00	0.00	0.00	0.00	2.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CCG...............	23	1	2.00	0.00	0.00	0.00	2.00	0.00
............................................................................................ATAAAAGTATGCCGAACTAG-------C.................	21	1	2.00	2.00	0.00	0.00	0.00	0.00
............................................................................................ATAAAAGTATTCCGAACTCG-------C.................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
............................................................................................ATAAAAGGATGCCGAACTCG-------CA................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................................AGTATGCCGAACTCG-------CAGT..............	19	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATGAAAGTATGCCGAACTCG-------CCG...............	23	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................ATAAAAGTATGCTGAACTCG-------..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAGGTATGCCGAACTCG-------CA................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATACCGAACTCG-------CAG...............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGA..............	23	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................ATAAAAGTATGCCAAACTC..........................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................TAAAAGTATGCCGAACTAG-------CAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGGGTTT----CGTACACTT----AATT.............................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGACCTCG-------..................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTTTGCCGAACTCG-------CAG...............	23	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................ATAAAAGGAGGCCGAACTCG-------C.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................A-----------ATAAAAGTATGCCGAACTCG-------CAGT..............	25	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................TAAAAGTATxCCGAACTCG-------CCG...............	21	1	1.00	1.00	0.00	0.00	0.00	0.00
...............GTGAGTTT----CGTACACTT----AATTAATT---GGGA---C..............................................................................	30	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................................................ATAAAAGTATGCCAAACTCG-------CA................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGGATGCCGAACTA..........................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TAAAGGTATGCCGAACCCG-------CAGG..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAC...............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATGCCGAACTCT-------C.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCT-------..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAATTATGCCGAACTCG-------CA................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................AAAGGATGCCGAACTCG-------CAGT..............	21	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................ATAAAAGTATGCCGAACGCG-------CT................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAACGTATGCCGACCTCG-------C.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAATATGCCGAACTCG-------C.................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTCTGCCGAACTCG-------CA................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTCTGCCGAACTCG-------..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATGCCGAACT...........................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................AAAAGTATGCCGAACTCG-------C.................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACGCG-------C.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................AATT---GGGA---CGGC-----------C---GTTA-----------ATAAAAGTATGC.................................	29	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................................................ATAAAAGTATACCGAACTCG-------..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................TAAAAGTATGCTGAACTCG-------CAGT..............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................TAAAAGTATGCCTAACTGG-------..................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGGATACCGAACT...........................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTGG-------..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGG..............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................................AAAGTATGCCGAACTCG-------CAGTA.............	22	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................GATTAATA---GGGA---CGGC-----------C---G...........................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TAAAAGGATGCCGAACTCG-------CAGT..............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATCCCGAACTCG-------C.................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATGAAAGTATGCCGAACTCG-------A.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAGGTATGCCGAACTCG-------..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATACCGAACTCG-------CT................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................................GTATGCCGAACTCG-------CCGT..............	18	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTACGCCGAACTCG-------..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATGCCGAGCTCG-------CA................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
............................................................................................ATAAAAGTATGCCGCACTCG-------C.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAACGTATGCCGAACTCG-------..................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TAAAAGTATGCCCAACTCG-------CAGA..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATACAAGTCTGCCGAACTCG-------..................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACGCT-------CA................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATTCCGAACTCG-------CA................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATGCCGAACTCA-------C.................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................ATAAAAGTATGCCGAACACG-------C.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................A-----------ATAAAAGAATGCCGAACTCG-------..................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTTT----CGTACACTT----AATT.............................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGAACTCC-------C.................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................TAACAGTATGCCGCACTCG-------CAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..CCGTGxTGGAGAGGAGAG.....................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................TAAAAGTATGCCGTACTCG-------CAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................ATAAAAGTATGCCGACCTCG-------C.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CACCGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATT---GGAG---CGGC-----------C---GTTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
............................................................................................ATAAAAGTATGCCGAACTCG-------CA................	22	1	431.00	11.00	18.00	0.00	402.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAG...............	23	1	269.00	5.00	14.00	0.00	250.00
............................................................................................ATAAAAGTATGCCGAACTCG-------C.................	21	1	215.00	8.00	13.00	0.00	194.00
............................................................................................ATAAAAGTATGCCGAACTCG-------..................	20	1	94.00	2.00	9.00	0.00	83.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAG...............	22	1	48.00	3.00	3.00	0.00	42.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CT................	22	1	25.00	0.00	3.00	0.00	22.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGT..............	23	1	10.00	1.00	0.00	0.00	9.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CA................	21	1	6.00	0.00	0.00	0.00	6.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAT...............	23	1	6.00	0.00	0.00	0.00	6.00
............................................................................................ATAAAAGTATGCCTAACTCG-------CAG...............	23	1	5.00	0.00	0.00	0.00	5.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAGA..............	24	1	5.00	0.00	0.00	0.00	5.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAA...............	23	1	4.00	0.00	0.00	0.00	4.00
............................................................................................ATAAAAGTATGCCGAACTCT-------CA................	22	1	4.00	0.00	0.00	0.00	4.00
.............................................................................................TAAAAGTATGCCGAACTCG-------CAGA..............	23	1	4.00	1.00	0.00	0.00	3.00
............................................................................................ATAAAAGTATGCCGAACTCG-------CAGT..............	24	1	3.00	0.00	0.00	0.00	3.00
............................................................................................ATAAAAGTATGACGAACTCG-------CAG...............	23	1	3.00	0.00	0.00	0.00	3.00
............................................................................................ATAAAAGTATGCCGAACTCG-------T.................	21	1	3.00	0.00	1.00	0.00	2.00
............................................................................................ATAAAAGTATGCCTAACTCG-------CA................	22	1	3.00	0.00	0.00	0.00	3.00
............................................................................................ATAAAAGTATGCCGAACTAG-------CAG...............	23	1	3.00	0.00	0.00	0.00	3.00
............................................................................................ATAAAAGTATGCCGAACTCG-------A.................	21	1	3.00	0.00	1.00	0.00	2.00
............................................................................................ATAAAAGTATGCCGAACTC..........................	19	1	3.00	0.00	0.00	0.00	3.00
............................................................................................ATAAAAGTATGCAGAACTCG-------CA................	22	1	3.00	0.00	0.00	0.00	3.00

droEug1

CACAGTGCTGGAAAGGTGAGTT-----CATAGACTA----AATCAGTA---TGAA---AAGT-----------G---ACTA-----------AT------ATACCGAATTCG-------CAGGAGACGGATGCGCGA

Size

Hit Count

Total Norm

droBia1

CACCGTGCTGGAGCGGTGAGTTT----CGTACACTT----AGTTAATT---CG-G---AGGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGGCGGATGCGCGA

Size

Hit Count

Total Norm

droTak1

CACTGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---TGGA---AAGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA

Size

Hit Count

Total Norm

droEle1

CACAGTGCTGGAGAGGTGAGTTT----CGTACGCTT----AATTAATA---AATG---AAGC-----------A---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA

Size

Hit Count

Total Norm

droRho1

CACAGTGCTGGAGAGGTGAGTTT----CGTACACTT----AATTAATA---AAGG---AAGC-----------C---ATTA-----------ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGCGCGA

Size

Hit Count

Total Norm

droFic1

CACGGTTCTGGAGCGGTGAGTTT----CGTACACTT----AATTAATA---CAAGAAGCGGG-----------G---ATTA-----------ATAAAAGTATGTCGAACTCG-------CAGGCGGCGGATGCGCGA

Size

Hit Count

Total Norm

droKik1

CACGGTGCTGGAAAGGCGAGTTT----TGTATATTT----AATTAATT---TTCA---AAGT-----ATCGTTCATAATTA-----------ATAAAAGTATGCTGAACTCG-------CAGGCGGCGAATGCGCGA

Size

Hit Count

Total Norm

droAna3

CACTGTGCTGGAGAGGTAATCTT----TGAATAATT----ATCTGTGA---GTTG---TGGC-----------A---TCTA-----------ATGATTGT-----TATCTTC-------CAGACGTCGCATGCGTGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................TGTGG---GTTG---GGGC-----------A---TCT.........................................................	17	1	1.00	0.00	0.00	1.00	0.00
...........................................TGTGG---GTTG---TGGG-----------A---TCT.........................................................	17	1	1.00	0.00	0.00	1.00	0.00
....................CTT----GGAATAATT----ATCTGGGA---......................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.....................TT----GGAATAATT----ATCGGTG..........................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droBip1

CACAGTGCTGGAGCGGTAAGTTG----GA-G-GAAT----GCCTATGAGTCACG-------------------------TC-----------ATGTACTGATCTTTATCTTC-------CAGACGACGGATGCGCGA

Size

Hit Count

Total Norm

dp4

CACTGTGCTGGAGCGGTAAGTC-----CATG-------------AATT---GCAT---CCCCCTTTGATTATTCTTT-------AATCTGGA----AATCCCTGTGATCCCA-------TAGACGACGGATGCGCGA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
............................................GATC---GCAT---CCCCCTTTGA.....................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CACTGTGCTGGAGCGGTAAGTC-----CATG-------------AATT---GCAT---CCCCCTTTGATTATTCTTT-------AATCTGGA----AATCCCTGTGATCCCA-------TAGACGACGGATGCGCGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................................................................................GTGAGCCCA-------TAGxCGACGGA.......	19	1	7.00	7.00	0.00	0.00	0.00	0.00

droWil1

AACTGTATTAGAAAGGTATAATG----AATAAACCA----ATTTGAAT---AG-C---AAAC-----------C---ATTA-----------AATCAATTTCCTTTTTTGTC-------TAGACGACGTATGCGTGA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........................................TGAAT---Ax-C---AAAC-----------C---ATGA-----------AA...........................................	18	1	2.00	0.00	2.00	0.00	0.00
...................AATA----AATAAATCA----ATTTG............................................................................................	18	4	0.25	0.00	0.25	0.00	0.00

droVir3

CACAGTGCTGGAGAGGTGGGTG-----CATCCACAT----CAGCTGCT---TG-A---TAAC-----------C---ATTTGTAAA--TGTA---AATCCTCCTTTAACTCG-TTTGAACAGGCGACGCATGCGCGA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.....................................................................................................CGGTTAACTCG-TTTGAAC.................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................................AGCAxGCGACGCATGCGCG.	18	1	1.00	0.00	0.00	1.00	0.00	0.00
...AGGGGTGGAGAGGTGGG.....................................................................................................................	17	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

CACAGTGCTGGAGAGGTGGGAG-----CATTGATTTCACCACCCATAAGACACA-------------------------TTCTCAC--AGTT---TTTCTTGC-TTAATTCC-TTTGTACAGGCGGCGCATGCGCGA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CACAGTGCTGGAAAGGTGATTCAAATCCATA----------------AGCCACAA---TCTTCTT-AAATATTATTT-------TCGCT------AATGCTATTTGTACTCGCTTTGATTAGGCGTCGCATGCGGGA	Size	Hit Count	Total Norm	V109 Male body
.ACAGTGATGGAAAGATGA......................................................................................................................	18	1	6.00	6.00

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

dme-mir-1013

chr3R:26617358-26617418 -

Known_mirbase

mirtron

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