dme-mir-990- Best orthologs

dme-mir-990	chr2R:12782728-12782813 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 12782780-12782800
   star strand at position 12782742-12782765
   mutations
   read mismatches

Notes: "Large deletion in droAna3 - droGri2, however the orthologs look confident for these species. "

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:12782713-12782828 -		1	TGGGAAAC------TGGCGAA---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGCTTCGGTGCCATTT-CACCCCGA---GCACCAAGAG-----------------------------------------------------------------CATCAGA---------------------CT
droSim1	chr2R:11518341-11518456 -	LASTZ	1	TGGGAAAC------TGGCGAA---------TCTG------------CTCAGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGCTTCGGTGCCATTT-CACCCCGA---GCACCAAGAG-----------------------------------------------------------------CATCAGA---------------------CT
droSec1	super_1:10286785-10286900 -	LASTZ	1	TGGGAAAC------TGGCGAA---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGCTTCGGTGCCATTT-CACCCCGA---GCACCAAGAG-----------------------------------------------------------------TATCAGA---------------------CT
droYak2	chr2R:16191830-16191945 +	LASTZ	1	TGGGAAAC------TGGCGAA---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTT-CACCCCGA---ACAGCAAGAC-----------------------------------------------------------------CATCAGA---------------------CT
droEre2	scaffold_4845:13064860-13064974 +	LASTZ	1	TGGGTAAC------TGGCGAG---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTT-CACCCCCA---GCACCAAGAG-----------------------------------------------------------------CA-CCGA---------------------CT
droEug1	scf7180000409672:2349853-2349966 +	LASTZ	4	TGGGAAAC------TGGCGAA---------GCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCGATTT-CAACCCGA---CTACTAACAG-----------------------------------------------------------------C--CAGA---------------------CT
droBia1	scf7180000301506:2208156-2208269 -	LASTZ	4	TGGGAAAC------TGGCGAT---------GCTG------------CTGTGC-GACATTCACCGTTCTGAGTTGGCCCCAACTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTTAACCCCTGA---ACACCAAGAG--------------------------------------------------------------------CAGC---------------------CC
droTak1	scf7180000415389:316919-317036 -	LASTZ	4	TGGGAAAC------TGTCGAA---------GCTG------------CCCTGC-GACATTCACCGTTCTGAGTTGGCCCCAACTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGACATTT-CACCCCGACAAACACCAAAGG--------------------------------------------------------------------CAGACT-------------------AT
droEle1	scf7180000491214:1580257-1580370 +	LASTZ	4	TGGGAAAC------TGGCGTT---------GCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAGTTGCACGTGGG-CCAG----C------------CTTCAGTTTCGGTGCCATTTTCACCCCGA---GTGCCAGGAG--------------------------------------------------------------------CAGA---------------------CT
droRho1	scf7180000780084:554991-555104 +	LASTZ	4	TGGGAAAC------TGGCCAA---------GCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTTTCACCCCAA---GTGCCAGGAG--------------------------------------------------------------------CAGA---------------------CT
droFic1	scf7180000453948:2648196-2648326 +	LASTZ	4	TGGGAAGC------TGGCGCT---------GCTG------------CCTGGC-GACATTCACCGTTCTGAGTTGGCCCCCGTTGCACGTGGG-CTGG----C------------C--CAGCTACGGTGCTATTA-AGCCTC-A---GCATCGAAGG-----------------------------------------------------------------C---GGACCACCACTACCACAACTGAGACT
droKik1	scf7180000302470:1199420-1199550 -	LASTZ	4	TGGGAAAT------TGGCGAA---------GCTG------------CTCTGC-GACATTCACCGTTCTGCGTTGGCCCCAAGTGCACGTGGG-CCAA----C------------TCTCAGTTACGGTGTAATAA-CAGTGCCA---C-ATCTTAGCCAGATTCCACCACA-------------------TATATCGC------------------------------C---------------------TC
droAna3	scaffold_13266:13815719-13815830 +	LASTZ	5	TGGGAAAT------TGTCGAA---------GCCA------------CTTTGC-GACATTCCCCGTTCTGCGTTGGCCCAAGGTGCACGTGGG-GCCGACGAC------------TCTCCGCTTCCGGACCCAT--------------TGCCGAAAA---------------------------------TACATTCT------------------------------T---------------------CA
droBip1	scf7180000396759:2320923-2321034 -	LASTZ	5	TGGGAAAT------TTGGTAG----AA---GCTGC---------TACTTTGC-GACATTCCCCGTTCTGCGTTGGCCAAAGGTGCACGTGGGGCCGA----C------------TTTCCGCTTCCGGACC-----------TA---TTGCCGAAAA---------------------------------TATAT--------------------------------CC---------------------TT
dp4	chr3:6727705-6727891 -	LASTZ	5	TGGGAAAC------TGGCGAG---------GCGA-GGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGG-TTAC----GCCTGAAGCTCCAATTCGGTTACGGTTT------C---------------GGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGA---------------------CA
droPer1	super_2:6950668-6950854 -	LASTZ	5	TGGGAAAC------TGGCGAG---------GCGA-GGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGG-TTAC----GCCTGAAGCTCCAATTCGGTTACGGTTT------C---------------GGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGA---------------------CA
droWil1	scaffold_180700:6478759-6478837 -	LASTZ	5	TGGGAAATACATCTTCGTTTGGCTTTAGTTTCTC------------TTCTGCGGACATTCAATGTTCTGCGTTTGCCCCAAGCGCACGTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12875:2573949-2574010 +	LASTZ	5	TGGGAAAC------TG-CGAA---------GCTG------------CTTTGC-GACATTCGACTTGCTGCGTTCGTCGCCGACGCACGTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:22657688-22657749 -	LASTZ	5	TGGGAAAC-------GGCGAA---------GCTT------------CTGTGC-GACATTCAACGTTCTGCGTTCGTCGCCGACGCACGTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15112:4702153-4702224 +	LASTZ	5	TGGGAATT------TTGCGAA---------GCTGCTGCTGTGGCT--GCTGC-GACATTCAACGTTCTGCGTTGGCCGCCGACGCACGTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------

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	TGGGAAAC------TGGCGAA---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGCTTCGGTGCCATTT-CACCCCGA---GCACCAAGAG-----------------------------------------------------------------CATCAGA---------------------CT
droSim1	TGGGAAAC------TGGCGAA---------TCTG------------CTCAGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGCTTCGGTGCCATTT-CACCCCGA---GCACCAAGAG-----------------------------------------------------------------CATCAGA---------------------CT
droSec1	TGGGAAAC------TGGCGAA---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGCTTCGGTGCCATTT-CACCCCGA---GCACCAAGAG-----------------------------------------------------------------TATCAGA---------------------CT
droYak2	TGGGAAAC------TGGCGAA---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTT-CACCCCGA---ACAGCAAGAC-----------------------------------------------------------------CATCAGA---------------------CT
droEre2	TGGGTAAC------TGGCGAG---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTT-CACCCCCA---GCACCAAGAG-----------------------------------------------------------------CA-CCGA---------------------CT
droEug1	TGGGAAAC------TGGCGAA---------GCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCGATTT-CAACCCGA---CTACTAACAG-----------------------------------------------------------------C--CAGA---------------------CT
droBia1	TGGGAAAC------TGGCGAT---------GCTG------------CTGTGC-GACATTCACCGTTCTGAGTTGGCCCCAACTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTTAACCCCTGA---ACACCAAGAG--------------------------------------------------------------------CAGC---------------------CC
droTak1	TGGGAAAC------TGTCGAA---------GCTG------------CCCTGC-GACATTCACCGTTCTGAGTTGGCCCCAACTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGACATTT-CACCCCGACAAACACCAAAGG--------------------------------------------------------------------CAGACT-------------------AT
droEle1	TGGGAAAC------TGGCGTT---------GCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAGTTGCACGTGGG-CCAG----C------------CTTCAGTTTCGGTGCCATTTTCACCCCGA---GTGCCAGGAG--------------------------------------------------------------------CAGA---------------------CT
droRho1	TGGGAAAC------TGGCCAA---------GCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTTTCACCCCAA---GTGCCAGGAG--------------------------------------------------------------------CAGA---------------------CT
droFic1	TGGGAAGC------TGGCGCT---------GCTG------------CCTGGC-GACATTCACCGTTCTGAGTTGGCCCCCGTTGCACGTGGG-CTGG----C------------C--CAGCTACGGTGCTATTA-AGCCTC-A---GCATCGAAGG-----------------------------------------------------------------C---GGACCACCACTACCACAACTGAGACT
droKik1	TGGGAAAT------TGGCGAA---------GCTG------------CTCTGC-GACATTCACCGTTCTGCGTTGGCCCCAAGTGCACGTGGG-CCAA----C------------TCTCAGTTACGGTGTAATAA-CAGTGCCA---C-ATCTTAGCCAGATTCCACCACA-------------------TATATCGC------------------------------C---------------------TC
droAna3	TGGGAAAT------TGTCGAA---------GCCA------------CTTTGC-GACATTCCCCGTTCTGCGTTGGCCCAAGGTGCACGTGGG-GCCGACGAC------------TCTCCGCTTCCGGACCCAT--------------TGCCGAAAA---------------------------------TACATTCT------------------------------T---------------------CA
droBip1	TGGGAAAT------TTGGTAG----AA---GCTGC---------TACTTTGC-GACATTCCCCGTTCTGCGTTGGCCAAAGGTGCACGTGGGGCCGA----C------------TTTCCGCTTCCGGACC-----------TA---TTGCCGAAAA---------------------------------TATAT--------------------------------CC---------------------TT
dp4	TGGGAAAC------TGGCGAG---------GCGA-GGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGG-TTAC----GCCTGAAGCTCCAATTCGGTTACGGTTT------C---------------GGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGA---------------------CA
droPer1	TGGGAAAC------TGGCGAG---------GCGA-GGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGG-TTAC----GCCTGAAGCTCCAATTCGGTTACGGTTT------C---------------GGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGA---------------------CA
droWil1	TGGGAAATACATCTTCGTTTGGCTTTAGTTTCTC------------TTCTGCGGACATTCAATGTTCTGCGTTTGCCCCAAGCGCACGTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	TGGGAAAC------TG-CGAA---------GCTG------------CTTTGC-GACATTCGACTTGCTGCGTTCGTCGCCGACGCACGTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	TGGGAAAC-------GGCGAA---------GCTT------------CTGTGC-GACATTCAACGTTCTGCGTTCGTCGCCGACGCACGTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	TGGGAATT------TTGCGAA---------GCTGCTGCTGTGGCT--GCTGC-GACATTCAACGTTCTGCGTTGGCCGCCGACGCACGTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------

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

TGGGAAAC------TGGCGAA---------TCTG------------CTCAGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGCTTCGGTGCCATTT-CACCCCGA---GCACCAAGAG-----------------------------------------------------------------CATCAGA---------------------CT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................ATTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1433.00	0.00	1392.00	35.00	6.00
........................................................ATTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	793.00	0.00	774.00	16.00	3.00
........................................................ATTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	326.00	12.00	282.00	5.00	27.00
........................................................ATTCACCGTTCTGAGTTGGAC..............................................................................................................................................................................	21	1	38.00	0.00	38.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGG................................................................................................................................................................................	19	1	18.00	0.00	18.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGAC...............................................................................................................................................................................	20	1	15.00	0.00	15.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCT.............................................................................................................................................................................	22	1	14.00	0.00	14.00	0.00	0.00
........................................................TTTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	14.00	0.00	13.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTGGCT..............................................................................................................................................................................	21	1	14.00	0.00	13.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCCT............................................................................................................................................................................	23	1	9.00	0.00	8.00	1.00	0.00
........................................................TTTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	6.00	0.00	6.00	0.00	0.00
........................................................ATTCACCGTTCTGAGGTGGCC..............................................................................................................................................................................	21	1	6.00	0.00	6.00	0.00	0.00
........................................................ATTCACCxTTCTGAGTTGGC...............................................................................................................................................................................	19	1	5.00	0.00	5.00	0.00	0.00
........................................................ATTCACCTTTCTGAGTTGGC...............................................................................................................................................................................	20	1	4.00	0.00	4.00	0.00	0.00
........................................................ATTCGCCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
........................................................ATTCACCGCTCTGAGTTGGCC..............................................................................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGA...............................................................................................................................................................................	20	1	3.00	0.00	1.00	2.00	0.00
........................................................ATTCACCGTTCTTAGTTGGCC..............................................................................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
..................................................................................................................................................GCACCAAGAG-----------------------------------------------------------------CATCAGA---------------------C.	18	1	3.00	0.00	3.00	0.00	0.00
.........................................................TTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	20	1	3.00	0.00	3.00	0.00	0.00
........................................................ATTCACCGTTCTGATTTGGC...............................................................................................................................................................................	20	1	3.00	0.00	3.00	0.00	0.00
........................................................ATTCACCGTTCTGAGGTGGC...............................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
........................................................ACTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGG...............................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTTGCCC.............................................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
...........................................................GACCGTTCGGAGTTGGCC..............................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
........................................................ATTCACCGTTCTGAGTTGGCCCG............................................................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
.....................................................GACATTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	25	1	2.00	0.00	1.00	0.00	1.00
..........................................................TCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
........................................................ATTCACCCTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	2.00	0.00	2.00	0.00	0.00
.........................................................TTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	21	1	2.00	0.00	2.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCTT............................................................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
........................................................ATTCACTGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	2.00	0.00	2.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGCCCC.............................................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCA.............................................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
........................................................ATTCACCGTTCTxAGTTGGCC..............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTTACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTG.................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................TTTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................................CATTCACCGTTCTGATTTGGCC..............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCATCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................ATCCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.......................................................GATTCACCGTTCTxAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCCC............................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTTGGCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGCGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................ATCCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.................................................................TCTGAGTTGGCCCCAAGTG.......................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGCTCTGAGTTTGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGGGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGTC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAATTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................................ATTTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTAGCC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...........................................................CACCGCTCTGAGTTGGCCC.............................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGGGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCTT.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTAGCCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCCGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGGTGGCCT.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..........................................................TCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTATGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTAAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGCTGGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAATTGGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTAAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................CTTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGCTCTGAGTTGGAC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGCC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.........................................................TTCACCGTTCTGAGTTGAC...............................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTGACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTCCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGACC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGATGGCC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................ACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................ATTCACCGTTCTGAGGTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

TGGGAAAC------TGGCGAA---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGCTTCGGTGCCATTT-CACCCCGA---GCACCAAGAG-----------------------------------------------------------------TATCAGA---------------------CT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................ATTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	381.00	3.00	157.00	221.00
........................................................ATTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	147.00	4.00	15.00	128.00
........................................................ATTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	120.00	0.00	2.00	118.00
........................................................ATTCACCGTTCTGAGTTGGCCT.............................................................................................................................................................................	22	1	20.00	0.00	2.00	18.00
........................................................ATTCACCGTTCTGAGTTGG................................................................................................................................................................................	19	1	16.00	0.00	0.00	16.00
...........................................................GACCGTTCGGAGTTGGCC..............................................................................................................................................................................	18	1	11.00	0.00	10.00	1.00
........................................................ATTCACCGTTCTGAGTTGGCCCT............................................................................................................................................................................	23	1	9.00	0.00	1.00	8.00
........................................................TTTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	7.00	0.00	7.00	0.00
........................................................ATTCACCTTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	2.00	0.00	0.00	2.00
........................................................ACTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	2.00	0.00	0.00	2.00
........................................................ATTCACCGTTCTCAGTTGGCCC.............................................................................................................................................................................	22	1	2.00	0.00	1.00	1.00
...........................................................GACCGTTCGGAGTTGGCCC.............................................................................................................................................................................	19	1	2.00	0.00	2.00	0.00
........................................................ATTCACCGTTCTGAGTTTGCCC.............................................................................................................................................................................	22	1	2.00	0.00	1.00	1.00
........................................................ATTCACCGTTCTGAGTTGGCCCA............................................................................................................................................................................	23	1	2.00	0.00	1.00	1.00
........................................................ATTCACCGTTATGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
.......................................................ATTTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
........................................................ATTTACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTG.................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
........................................................TTTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00
..........................................................TCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTGGT...............................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00
........................................................ATTCACCGTACTGAGTTGACCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00
.........................................................TTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00
..................................................................CTGAGTTGGCCCCAAGTGCACGTG.................................................................................................................................................................	24	1	1.00	0.00	0.00	1.00
........................................................GTTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
........................................................ATTCACCGTTCCGAGTTGG................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00
........................................................ATTCACCATTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTGGGCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
........................................................ATTAACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTGGCCCTA...........................................................................................................................................................................	24	1	1.00	0.00	0.00	1.00
.......................................................ATTTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGGGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00
........................................................TTTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
...............................................................................AAGTGCACGTGGG-CCAG----C------------T........................................................................................................................................	19	1	1.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTGGCCA.............................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00
........................................................ATTAACCGTCCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
........................................................ATTGACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTTGCCCT............................................................................................................................................................................	23	1	1.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTGACCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
........................................................ATTCACCGTTCCGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTCGC...............................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00
............................................................................CCCAAGTGCACGTGGG-CCAG----C------------.........................................................................................................................................	21	1	1.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGGTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00

droYak2

TGGGAAAC------TGGCGAA---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTT-CACCCCGA---ACAGCAAGAC-----------------------------------------------------------------CATCAGA---------------------CT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................................ATTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	497.00	0.00	16.00	1.00	13.00	467.00
........................................................ATTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	304.00	8.00	8.00	0.00	19.00	269.00
........................................................ATTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	260.00	2.00	23.00	1.00	41.00	193.00
........................................................ATTCACCGTTCTGAGTTGG................................................................................................................................................................................	19	1	30.00	0.00	3.00	1.00	18.00	8.00
........................................................ATTCACCGTTCTGAGTTGGCCCT............................................................................................................................................................................	23	1	16.00	0.00	0.00	0.00	0.00	16.00
........................................................ATTCACCGTTCTGAGTTGGAC..............................................................................................................................................................................	21	1	10.00	0.00	0.00	0.00	0.00	10.00
........................................................ATTCACCGTTCTGAGTTGAC...............................................................................................................................................................................	20	1	7.00	0.00	0.00	0.00	0.00	7.00
........................................................TTTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	5.00	0.00	0.00	0.00	0.00	5.00
...........................................................................................G-CCAG----C------------TTTCAGTTTCGGTGCCA........................................................................................................................	23	1	5.00	5.00	0.00	0.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCCC............................................................................................................................................................................	23	1	4.00	0.00	0.00	0.00	0.00	4.00
........................................................ATTCACCGTTCTGAGTTGGCCCA............................................................................................................................................................................	23	1	4.00	1.00	0.00	0.00	1.00	2.00
........................................................ATTCACCGCTCTGAGTTGGCC..............................................................................................................................................................................	21	1	4.00	0.00	0.00	0.00	0.00	4.00
........................................................ATTCACCGTTCTGAGTTGGCCCTT...........................................................................................................................................................................	24	1	4.00	0.00	0.00	0.00	0.00	4.00
........................................................TTTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
........................................................ATTCACCGTTCTGAGTTGGG...............................................................................................................................................................................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
...........................................................CACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	19	1	3.00	0.00	0.00	0.00	0.00	3.00
........................................................ATTCACCGTTCTGATTTGGC...............................................................................................................................................................................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
........................................................TTTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................ATTCACCGTTCTGAGTTGGCCG.............................................................................................................................................................................	22	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................ATTCACCGTTCTGAGTTGGCCT.............................................................................................................................................................................	22	1	2.00	0.00	0.00	0.00	1.00	1.00
........................................................ATTCACTGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................ATTCACCGTTCTGAGTTGGCCCG............................................................................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................ATTCACCGTTCTGAGTCGGC...............................................................................................................................................................................	20	1	2.00	0.00	0.00	0.00	2.00	0.00
.........................................................TTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................ATTCACCGTTCTGAGTTGCCC..............................................................................................................................................................................	21	1	2.00	0.00	0.00	0.00	1.00	1.00
........................................................ATTCACCGTTCTGAGTTGGCCTT............................................................................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................ATTCACCGGTCTGAGTTGGC...............................................................................................................................................................................	20	1	2.00	0.00	0.00	0.00	1.00	1.00
........................................................ATTCACCGTTCTGAGGTGGCC..............................................................................................................................................................................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................ATTCACCGTTCTGAGTTGGCT..............................................................................................................................................................................	21	1	2.00	0.00	0.00	0.00	1.00	1.00
........................................................ATTCACAGTTCTGAGTTGGCCCT............................................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTTACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGGGCTGAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................ATTCAACGTTCTGAGTTGG................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTGGT...............................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACAGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................................GTTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCATCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGTGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGCTGTCCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................GTGCGCGTGGG-CCAG----C------------G........................................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ACTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................ATTCACCGTTCTGAGATCGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................ATTCACCGGTCTGAGxTGGCCC.............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCTTTCTGAGTTGGAC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGATGGCCCT............................................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGCGTTGG................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................ATTCACCGTTCTTAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCCAC...........................................................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCCGAGCTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCA..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGGGTTGGCCC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTGGTC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCCGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCTA............................................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGGTGGCCTC............................................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGCTCTGAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................ATCCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTTGC...............................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTAGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTTGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGGTCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGGGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGCCTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTGTC...............................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGCTCTGACTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCCGAGTTGGC...............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCCTC...........................................................................................................................................................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTATGAGTTGGCTC.............................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................................G-CCAG----C------------TTTCAGTTTCGGTGCCAT.......................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................................ATCCACCGTTCTGAGTTGG................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCG..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGATTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTCCTGAGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTGGCCA.............................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................ATTTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................ATTCACCGTTCTGAGTTGGCAC.............................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................AGTCATCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................................ATTCACCGTTCTGCGTTGGCC..............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
............................................................ACCGTTCTGAGTTGGCC..............................................................................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................ACCCTTCTGAGTTTGC...............................................................................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................AxTTTGACCGTTCTGAGTTGGCC..............................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

TGGGTAAC------TGGCGAG---------TCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTT-CACCCCCA---GCACCAAGAG-----------------------------------------------------------------CA-CCGA---------------------CT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................................ATTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	1022.00	12.00	56.00	0.00	954.00
........................................................ATTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	372.00	2.00	29.00	0.00	341.00
........................................................ATTCACCGTTCTGAGTTGGC...............................................................................................................................................................................	20	1	264.00	0.00	20.00	0.00	244.00
........................................................ATTCACCGTTCTGAGTTGGCCT.............................................................................................................................................................................	22	1	36.00	0.00	2.00	0.00	34.00
........................................................ATTCACCGTTCTGAGTTGGCCCT............................................................................................................................................................................	23	1	28.00	0.00	2.00	0.00	26.00
........................................................ATTCACCGTTCTGAGTTGG................................................................................................................................................................................	19	1	18.00	0.00	4.00	0.00	14.00
........................................................ATTCACCGTTCTGAGTTGGCCA.............................................................................................................................................................................	22	1	16.00	0.00	1.00	0.00	15.00
........................................................ATTCACCGTTCTGAGTTTGCCC.............................................................................................................................................................................	22	1	16.00	2.00	0.00	0.00	14.00
...........................................................................................G-CCAG----C------------TTTCAGTTTCGGTGCCAT.......................................................................................................................	24	1	15.00	4.00	2.00	0.00	9.00
........................................................TTTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	14.00	0.00	1.00	0.00	13.00
........................................................ATTCACCGTTCTTAGTTGGCCC.............................................................................................................................................................................	22	1	13.00	0.00	0.00	0.00	13.00
........................................................ATTCACCGTTCTGAGTTGTCCC.............................................................................................................................................................................	22	1	13.00	0.00	2.00	0.00	11.00
........................................................ATTAACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	12.00	0.00	0.00	0.00	12.00
........................................................ATTCACCTTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	11.00	1.00	1.00	0.00	9.00
........................................................ATTCACAGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	10.00	1.00	0.00	0.00	9.00
........................................................ATTCACCGTTCTGAGTTGGCCCA............................................................................................................................................................................	23	1	10.00	0.00	1.00	0.00	9.00
...........................................................................................G-CCAG----C------------TTTCAGTTTCGGTGCCA........................................................................................................................	23	1	8.00	4.00	0.00	0.00	4.00
........................................................TTTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	6.00	0.00	0.00	0.00	6.00
........................................................ATTCACCGTTCTGAGTTGCC...............................................................................................................................................................................	20	1	6.00	0.00	0.00	0.00	6.00
........................................................ATTCACCGTTCTGAGTTTGCC..............................................................................................................................................................................	21	1	5.00	0.00	1.00	0.00	4.00
........................................................ATTCACCGTTCTGAGTTGGCAC.............................................................................................................................................................................	22	1	5.00	0.00	0.00	0.00	5.00
........................................................ATTCACCTTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	4.00	0.00	0.00	0.00	4.00
.........................................................TTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	21	1	4.00	0.00	0.00	0.00	4.00
........................................................ATTCACCGTTCTGAGTTGGCCCC............................................................................................................................................................................	23	1	4.00	0.00	0.00	0.00	4.00
........................................................ATTCACCGTTATGAGTTGGCCC.............................................................................................................................................................................	22	1	4.00	0.00	0.00	0.00	4.00
........................................................ATTCACCGTTCTTAGTTGGCC..............................................................................................................................................................................	21	1	4.00	0.00	0.00	0.00	4.00
........................................................ATTCACCGTTCTGAGTTGGACC.............................................................................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
........................................................ATTCACCGTTCCGAGTTGGCCC.............................................................................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
........................................................ATTCACCGTTCTGAGTTGTCC..............................................................................................................................................................................	21	1	3.00	0.00	0.00	0.00	3.00
........................................................ATTCACCGTTCTGGGTTGGCCC.............................................................................................................................................................................	22	1	3.00	0.00	1.00	0.00	2.00
........................................................ATTCACCGTTCTGAGTTTGC...............................................................................................................................................................................	20	1	3.00	0.00	2.00	0.00	1.00
........................................................ATTCACCGTTATGAGTTGGCC..............................................................................................................................................................................	21	1	3.00	0.00	0.00	0.00	3.00

droEug1

TGGGAAAC------TGGCGAA---------GCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCGATTT-CAACCCGA---CTACTAACAG-----------------------------------------------------------------C--CAGA---------------------CT

Size

Hit Count

Total Norm

droBia1

TGGGAAAC------TGGCGAT---------GCTG------------CTGTGC-GACATTCACCGTTCTGAGTTGGCCCCAACTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTTAACCCCTGA---ACACCAAGAG--------------------------------------------------------------------CAGC---------------------CC

Size

Hit Count

Total Norm

droTak1

TGGGAAAC------TGTCGAA---------GCTG------------CCCTGC-GACATTCACCGTTCTGAGTTGGCCCCAACTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGACATTT-CACCCCGACAAACACCAAAGG--------------------------------------------------------------------CAGACT-------------------AT

Size

Hit Count

Total Norm

droEle1

TGGGAAAC------TGGCGTT---------GCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAGTTGCACGTGGG-CCAG----C------------CTTCAGTTTCGGTGCCATTTTCACCCCGA---GTGCCAGGAG--------------------------------------------------------------------CAGA---------------------CT

Size

Hit Count

Total Norm

droRho1

TGGGAAAC------TGGCCAA---------GCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGG-CCAG----C------------TTTCAGTTTCGGTGCCATTTTCACCCCAA---GTGCCAGGAG--------------------------------------------------------------------CAGA---------------------CT

Size

Hit Count

Total Norm

droFic1

TGGGAAGC------TGGCGCT---------GCTG------------CCTGGC-GACATTCACCGTTCTGAGTTGGCCCCCGTTGCACGTGGG-CTGG----C------------C--CAGCTACGGTGCTATTA-AGCCTC-A---GCATCGAAGG-----------------------------------------------------------------C---GGACCACCACTACCACAACTGAGACT

Size

Hit Count

Total Norm

droKik1

TGGGAAAT------TGGCGAA---------GCTG------------CTCTGC-GACATTCACCGTTCTGCGTTGGCCCCAAGTGCACGTGGG-CCAA----C------------TCTCAGTTACGGTGTAATAA-CAGTGCCA---C-ATCTTAGCCAGATTCCACCACA-------------------TATATCGC------------------------------C---------------------TC

Size

Hit Count

Total Norm

droAna3

TGGGAAAT------TGTCGAA---------GCCA------------CTTTGC-GACATTCCCCGTTCTGCGTTGGCCCAAGGTGCACGTGGG-GCCGACGAC------------TCTCCGCTTCCGGACCCAT--------------TGCCGAAAA---------------------------------TACATTCT------------------------------T---------------------CA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................................ATTCACCGTTCTGAGTTGGCC..............................................................................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
........................................................ATTCACCGTTCTGAGTTGGCCC.............................................................................................................................................................................	22	1	2.00	0.00	1.00	0.00	1.00
...................................................................................GCACGTGGG-GCCGACGAC------------TCTCC....................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................CGAC------------TCACCGCTTxCGGACCC........................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................TTCTGCGTTGGCCCAAGGTGCACG...................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.................................................................................GTGCACGTGGG-GCCGACGAC------------TCTCC....................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00

droBip1

TGGGAAAT------TTGGTAG----AA---GCTGC---------TACTTTGC-GACATTCCCCGTTCTGCGTTGGCCAAAGGTGCACGTGGGGCCGA----C------------TTTCCGCTTCCGGACC-----------TA---TTGCCGAAAA---------------------------------TATAT--------------------------------CC---------------------TT

Size

Hit Count

Total Norm

dp4

TGGGAAAC------TGGCGAG---------GCGA-GGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGG-TTAC----GCCTGAAGCTCCAATTCGGTTACGGTTT------C---------------GGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGA---------------------CA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................................................................................................................ACGGGTACGGGTACGGGTAC......................................................................	20	4	0.25	0.25	0.00	0.00	0.00
...........................................................................................................................................................ACGGGTACGGGTACGGGTAC............................................................................	20	4	0.25	0.25	0.00	0.00	0.00
...................................................................AGCGTTCGGCCAGCGAGCCCGTGGG-..............................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................ACGGGTACGGGTACGGGTAC................................................................	20	4	0.25	0.25	0.00	0.00	0.00
................................................................TTCAGCGTTCGGCCAGCCAGCACGTG.................................................................................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00

droPer1

TGGGAAAC------TGGCGAG---------GCGA-GGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGG-TTAC----GCCTGAAGCTCCAATTCGGTTACGGTTT------C---------------GGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGA---------------------CA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................................ACCAGGACTCCTCTGC-GA....................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
......AC------TGGCGAT---------GCGG-GGCGA...................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................ACGGCTACGGTTACGGCT..................................................................	18	4	0.25	0.00	0.00	0.25	0.00	0.00
...............................................................................................................................................................CTACGGCTACGTCTACGGCTAC......................................................................	22	3	0.33	0.00	0.33	0.00	0.00	0.00
...............................................................................................................................................................................................................CGGCGGGTTGTGGAGGTCGG........................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................................................................................................ACGGCTACGGTTACGGCT..............................................................................	18	4	0.25	0.00	0.00	0.25	0.00	0.00
.................................................................................................................................................................ACGGCTACGGTTACGGCT........................................................................	18	4	0.25	0.00	0.00	0.25	0.00	0.00
......AC------TGGCGAG---------GCGG-GACGA...................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................CTACGGCTACGTCTACGGCTAC............................................................................	22	3	0.33	0.00	0.33	0.00	0.00	0.00
...............GGCGAG---------TCGA-GGCGAGGC................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................GTTCGGCCAGCGAGCACGTGGG-..............................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................CTACGGCTACGTCTACGGCTAC................................................................	22	3	0.33	0.00	0.33	0.00	0.00	0.00
................................................................................................................................A------C---------------GGCTACGGTTACGGCT....................................................................................	18	4	0.25	0.00	0.00	0.25	0.00	0.00
.....AAC------TGGCGAG---------GCGG-GGCG....................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

TGGGAAATACATCTTCGTTTGGCTTTAGTTTCTC------------TTCTGCGGACATTCAATGTTCTGCGTTTGCCCCAAGCGCACGTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
............TTTCGTTTGGCTTAAGTT.............................................................................................................................................................................................................................	18	2	19.00	4.00	1.00	0.00	14.00
...........TTTTCGTTTGGCTTAAGTT.............................................................................................................................................................................................................................	19	2	10.00	1.50	1.00	0.00	7.50
...........TTTTCGTTTGGCTTAAGT..............................................................................................................................................................................................................................	18	2	3.00	0.00	0.00	0.00	3.00
..........TTCTTCGTTTGGCTTAAGTT.............................................................................................................................................................................................................................	20	2	1.00	0.00	0.00	0.00	1.00
.........TATCTTCGTTTGGCTTAAGTT.............................................................................................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00

droVir3

TGGGAAAC------TG-CGAA---------GCTG------------CTTTGC-GACATTCGACTTGCTGCGTTCGTCGCCGACGCACGTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..........................................................TCGACTTGCTGCGTTCGAC..............................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00

droMoj3

TGGGAAAC-------GGCGAA---------GCTT------------CTGTGC-GACATTCAACGTTCTGCGTTCGTCGCCGACGCACGTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..........................................................TCAACGTTCTGCGTTCGTCGCC...........................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................ACGTTCTTCGTTCGTCGCG...........................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droGri2

TGGGAATT------TTGCGAA---------GCTGCTGCTGTGGCT--GCTGC-GACATTCAACGTTCTGCGTTGGCCGCCGACGCACGTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:07:42 EDT

dme-mir-990

chr2R:12782728-12782813 -

Known_mirbase

intron

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