dme-mir-959- Best orthologs

dme-mir-959	chr2L:5640940-5641037 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 5641000-5641020
   star strand at position 5640959-5640979
   mutations
   read mismatches

Notes: Many equally probable paralogs reported for 959/dwil.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:5640925-5641052 +		1	CGA-ATTAAATTGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTTCTT----CAGGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAACTGCAATGAT------------TATCG----------------------------------
droSim1	chr2L:5434012-5434138 +	LASTZ	1	AA---TTAAATAGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTTCTT----TGCGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAGCTGCAAGGAT------------CATCG----------------------------------
droSec1	super_5:3718667-3718793 +	LASTZ	1	AA---TTAAATAGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTTCTT----TGCGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAGCTGCAAGGAT------------CATCG----------------------------------
droYak2	chr2L:13552255-13552381 -	LASTZ	1	CGA-GTTAAATTGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCT---TTCC-T----TGCGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGAT------------CATCG----------------------------------
droEre2	scaffold_4929:5729400-5729526 +	LASTZ	1	CGA-GTTAAATTGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGAGCT---TTCC-T----TGCGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGAG------------CAACG----------------------------------
droEug1	scf7180000409063:317228-317361 +	LASTZ	4	CGT-GTAAAATTGATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCT---TTCC-T----TGAGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCCGAGCT------------CATCC---------------------------TTCCTGC
droBia1	scf7180000302422:3830480-3830600 +	LASTZ	4	TAT-GTAAAATTAATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTGC-A----TTGGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAGACTGCAACGC----------------------------------------------------
droTak1	scf7180000415871:385212-385337 +	LASTZ	4	TAT-GTTAAATTCATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT----TCA-T----CGGGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGCT------------CAGCA----------------------------------
droEle1	scf7180000490753:30119-30245 +	LASTZ	4	CGT-GTTAAATTGATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCC---TTCC-T----CGCGGCGGCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGGAAGGTG------------TGCTG----------------------------------
droRho1	scf7180000778253:34069-34192 -	LASTZ	4	C-----TAGATGGATTTCAATG---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTCC-T----TGAGGCGGCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGGAAGGCC------------CATCG----------------------------------
droFic1	scf7180000453932:197783-197909 -	LASTZ	4	C----TTGAATTGATTTCGGCT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTGC-T----TGGGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAGG-CC------------AATCG---------------------------CTC----
droKik1	scf7180000302389:431175-431301 -	LASTZ	4	CAG-GTTAAATTGATTTCCATT---------------------------------TTGTTCCACATTCTTAATACTCGGGTTGGCAAAGACCT---TTCC-A----GGAGGCGCCTTTGTCATCGGGGGTATTATGAAATATGGTCCAAAGCAACTGCAGGCGG------------TAGTG----------------------------------
droAna3	scaffold_12916:11084702-11084849 +	LASTZ	1	GAA-GTTAAATTTATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTCC-T----GGAGCCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAAACCAGCACAATG------------TATCGGCCAATAGGCCAATTAACCCG-------------
droBip1	scf7180000396572:742458-742584 +	LASTZ	4	AAA-GTTAAATTTATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGAGCT---ATCC-T----GGAGCTGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAACACACCACAACG------------CATCG----------------------------------
dp4	chr4_group4:3182582-3182745 -	LASTZ	1	TGG-TTTTCGTTTA----CGTT--------------------TTTT-TTTTGTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCA---CTCG-TAGTGTGAGAAGCCTTTGTCATCGCGGGTATTATGCAACATAGCTCAAAAGCGCAACAAAATACACA-------------AAA--------AATATACACGTAAATGTGTGTGG
droPer1	super_10:2201518-2201669 -	LASTZ	1	TGG-TTTTCGTTCA----CGTT--------------------TTTTTTTTTGTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCA---CTCG-TAGTGTGAGAAGCCTTTGTCATCGCGGGTATTATGCAACATAGCTCAAAAGCGCAACAAAATACACA-------------AAA--------AATATACACG-------------
droWil1	scaffold_180708:8626283-8626424 -	LASTZ	1	AGT-GAAAAAGTGACTTAAGTT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACAAAATGTTT-A----CCAATCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAGTTCAACATAATAATTAAGAATTAACTTTG----------------------------------
droVir3	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:14018136-14018207 +	LASTZ	5	TGATGTAATAAGTGTTTTAGCT---------------------------------TTAAGTTGTGCCATTT---------------------------------------------------------------TAAATTGAAAAA-AGTGAAGATTGAAAATT------------GACTA----------------------------------
droGri2	scaffold_15252:3146904-3147001 +	LASTZ	5	CAA-AGAGTAGCAGGAGTAGTTAAGTTGTAGTTTCTTACGGTTTTTTTTTT-----AATAACATGC-TTTAGTGCT-------------------------------------------------------TCAATGTAGGTGGCTCAAGATAT---------T------------TGTTG----------------------------------

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	CGA-ATTAAATTGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTTCTT----CAGGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAACTGCAATGAT------------TATCG----------------------------------
droSim1	AA---TTAAATAGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTTCTT----TGCGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAGCTGCAAGGAT------------CATCG----------------------------------
droSec1	AA---TTAAATAGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTTCTT----TGCGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAGCTGCAAGGAT------------CATCG----------------------------------
droYak2	CGA-GTTAAATTGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCT---TTCC-T----TGCGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGAT------------CATCG----------------------------------
droEre2	CGA-GTTAAATTGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGAGCT---TTCC-T----TGCGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGAG------------CAACG----------------------------------
droEug1	CGT-GTAAAATTGATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCT---TTCC-T----TGAGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCCGAGCT------------CATCC---------------------------TTCCTGC
droBia1	TAT-GTAAAATTAATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTGC-A----TTGGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAGACTGCAACGC----------------------------------------------------
droTak1	TAT-GTTAAATTCATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT----TCA-T----CGGGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGCT------------CAGCA----------------------------------
droEle1	CGT-GTTAAATTGATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCC---TTCC-T----CGCGGCGGCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGGAAGGTG------------TGCTG----------------------------------
droRho1	C-----TAGATGGATTTCAATG---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTCC-T----TGAGGCGGCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGGAAGGCC------------CATCG----------------------------------
droFic1	C----TTGAATTGATTTCGGCT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTGC-T----TGGGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAGG-CC------------AATCG---------------------------CTC----
droKik1	CAG-GTTAAATTGATTTCCATT---------------------------------TTGTTCCACATTCTTAATACTCGGGTTGGCAAAGACCT---TTCC-A----GGAGGCGCCTTTGTCATCGGGGGTATTATGAAATATGGTCCAAAGCAACTGCAGGCGG------------TAGTG----------------------------------
droAna3	GAA-GTTAAATTTATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTCC-T----GGAGCCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAAACCAGCACAATG------------TATCGGCCAATAGGCCAATTAACCCG-------------
droBip1	AAA-GTTAAATTTATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGAGCT---ATCC-T----GGAGCTGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAACACACCACAACG------------CATCG----------------------------------
dp4	TGG-TTTTCGTTTA----CGTT--------------------TTTT-TTTTGTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCA---CTCG-TAGTGTGAGAAGCCTTTGTCATCGCGGGTATTATGCAACATAGCTCAAAAGCGCAACAAAATACACA-------------AAA--------AATATACACGTAAATGTGTGTGG
droPer1	TGG-TTTTCGTTCA----CGTT--------------------TTTTTTTTTGTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCA---CTCG-TAGTGTGAGAAGCCTTTGTCATCGCGGGTATTATGCAACATAGCTCAAAAGCGCAACAAAATACACA-------------AAA--------AATATACACG-------------
droWil1	AGT-GAAAAAGTGACTTAAGTT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACAAAATGTTT-A----CCAATCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAGTTCAACATAATAATTAAGAATTAACTTTG----------------------------------
droMoj3	TGATGTAATAAGTGTTTTAGCT---------------------------------TTAAGTTGTGCCATTT---------------------------------------------------------------TAAATTGAAAAA-AGTGAAGATTGAAAATT------------GACTA----------------------------------
droGri2	CAA-AGAGTAGCAGGAGTAGTTAAGTTGTAGTTTCTTACGGTTTTTTTTTT-----AATAACATGC-TTTAGTGCT-------------------------------------------------------TCAATGTAGGTGGCTCAAGATAT---------T------------TGTTG----------------------------------

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

AA---TTAAATAGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTTCTT----TGCGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAGCTGCAAGGAT------------CATCG----------------------------------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................TTAGTACTCGGGTTGATAAAGA.............................................................................................................................	22	1	149.00	0.00	0.00	142.00	7.00
....................................................................TTAGTACTCGGGTTGATAAA...............................................................................................................................	20	1	137.00	0.00	1.00	136.00	0.00
...................................................................CTTAGTACTCGGGTTGATAAA...............................................................................................................................	21	1	71.00	0.00	2.00	66.00	3.00
....................................................................................................................TTGTCATCGGGGGTATTATGAA.............................................................................	22	1	66.00	1.00	0.00	63.00	2.00
....................................................................................................................TTGTCATCGGGGGTATTAT................................................................................	19	1	50.00	0.00	1.00	49.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGA..............................................................................	21	1	47.00	1.00	0.00	44.00	2.00
....................................................................TTAGTACTCGGGTTGATAA................................................................................................................................	19	1	41.00	0.00	0.00	41.00	0.00
...................................................................CTTAGTACTCGGGTTGATAA................................................................................................................................	20	1	35.00	0.00	1.00	34.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTAT................................................................................	20	1	27.00	0.00	1.00	26.00	0.00
....................................................................TTAGTACTCGGGTTGATA.................................................................................................................................	18	1	23.00	0.00	0.00	23.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAA............................................................................	23	1	21.00	0.00	0.00	21.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAG..............................................................................................................................	21	1	17.00	0.00	1.00	16.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTA.................................................................................	18	1	17.00	0.00	0.00	17.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGA..............................................................................	22	1	13.00	0.00	0.00	12.00	1.00
.....................................................................................................................TGTCATCGGGGGTATTATGAAA............................................................................	22	1	12.00	0.00	0.00	12.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGG..............................................................................	21	1	10.00	0.00	0.00	10.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGAA.............................................................................	23	1	9.00	0.00	0.00	7.00	2.00
.....................................................................................................................TGTCATCGGGGGTATTATGA..............................................................................	20	1	9.00	0.00	0.00	9.00	0.00
....................................................................TTAGTACTCGGGTTGATT.................................................................................................................................	18	1	9.00	0.00	1.00	8.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAGG.............................................................................................................................	22	1	8.00	0.00	0.00	8.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAGAA............................................................................................................................	23	1	8.00	0.00	0.00	8.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGAAA............................................................................	24	1	7.00	0.00	0.00	6.00	1.00
.....................................................................................................................TGTCATCGGGGGTATTATGAA.............................................................................	21	1	6.00	0.00	0.00	6.00	0.00
...................................................................CTTAGTACTCGGGTTGATA.................................................................................................................................	19	1	5.00	0.00	0.00	5.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAA..............................................................................................................................	21	1	5.00	0.00	0.00	5.00	0.00
.....................................................................................................................TGTCATCGGGGGTATTAT................................................................................	18	1	4.00	0.00	0.00	4.00	0.00
..................................................................TCTTAGTACTCGGGTTGATAA................................................................................................................................	21	1	4.00	0.00	0.00	4.00	0.00
...................................................................CTTAGTACTCGGGTTGATAAAG..............................................................................................................................	22	1	4.00	0.00	0.00	3.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATG...............................................................................	20	1	3.00	0.00	0.00	3.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTA.................................................................................	19	1	3.00	0.00	0.00	3.00	0.00
...................................................................CTTAGTACTCGGGTTGATAAAGA.............................................................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
...................................................................CTTAGTACTCGGGTTGAT..................................................................................................................................	18	1	3.00	0.00	0.00	3.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATG...............................................................................	21	1	3.00	0.00	0.00	3.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATT...............................................................................	20	1	3.00	0.00	0.00	3.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAGT.............................................................................................................................	22	1	3.00	0.00	0.00	3.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATT..................................................................................	18	1	2.00	0.00	0.00	2.00	0.00
....................................................................TTAGTACTCGGGGTGATAAAGA.............................................................................................................................	22	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAAA...........................................................................	24	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................TTGTCATCGGGGGGATTATGAA.............................................................................	22	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGT..............................................................................	21	1	2.00	0.00	0.00	2.00	0.00
...................................................................CTTGGTACTCGGGTTGATAAA...............................................................................................................................	21	1	2.00	0.00	0.00	2.00	0.00
..........................................................................................CCT---TTTCTT----TGCGGAGCC....................................................................................................	18	1	2.00	0.00	0.00	2.00	0.00
.....................................................................................................................TGTCATCGGGGGAATTATGA..............................................................................	20	1	2.00	0.00	0.00	2.00	0.00
.....................................................................TAGTACTCGGGTTGATAA................................................................................................................................	18	1	2.00	0.00	0.00	2.00	0.00
...................................................................CTTAGTACTCGGGTTGATT.................................................................................................................................	19	1	2.00	0.00	0.00	2.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAGAAA...........................................................................................................................	24	1	2.00	0.00	0.00	2.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAT............................................................................	23	1	2.00	0.00	0.00	2.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTT.................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGGATTATGAAA............................................................................	23	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGAC.............................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................TTAGTACTCGGGCTGATAAA...............................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................TTTGTCATTGGGGGTATTAT................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................................................TTAGTACTCGGGTTGATAAGGA.............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCxGGGGTATTATG...............................................................................	19	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGGATTAT................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TGGTCATCGGGGGTATTATGAA.............................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................TTTGTCATCGGGGGGATTAT................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGAG.............................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...................................................................CTTAGTACTCGGGTTGATAAAA..............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................TTAGTACTCGGGTTGATG.................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGAATTATGA..............................................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................CAGCCTTTGTCATCGTGG.......................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATT...............................................................................	21	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................TTTGTCATCGGGGGTACTATGAA.............................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGAAAAT..........................................................................	26	1	1.00	0.00	0.00	1.00	0.00
....................................................................GTAGTACTCGGGTTGATAAAGA.............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................TTTGTCATCGGGGTTATTAT................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................................................TTAGTACTCGAGTTGATA.................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTCTGAA.............................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGACT............................................................................	24	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTG.................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..................................................................TCTTAGTACTCGGGTTGATA.................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................................................TTAGTATTCGGGTTGATAAA...............................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGCATTAT................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
....................................................................TTAGTACTCAGGTTGATAAA...............................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................TTTGTCATCGGAGGTATTAT................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGC..............................................................................	21	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTAC................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................TGTCATCGGGGGGATTAT................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................TGTCATCGGGGGGATTATGAAA............................................................................	22	1	1.00	0.00	0.00	1.00	0.00
..................................................................TCTTAGTACTCGGGTTGATAAA...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00

droSec1

AA---TTAAATAGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTTCTT----TGCGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAGCTGCAAGGAT------------CATCG----------------------------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
....................................................................TTAGTACTCGGGTTGATAAAGA.............................................................................................................................	22	1	373.00	252.00	107.00	14.00
....................................................................TTAGTACTCGGGTTGATAAAG..............................................................................................................................	21	1	246.00	221.00	16.00	9.00
....................................................................................................................TTGTCATCGGGGGTATTATGA..............................................................................	21	1	196.00	160.00	18.00	18.00
...................................................................................................................TTTGTCATCGGGGGTATTATGA..............................................................................	22	1	67.00	49.00	14.00	4.00
....................................................................TTAGTACTCGGGTTGATAAA...............................................................................................................................	20	1	66.00	62.00	2.00	2.00
...................................................................CTTAGTACTCGGGTTGATAAAG..............................................................................................................................	22	1	63.00	58.00	4.00	1.00
...................................................................CTTAGTACTCGGGTTGATAAA...............................................................................................................................	21	1	53.00	44.00	8.00	1.00
.....................................................................................................................TGTCATCGGGGGTATTATGA..............................................................................	20	1	43.00	34.00	6.00	3.00
....................................................................................................................TTGTCATCGGGGGTATTATG...............................................................................	20	1	34.00	29.00	4.00	1.00
...................................................................CTTAGTACTCGGGTTGATAA................................................................................................................................	20	1	29.00	28.00	1.00	0.00
...................................................................CTTAGTACTCGGGTTGATA.................................................................................................................................	19	1	19.00	14.00	0.00	5.00
....................................................................................................................TTGTCATCGGGGGTATTATGAA.............................................................................	22	1	14.00	7.00	6.00	1.00
...................................................................CTTAGTACTCGGGTTGATAAAGA.............................................................................................................................	23	1	12.00	6.00	6.00	0.00
.....................................................................................................................TGTCATCGGGGGTATTATGAAA............................................................................	22	1	11.00	3.00	8.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAA............................................................................	23	1	10.00	5.00	4.00	1.00
...................................................................................................................TTTGTCATCGGGGGTATTATG...............................................................................	21	1	10.00	7.00	0.00	3.00
....................................................................TTAGTACTCGGGTTGATAAAGAA............................................................................................................................	23	1	10.00	9.00	1.00	0.00
....................................................................TTAGTACTCGGGTTGATAA................................................................................................................................	19	1	8.00	8.00	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGAA.............................................................................	23	1	7.00	1.00	5.00	1.00
....................................................................TTAGTACTCGGGTTGATAAAA..............................................................................................................................	21	1	7.00	5.00	0.00	2.00
.....................................................................................................................TGTCATCGGGGGTATTATG...............................................................................	19	1	7.00	4.00	2.00	1.00
....................................................................TTAGTACTCGGGTTGATAAAGT.............................................................................................................................	22	1	5.00	5.00	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGAAA............................................................................	24	1	4.00	3.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTAAGA..............................................................................	21	1	4.00	4.00	0.00	0.00
.....................................................................................................................TGTCATCGGGGGTATTATGAA.............................................................................	21	1	4.00	1.00	3.00	0.00
....................................................................TTAGTACTCGGGTTGATACAG..............................................................................................................................	21	1	3.00	3.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAT..............................................................................................................................	21	1	3.00	3.00	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTAT................................................................................	20	1	3.00	3.00	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGT..............................................................................	22	1	3.00	2.00	0.00	1.00
....................................................................TTAGTACTCGGGTTGATAAAGAAA...........................................................................................................................	24	1	3.00	2.00	1.00	0.00

droYak2

CGA-GTTAAATTGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCT---TTCC-T----TGCGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGAT------------CATCG----------------------------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....................................................................................................................TTGTCATCGGGGGTATTATGA..............................................................................	21	1	275.00	1.00	1.00	263.00	2.00	8.00
....................................................................TTAGTACTCGGGTTGACAAAG..............................................................................................................................	21	1	175.00	0.00	0.00	175.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGACAAAGA.............................................................................................................................	22	1	158.00	0.00	0.00	156.00	0.00	2.00
...................................................................CTTAGTACTCGGGTTGACAAA...............................................................................................................................	21	1	101.00	0.00	0.00	96.00	0.00	5.00
...................................................................CTTAGTACTCGGGTTGACAAAG..............................................................................................................................	22	1	93.00	0.00	0.00	92.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATG...............................................................................	20	1	81.00	0.00	2.00	77.00	1.00	1.00
.....................................................................................................................TGTCATCGGGGGTATTATGA..............................................................................	20	1	71.00	0.00	0.00	68.00	0.00	3.00
....................................................................................................................TTGTCATCGGGGGTATTATGAA.............................................................................	22	1	32.00	0.00	1.00	22.00	0.00	9.00
....................................................................TTAGTACTCGGGTTGACAAA...............................................................................................................................	20	1	30.00	0.00	0.00	29.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAA............................................................................	23	1	28.00	0.00	0.00	17.00	1.00	10.00
...................................................................CTTAGTACTCGGGTTGACAA................................................................................................................................	20	1	28.00	0.00	0.00	23.00	0.00	5.00
...................................................................CTTAGTACTCGGGTTGACA.................................................................................................................................	19	1	21.00	0.00	1.00	17.00	0.00	3.00
..................................................................TCTTAGTACTCGGGTTGACA.................................................................................................................................	20	1	19.00	0.00	0.00	16.00	0.00	3.00
....................................................................................................................TTGTCATCGGGGGTATTAT................................................................................	19	1	14.00	0.00	0.00	4.00	0.00	10.00
...................................................................................................................TTTGTCATCGGGGGTATTATGA..............................................................................	22	1	14.00	0.00	0.00	12.00	0.00	2.00
..................................................................TCTTAGTACTCGGGTTGACAAA...............................................................................................................................	22	1	13.00	0.00	0.00	13.00	0.00	0.00
.....................................................................................................................TGTCATCGGGGGTATTATG...............................................................................	19	1	8.00	0.00	0.00	8.00	0.00	0.00
.....................................................................................................................TGTCATCGGGGGTATTATGAA.............................................................................	21	1	7.00	0.00	0.00	4.00	0.00	3.00
..................................................................TCTTAGTACTCGGGTTGACAA................................................................................................................................	21	1	6.00	0.00	0.00	2.00	0.00	4.00
....................................................................TTAGTACTCGGGTTGACAA................................................................................................................................	19	1	5.00	0.00	0.00	2.00	0.00	3.00
....................................................................TTAGTACTCGGGTTGACAAAGT.............................................................................................................................	22	1	5.00	0.00	1.00	4.00	0.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGT..............................................................................	21	1	5.00	0.00	0.00	4.00	0.00	1.00
....................................................................TTAGTACTCGGGTTGATAAAG..............................................................................................................................	21	1	4.00	0.00	0.00	4.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGACA.................................................................................................................................	18	1	4.00	0.00	0.00	0.00	2.00	2.00
...................................................................CTTAGTACTCGGGTTGACAAAA..............................................................................................................................	22	1	3.00	0.00	0.00	3.00	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTAT................................................................................	20	1	3.00	0.00	0.00	2.00	0.00	1.00
...................................................................CTTAGTACTCGGGTTGAC..................................................................................................................................	18	1	3.00	0.00	0.00	0.00	0.00	3.00
....................................................................TTAGTACTCGGGTTGACAAAA..............................................................................................................................	21	1	3.00	0.00	0.00	3.00	0.00	0.00
....................................................................................................................TTGTCATCGGGGGCATTATGA..............................................................................	21	1	3.00	0.00	0.00	3.00	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATG...............................................................................	21	1	3.00	0.00	0.00	2.00	0.00	1.00
.....................................................................................................................TGTCATCGGGGGTATTATGAAA............................................................................	22	1	3.00	0.00	0.00	2.00	0.00	1.00

droEre2

CGA-GTTAAATTGATTTTAACT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGAGCT---TTCC-T----TGCGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGAG------------CAACG----------------------------------	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................................................................................TTGTCATCGGGGGTATTATGA..............................................................................	21	1	171.00	0.00	20.00	0.00	151.00
....................................................................TTAGTACTCGGGTTGACAAAGA.............................................................................................................................	22	1	57.00	2.00	3.00	0.00	52.00
....................................................................TTAGTACTCGGGTTGACAAAG..............................................................................................................................	21	1	40.00	0.00	2.00	0.00	38.00
....................................................................................................................TTGTCATCGGGGGTATTATG...............................................................................	20	1	30.00	0.00	7.00	0.00	23.00
...................................................................CTTAGTACTCGGGTTGACAAAG..............................................................................................................................	22	1	18.00	1.00	2.00	0.00	15.00
....................................................................TTAGTACTCGGGTTGACAAA...............................................................................................................................	20	1	12.00	0.00	2.00	0.00	10.00
....................................................................................................................TTGTCATCGGGGGTATTATGAA.............................................................................	22	1	12.00	0.00	5.00	0.00	7.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAA............................................................................	23	1	10.00	0.00	1.00	0.00	9.00
...................................................................CTTAGTACTCGGGTTGACAAA...............................................................................................................................	21	1	8.00	0.00	0.00	0.00	8.00
.....................................................................................................................TGTCATCGGGGGTATTATGA..............................................................................	20	1	6.00	0.00	1.00	0.00	5.00
....................................................................................................................TTGTCATCGTGGGTATTATGA..............................................................................	21	1	5.00	0.00	0.00	0.00	5.00
..................................................................TCTTAGTACTCGGGTTGACA.................................................................................................................................	20	1	5.00	0.00	1.00	0.00	4.00
....................................................................................................................TTGTCATCTGGGGTATTATGA..............................................................................	21	1	5.00	0.00	0.00	0.00	5.00
..................................................................TCTTAGTACTCGGGTTGACAAA...............................................................................................................................	22	1	4.00	0.00	0.00	0.00	4.00
...................................................................CTTAGTACTCGGGTTGACAA................................................................................................................................	20	1	4.00	1.00	1.00	0.00	2.00
.....................................................................................................................TGTCATCGGGGGTATTATG...............................................................................	19	1	4.00	0.00	2.00	0.00	2.00
....................................................................TTAGTACTCTGGTTGACAAAG..............................................................................................................................	21	1	3.00	0.00	0.00	0.00	3.00
...................................................................................................................TTTGTCATCGGGGGTATTATGA..............................................................................	22	1	3.00	0.00	0.00	0.00	3.00
...................................................................CTTAGTACTCGGGTTGACAAAA..............................................................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
..................................................................TCTTAGTACTCGGGTTGACAA................................................................................................................................	21	1	2.00	0.00	0.00	0.00	2.00
....................................................................TTAGTACTCGGGTTGACAA................................................................................................................................	19	1	2.00	0.00	0.00	0.00	2.00
....................................................................................................................TCGTCATCGGGGGTATTATGA..............................................................................	21	1	2.00	0.00	0.00	0.00	2.00
....................................................................................................................TTGTCATCGGGTGTATTATGA..............................................................................	21	1	2.00	0.00	0.00	0.00	2.00
....................................................................................................................TTGTCATCGGTGGTATTATGA..............................................................................	21	1	2.00	0.00	0.00	0.00	2.00
....................................................................................................................TTGTCATCGGGGGTATTAT................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATTA..............................................................................	21	1	2.00	0.00	0.00	0.00	2.00
...................................................................................................................TTTGTCATCGGGGGTATTATG...............................................................................	21	1	2.00	0.00	1.00	0.00	1.00
....................................................................TTAGTACTCTGGTTGACAAAGA.............................................................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
...................................................................CTTAGTACTCGGGTTGACA.................................................................................................................................	19	1	2.00	0.00	0.00	0.00	2.00
....................................................................................................................TTGTCATCGGTGGTATTATGT..............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATT...............................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................TTGTCATCGGGGTTATTATGAAA............................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................TCGTCATCGGGGGTATTATGT..............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
..................................................................TCTTAGTACTCGGGTTGAC..................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
....................................................................TTAGTACTCGAGTTGACAAAGA.............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTCTCATCGGGGGTATTATGT..............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................................................................CTTAGTACTCGGGTTGAC..................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...................................................................CTTAGTACTCGGGTTGACAAAGA.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAAC...........................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................TGTCATCGGTGGTATTATGA..............................................................................	20	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAAA...........................................................................	24	1	1.00	0.00	0.00	0.00	1.00
....................................................................TTAGTACTAGGGTTGACAAAG..............................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTAATCGGGGGCATTATGA..............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATGTT.............................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................CTTAGTACTCTGGTTGACAAAG..............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..................................................................TCTTAGTACTCGGGTTTACAAA...............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATGT..............................................................................	21	1	1.00	0.00	1.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGACAAAT..............................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................GTCATCGGGGGTATTATGA..............................................................................	19	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATAGGGGGTATTATGA..............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGCTTTATGA..............................................................................	21	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................TTGTCATCTGTGGTATTATGA..............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCTGGTGTATTATGA..............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................TTAGTACTCGGGTTGACAAATA.............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
......................................................................AGTACTCGGGTTGACAAAGT.............................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
...................................................................CTTAGTACTCTGGTTGACAAA...............................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................TTTGTCATCGGTGGTATTATGA..............................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................CTTAGTACTCGGGTCGACAAAG..............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGAGTATTATGA..............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.............ATTTTAACT---------------------------------TTxTTCTAGA......................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................TCCTAGTACTCGTGTTGACA.................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTGTGGA.............................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGT..............................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCTGGGGTATTATGAAA............................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...................................................................CTTAGTACCCGGGTTGACAAAGT.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................................................TTAGTACTCGGTCTGACAAAG..............................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATGG..............................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................TTAGTACTCGGGTTGACA.................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................TTTGTCATCGGGGGTATTATGAT.............................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATTAAAA...........................................................................	24	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................TTGTCATCAGGGGTATTATGAAA............................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................................................TTAGTACTCGGGTTGACAAT...............................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
....................................................................TTACTACTCGGGTTGACAAAGAT............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAT............................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...................................................................CTTAGTACTCGGGTTTACAAAG..............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................ATTAGTACTCGGGTTGACAAAG..............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................TTGTCATCGGAGGTATTATGAA.............................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droEug1

CGT-GTAAAATTGATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCT---TTCC-T----TGAGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCCGAGCT------------CATCC---------------------------TTCCTGC

Size

Hit Count

Total Norm

droBia1

TAT-GTAAAATTAATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTGC-A----TTGGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAGACTGCAACGC----------------------------------------------------

Size

Hit Count

Total Norm

droTak1

TAT-GTTAAATTCATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT----TCA-T----CGGGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGCT------------CAGCA----------------------------------

Size

Hit Count

Total Norm

droEle1

CGT-GTTAAATTGATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCC---TTCC-T----CGCGGCGGCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGGAAGGTG------------TGCTG----------------------------------

Size

Hit Count

Total Norm

droRho1

C-----TAGATGGATTTCAATG---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTCC-T----TGAGGCGGCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGGAAGGCC------------CATCG----------------------------------

Size

Hit Count

Total Norm

droFic1

C----TTGAATTGATTTCGGCT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTGC-T----TGGGGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAGG-CC------------AATCG---------------------------CTC----

Size

Hit Count

Total Norm

droKik1

CAG-GTTAAATTGATTTCCATT---------------------------------TTGTTCCACATTCTTAATACTCGGGTTGGCAAAGACCT---TTCC-A----GGAGGCGCCTTTGTCATCGGGGGTATTATGAAATATGGTCCAAAGCAACTGCAGGCGG------------TAGTG----------------------------------

Size

Hit Count

Total Norm

droAna3

GAA-GTTAAATTTATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCT---TTCC-T----GGAGCCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAAACCAGCACAATG------------TATCGGCCAATAGGCCAATTAACCCG-------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................................................................................................................TTGTCATCGGGGGTATTATGA..............................................................................	21	1	313.00	284.00	16.00	13.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAGA.............................................................................................................................	22	1	289.00	258.00	24.00	7.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAG..............................................................................................................................	21	1	182.00	165.00	17.00	0.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATG...............................................................................	20	1	83.00	76.00	1.00	6.00	0.00
....................................................................TTAGTACTCGGGTTGATAAA...............................................................................................................................	20	1	53.00	49.00	3.00	1.00	0.00
...................................................................CTTAGTACTCGGGTTGATAAAG..............................................................................................................................	22	1	49.00	46.00	2.00	1.00	0.00
...................................................................CTTAGTACTCGGGTTGATAAA...............................................................................................................................	21	1	29.00	28.00	1.00	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGA..............................................................................	22	1	28.00	23.00	5.00	0.00	0.00
.....................................................................................................................TGTCATCGGGGGTATTATGA..............................................................................	20	1	26.00	23.00	2.00	1.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATG...............................................................................	21	1	24.00	19.00	3.00	2.00	0.00
...................................................................CTTAGTACTCGGGTTGATAA................................................................................................................................	20	1	23.00	19.00	2.00	2.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGAA.............................................................................	22	1	22.00	21.00	0.00	1.00	0.00
...................................................................CTTAGTACTCGGGTTGATA.................................................................................................................................	19	1	15.00	13.00	2.00	0.00	0.00
...................................................................CTTAGTACTCGGGTTGATAAAGA.............................................................................................................................	23	1	13.00	12.00	1.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAGT.............................................................................................................................	22	1	11.00	10.00	1.00	0.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGAAA............................................................................	23	1	9.00	8.00	0.00	1.00	0.00
.....................................................................................................................TGTCATCGGGGGTATTATG...............................................................................	19	1	9.00	7.00	1.00	1.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGT..............................................................................	21	1	7.00	6.00	0.00	1.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAT..............................................................................................................................	21	1	6.00	6.00	0.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATAA................................................................................................................................	19	1	6.00	6.00	0.00	0.00	0.00
.....................................................................................................................TGTCATCGGGGGTATTATGAA.............................................................................	21	1	5.00	3.00	0.00	2.00	0.00
....................................................................TTAGTACTCGGGTTGATAAT...............................................................................................................................	20	1	4.00	4.00	0.00	0.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTAT................................................................................	19	1	4.00	3.00	0.00	1.00	0.00
...................................................................CTTAGTACTCGGGTTGATT.................................................................................................................................	19	1	4.00	4.00	0.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATAAATA.............................................................................................................................	22	1	4.00	4.00	0.00	0.00	0.00
...................................................................CTTAGTACTCGGGTTGATAAAGT.............................................................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATA.................................................................................................................................	18	1	3.00	0.00	1.00	2.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATGC..............................................................................	21	1	3.00	2.00	0.00	1.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGT..............................................................................	22	1	3.00	3.00	0.00	0.00	0.00
....................................................................TTAGTACTCGGGCTGATAAAG..............................................................................................................................	21	1	3.00	3.00	0.00	0.00	0.00
..................................................................TCTTAGTACTCGGGTTGATAA................................................................................................................................	21	1	3.00	2.00	0.00	1.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAGTT............................................................................................................................	23	1	3.00	3.00	0.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATATT...............................................................................................................................	20	1	3.00	3.00	0.00	0.00	0.00
..................................................................TCTTAGTACTCGGGTTGATA.................................................................................................................................	20	1	3.00	3.00	0.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATAAACA.............................................................................................................................	22	1	3.00	3.00	0.00	0.00	0.00

droBip1

AAA-GTTAAATTTATTTCAATT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGAGCT---ATCC-T----GGAGCTGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAACACACCACAACG------------CATCG----------------------------------

Size

Hit Count

Total Norm

dp4

TGG-TTTTCGTTTA----CGTT--------------------TTTT-TTTTGTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCA---CTCG-TAGTGTGAGAAGCCTTTGTCATCGCGGGTATTATGCAACATAGCTCAAAAGCGCAACAAAATACACA-------------AAA--------AATATACACGTAAATGTGTGTGG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
....................................................................TTAGTACTTGGGTTGATAAAGA.............................................................................................................................	22	1	642.00	622.00	0.00	17.00	3.00
....................................................................................................................TTGTCATCGCGGGTATTATGCA.............................................................................	22	1	496.00	456.00	0.00	24.00	16.00
....................................................................TTAGTACTTGGGTTGATAAAG..............................................................................................................................	21	1	402.00	385.00	2.00	14.00	1.00
....................................................................................................................TTGTCATCGCGGGTATTATG...............................................................................	20	1	370.00	353.00	0.00	17.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGC..............................................................................	21	1	348.00	316.00	0.00	31.00	1.00
....................................................................TTAGTACTTGGGTTGATAAA...............................................................................................................................	20	1	106.00	102.00	0.00	3.00	1.00
....................................................................................................................TTGTCATCGCGGGTATTATGT..............................................................................	21	1	65.00	62.00	0.00	3.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGCAA............................................................................	23	1	59.00	54.00	0.00	4.00	1.00
....................................................................TTAGTACTTGGGTTGATAAAGT.............................................................................................................................	22	1	29.00	28.00	0.00	1.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGCT.............................................................................	22	1	17.00	16.00	0.00	1.00	0.00
...................................................................CTTAGTACTTGGGTTGATAAAG..............................................................................................................................	22	1	16.00	14.00	0.00	2.00	0.00
....................................................................TTAGTACTTGGGTTGATAA................................................................................................................................	19	1	15.00	13.00	0.00	1.00	1.00
...................................................................CTTAGTACTTGGGTTGATAA................................................................................................................................	20	1	13.00	11.00	0.00	2.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGCAT............................................................................	23	1	12.00	11.00	0.00	1.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAGAA............................................................................................................................	23	1	10.00	10.00	0.00	0.00	0.00
...................................................................................................................TTTGTCATCGCGGGTATTATG...............................................................................	21	1	8.00	7.00	0.00	1.00	0.00
...................................................................CTTAGTACTTGGGTTGATA.................................................................................................................................	19	1	7.00	6.00	0.00	0.00	1.00
...................................................................................................................TTTGTCATCGCGGGTATTATGC..............................................................................	22	1	6.00	6.00	0.00	0.00	0.00
...................................................................CTTAGTACTTGGGTTGATAAAGT.............................................................................................................................	23	1	6.00	6.00	0.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTAT................................................................................	19	1	5.00	4.00	0.00	0.00	1.00
...................................................................................................................TTTGTCATCGCGGGTATTATGCA.............................................................................	23	1	5.00	5.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAGAT............................................................................................................................	23	1	5.00	5.00	0.00	0.00	0.00
.....................................................................TAGTACTTGGGTTGATAAAGA.............................................................................................................................	21	1	4.00	4.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAGTT............................................................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
.....................................................................................................................TGTCATCGCGGGTATTATGCA.............................................................................	21	1	4.00	3.00	0.00	1.00	0.00
...................................................................CTTAGTACTTGGGTTGATAAA...............................................................................................................................	21	1	3.00	3.00	0.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGTT.............................................................................	22	1	3.00	3.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAA..............................................................................................................................	21	1	3.00	3.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAGAGA.............................................................................................................................	22	1	3.00	3.00	0.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAGA.............................................................................................................................	22	1	3.00	3.00	0.00	0.00	0.00

droPer1

TGG-TTTTCGTTCA----CGTT--------------------TTTTTTTTTGTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCA---CTCG-TAGTGTGAGAAGCCTTTGTCATCGCGGGTATTATGCAACATAGCTCAAAAGCGCAACAAAATACACA-------------AAA--------AATATACACG-------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................................................................TTAGTACTTGGGTTGATAAAGA.............................................................................................................................	22	1	1713.00	1710.00	0.00	3.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAG..............................................................................................................................	21	1	1025.00	1025.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAA...............................................................................................................................	20	1	304.00	302.00	0.00	1.00	1.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATG...............................................................................	20	1	191.00	187.00	0.00	4.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGC..............................................................................	21	1	150.00	145.00	0.00	4.00	1.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGCA.............................................................................	22	1	126.00	121.00	0.00	2.00	2.00	1.00
....................................................................TTAGTACTTGGGTTGATAAAGT.............................................................................................................................	22	1	119.00	119.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAA................................................................................................................................	19	1	100.00	100.00	0.00	0.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGT..............................................................................	21	1	53.00	53.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAGAT............................................................................................................................	23	1	32.00	32.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATTT................................................................................................................................	19	1	24.00	24.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAGAA............................................................................................................................	23	1	21.00	21.00	0.00	0.00	0.00	0.00
...................................................................CTTAGTACTTGGGTTGATT.................................................................................................................................	19	1	17.00	17.00	0.00	0.00	0.00	0.00
...................................................................CTTAGTACTTGGGTTGATAAAG..............................................................................................................................	22	1	12.00	12.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAGTT............................................................................................................................	23	1	12.00	12.00	0.00	0.00	0.00	0.00
...................................................................CTTAGTACTTGGGTTGATAA................................................................................................................................	20	1	11.00	11.00	0.00	0.00	0.00	0.00
...................................................................CTTAGTACTTGGGTTGATA.................................................................................................................................	19	1	11.00	11.00	0.00	0.00	0.00	0.00
...................................................................CTTAGTACTTGGGTTGATTT................................................................................................................................	20	1	8.00	7.00	0.00	1.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGCAA............................................................................	23	1	8.00	7.00	0.00	1.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAA..............................................................................................................................	21	1	8.00	8.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAT..............................................................................................................................	21	1	8.00	8.00	0.00	0.00	0.00	0.00
...................................................................................................................TTTGTCATCGCGGGTATTATGT..............................................................................	22	1	6.00	6.00	0.00	0.00	0.00	0.00
...................................................................................................................TTTGTCATCGCGGGTATTATG...............................................................................	21	1	6.00	6.00	0.00	0.00	0.00	0.00
....................................................................TTAGTGCTTGGGTTGATAAAGA.............................................................................................................................	22	1	6.00	6.00	0.00	0.00	0.00	0.00
...................................................................CTTAGTACTTGGGTTGATAAAGT.............................................................................................................................	23	1	5.00	5.00	0.00	0.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGCT.............................................................................	22	1	5.00	5.00	0.00	0.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGAATTATG...............................................................................	20	1	4.00	4.00	0.00	0.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGCAT............................................................................	23	1	4.00	4.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAT...............................................................................................................................	20	1	4.00	4.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATA.................................................................................................................................	18	1	4.00	3.00	0.00	0.00	1.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAGA.............................................................................................................................	22	1	4.00	4.00	0.00	0.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTAT................................................................................	19	1	3.00	3.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGGGTTGATAAAGATT...........................................................................................................................	24	1	3.00	3.00	0.00	0.00	0.00	0.00
....................................................................TTAGTACTTGTGTTGATAAAGA.............................................................................................................................	22	1	3.00	3.00	0.00	0.00	0.00	0.00
....................................................................................................................TTGTCATCGCGGGTATTATGA..............................................................................	21	1	3.00	3.00	0.00	0.00	0.00	0.00

droWil1

AGT-GAAAAAGTGACTTAAGTT---------------------------------TTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACAAAATGTTT-A----CCAATCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAGTTCAACATAATAATTAAGAATTAACTTTG----------------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
....................................................................TTAGTACTCGGGTTGATAAAGA.............................................................................................................................	22	7	155.43	133.00	7.71	8.43	6.29
....................................................................TTAGTACTCGGGTTGATAAAG..............................................................................................................................	21	7	95.57	83.57	4.86	6.57	0.57
....................................................................................................................TTGTCATCGGGGGTATTATGA..............................................................................	21	7	45.14	38.43	2.00	2.86	1.86
....................................................................TTAGTACTCGGGTTGATAAA...............................................................................................................................	20	7	28.71	21.14	0.57	1.86	5.14
.....................................................................................................................TGTCATCGGGGGTATTATGA..............................................................................	20	7	7.86	7.00	0.29	0.29	0.29
...................................................................................................................TTTGTCATCGGGGGTATTATGA..............................................................................	22	7	7.57	6.14	0.43	1.00	0.00
....................................................................................................................TTGTCATCGGGGGTATTATG...............................................................................	20	7	6.86	6.43	0.29	0.14	0.00
...................................................................CTTAGTACTCGGGTTGATAAAG..............................................................................................................................	22	7	5.57	4.86	0.43	0.29	0.00
....................................................................TTAGTACTCGGGTTGATAAAGAA............................................................................................................................	23	7	5.14	4.43	0.14	0.29	0.29
....................................................................................................................TTGTCATCGGGGGTATTATGAA.............................................................................	22	7	5.00	3.14	0.14	0.00	1.71
....................................................................................................................TTGTCATCGGGGGTATTATGAAA............................................................................	23	7	5.00	3.00	0.29	0.00	1.71
....................................................................TTAGTACTCGGGTTGATAA................................................................................................................................	19	7	4.57	2.57	0.29	0.29	1.43
....................................................................TTAGTACTCGGGTTGATAAAA..............................................................................................................................	21	7	3.57	2.00	0.29	0.71	0.57
....................................................................TTAGTACTCGGGTTGATAAAGAAA...........................................................................................................................	24	7	2.43	1.86	0.29	0.14	0.14
...................................................................................................................TTTGTCATCGGGGGTATTAT................................................................................	20	7	2.43	0.71	0.00	0.00	1.71
...................................................................CTTAGTACTCGGGTTGATAAAGA.............................................................................................................................	23	7	2.14	2.00	0.00	0.14	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATG...............................................................................	21	7	1.71	1.43	0.29	0.00	0.00
...................................................................................................................TTTGTCATCGGGGGTATTATGAA.............................................................................	23	7	1.57	0.71	0.29	0.14	0.43
...................................................................CTTAGTACTCGGGTTGATAAA...............................................................................................................................	21	7	1.57	1.57	0.00	0.00	0.00
...................................................................CTTAGTACTCGGGTTGATAA................................................................................................................................	20	7	1.43	1.29	0.00	0.00	0.14
....................................................................................................................TTGTCATCGGGGGTATTAT................................................................................	19	7	1.43	0.14	0.00	0.00	1.29
...................................................................CTTAGTACTCGGGTTGATA.................................................................................................................................	19	7	1.00	0.57	0.14	0.29	0.00
....................................................................TTAGTACTCGGGTTGATA.................................................................................................................................	18	7	0.86	0.00	0.14	0.00	0.71
....................................................................................................................TTGTCATCGGGGGTATTA.................................................................................	18	7	0.71	0.00	0.00	0.00	0.71
...................................................................................................................TTTGTCATCGGGGGTATTATC...............................................................................	21	7	0.71	0.14	0.14	0.14	0.29
....................................................................TTAGTACTCGGGTTGATC.................................................................................................................................	18	7	0.71	0.00	0.00	0.14	0.57
.....................................................................TAGTACTCGGGTTGATAAAGA.............................................................................................................................	21	7	0.57	0.43	0.00	0.14	0.00
....................................................................TTAGTACTCGGGTTGATAAAGT.............................................................................................................................	22	7	0.57	0.57	0.00	0.00	0.00
.....................................................................................................................TGTCATCGGGGGTATTATG...............................................................................	19	7	0.57	0.14	0.00	0.00	0.43
....................................................................TTAGTACTCGGGTTGATAAGGA.............................................................................................................................	22	7	0.57	0.57	0.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATAAAAA.............................................................................................................................	22	7	0.43	0.43	0.00	0.00	0.00
....................................................................TTAGTACTCGGGTTGATAAG...............................................................................................................................	20	7	0.43	0.43	0.00	0.00	0.00
....................................................................TTAGTGCTCGGGTTGATAAAGA.............................................................................................................................	22	7	0.43	0.14	0.14	0.00	0.14
....................................................................TTAGTACTCGGGTTGATCC................................................................................................................................	19	7	0.43	0.00	0.00	0.43	0.00
....................................................................TTAGTACTCGGGTTGATAAAGG.............................................................................................................................	22	7	0.43	0.14	0.00	0.00	0.29
....................................................................................................................TTGTCATCGGGGGTATTATGAAAA...........................................................................	24	7	0.43	0.00	0.00	0.00	0.43
....................................................................TTAGTACTCGGGTTGATAAGA..............................................................................................................................	21	7	0.43	0.29	0.00	0.14	0.00
.....................................................................................................................TGTCATCGGGGGTATTATGAA.............................................................................	21	7	0.43	0.43	0.00	0.00	0.00

droVir3

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TGATGTAATAAGTGTTTTAGCT---------------------------------TTAAGTTGTGCCATTT---------------------------------------------------------------TAAATTGAAAAA-AGTGAAGATTGAAAATT------------GACTA----------------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......................................................TTAAGTTGTGGCATTT---------------------------------------------------------------TT...............................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................A-AGTGAAGATCGAAGATT------------.......................................	18	1	1.00	0.00	0.00	1.00	0.00

droGri2

CAA-AGAGTAGCAGGAGTAGTTAAGTTGTAGTTTCTTACGGTTTTTTTTTT-----AATAACATGC-TTTAGTGCT-------------------------------------------------------TCAATGTAGGTGGCTCAAGATAT---------T------------TGTTG----------------------------------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:14 EDT

dme-mir-959

chr2L:5640940-5641037 +

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