dme-mir-1004- Best orthologs

dme-mir-1004	chr2L:3767621-3767688 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 3767667-3767688
   star strand at position 3767621-3767643
   mutations
   read mismatches

Notes: droAna3 has scattered reads throughout the hairpin. droBip has lost too much of the intron to fold into a hairpin. Conclusion: gone in droWil1 - droGri2 and in the anannasae subgroup.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:3767606-3767703 +		1	GTGGCTGGACAAAAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCACGGTGCTTGTA
droSim1	chr2L:3722744-3722841 +	LASTZ	1	GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droSec1	super_5:1870685-1870782 +	LASTZ	1	GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCTGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droYak2	chr2L:3769291-3769388 +	LASTZ	1	GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGATGTTTGTA
droEre2	scaffold_4929:3814030-3814127 +	LASTZ	1	GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCAATCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droEug1	scf7180000409554:2307491-2307593 -	LASTZ	4	GTGGCTGGACAAAAGGT-TGGGGG--ACAC------------TGATCTCGGAGATCGCTGA---------TCC-----------------------------GATTT----AC----TGATCTATTCTC-----TCACATCACT---T--CCCTCACAGCGCGCGGTGCCTGTA
droBia1	scf7180000302261:2154110-2154211 +	LASTZ	4	GTGGCTGGACAAGAGGT-TGGGGG--ACAC------------TGATCTCGGAGACTGATCC--------ATT-------------------------------CCTT----AC----TGATCCACTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droTak1	scf7180000415709:76418-76520 -	LASTZ	4	GTGGCTGGACAAAAGGT-TGGGGG--ACAC------------TGATCTCGGAGACTGATCC----------CG-----------------------------ATCT---TTAC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droEle1	scf7180000490728:519645-519748 +	LASTZ	4	GTGGCTGGACAAAAGGT-GCGGTT--TCAT------------TGATCTTGGAGACCTTTTC--------GACT-----------------------------ATCCT----AG----TGATCCATTCTC-----TCACATCACT---T--CCCTTATAGCGCGAGGTGCCTGTA
droRho1	scf7180000777886:5849-5946 -	LASTZ	4	GTGGCTGGACAAAAGGT-TGGGGG--ACAT------------TGATCTTGGAGAC--------------GGCT-----------------------------GGCTT----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGCGCGCGGTGCCTGTA
droFic1	scf7180000453924:1748603-1748705 +	LASTZ	4	GTGGCTGGACAAGAGGT-TGGGGG--ACAC------------TGATCTCGGAGAATCGCTC--------ATT------------------------------CGCTC----AC----TGATCCATTCTC-----TCACATCTCT---T--CCCTCACAGCGCGCGGGGCCTGTA
droKik1	scf7180000302401:685585-685686 +	LASTZ	4	GTGGCTCGACAAGAGGT--GAAGG--ACAC------------TGATCTTAGAGAAAGGCAA-------CAGCA-----------------------------AATTA----TA----TG--TAATTCTC-----TCACATCACT---T--CCTTCACAGTGCGAGGTGCTTGTA
droAna3	scaffold_12916:5837615-5837739 +	LASTZ	3	GTGGCTGGACAAGAGGT-GAGATA--ACACGTTCTAACCAACTGATAT--GAAACTAC-G-A--------------------ATGTTTTTATCGCTGTC---G--------AT----TCGAACGATCTC-----TCATATAACCGTAC--CTATTACAGTGCGCGGTGTCTGTA
droBip1	scf7180000396568:1004375-1004463 -	LASTZ	5	GTGGCTGGACAAGAGGT-ACG-------AT------------CGAATCT---------------------CTC-----------------------------GTATA----AT----TCAAACGATCTC-----TCATATAACCGTCT--CTCCTACAGTGCCCGGTGTTTGTA
dp4	chr4_group3:4962038-4962146 -	LASTZ	1	GTGGCTGGACAAGAGGTGTGTGGG--ATAC------------TGATTTTAGAGAAAAAAAA--------AACC--------------------------ATTAACGT----GA----GGCTTCG-TTTC-----TCACATCATT---TTCCCCTCACAGTGCCCGGTGCCTGTA
droPer1	super_1:6454682-6454788 -	LASTZ	1	GTGGCTGGACAAGAGGTGTGTGGG--ATAC------------TGATTTTAGAGAAAAATA----------ACC--------------------------ATTAACGT----GA----GGCTTCG-TTTC-----TCACATCATT---TTCCCCTCACAGTGCCCGGTGCCTGTA
droWil1	scaffold_180708:9298763-9298869 -	LASTZ	5	ATGGTTGGATAAAAGGT--GGGGT--ACAA------------CAACAACAAAAATAC--G-AATATAATGGTA-----------------------------AACTC----TC------------TCTCTCATCTCTTATCATT---TTCTCCTCACAGTGCGCGTTCACTTTA
droVir3	scaffold_12963:14941260-14941364 -	LASTZ	5	GTGGCTGGACAAAAGGT-TGGGGC--ACAT------------TGATCTTCAAGAAACTCAC--------AGCC-----------------------------AGCTC----AT----TTACTCACTCTC-----TCTCTCTTCT----CTCCCTCACAGTGCCCGCTGTCTGTA
droMoj3	scaffold_6500:17898451-17898546 -	LASTZ	5	GTGGCTGGACAAGAGGT-AATTGATCACTC------------CTATCTCTGTCTC-----------------T-----------------------------CTTTCTCTTTC----TG----ACTCTC-----TCCCA-CTCT---T--TATTTGTAGTGCTCGCTGCCTGTA
droGri2	scaffold_15126:4437367-4437497 +	LASTZ	5	GTGGCTGGACAAAAGGT-AGGAGAGCACAT------------TGATCTTGAAGAAACTTGC--------AGAAAACTCTCTAATACTCTCAC-----------TCCATTTCTCTAACTCTCCCTCTCTC-----TTATTTAACT---T--C-ATTTTAGTGCGCGCTGTTTATA

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	GTGGCTGGACAAAAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCACGGTGCTTGTA
droSim1	GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droSec1	GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCTGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droYak2	GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGATGTTTGTA
droEre2	GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCAATCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droEug1	GTGGCTGGACAAAAGGT-TGGGGG--ACAC------------TGATCTCGGAGATCGCTGA---------TCC-----------------------------GATTT----AC----TGATCTATTCTC-----TCACATCACT---T--CCCTCACAGCGCGCGGTGCCTGTA
droBia1	GTGGCTGGACAAGAGGT-TGGGGG--ACAC------------TGATCTCGGAGACTGATCC--------ATT-------------------------------CCTT----AC----TGATCCACTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droTak1	GTGGCTGGACAAAAGGT-TGGGGG--ACAC------------TGATCTCGGAGACTGATCC----------CG-----------------------------ATCT---TTAC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA
droEle1	GTGGCTGGACAAAAGGT-GCGGTT--TCAT------------TGATCTTGGAGACCTTTTC--------GACT-----------------------------ATCCT----AG----TGATCCATTCTC-----TCACATCACT---T--CCCTTATAGCGCGAGGTGCCTGTA
droRho1	GTGGCTGGACAAAAGGT-TGGGGG--ACAT------------TGATCTTGGAGAC--------------GGCT-----------------------------GGCTT----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGCGCGCGGTGCCTGTA
droFic1	GTGGCTGGACAAGAGGT-TGGGGG--ACAC------------TGATCTCGGAGAATCGCTC--------ATT------------------------------CGCTC----AC----TGATCCATTCTC-----TCACATCTCT---T--CCCTCACAGCGCGCGGGGCCTGTA
droKik1	GTGGCTCGACAAGAGGT--GAAGG--ACAC------------TGATCTTAGAGAAAGGCAA-------CAGCA-----------------------------AATTA----TA----TG--TAATTCTC-----TCACATCACT---T--CCTTCACAGTGCGAGGTGCTTGTA
droAna3	GTGGCTGGACAAGAGGT-GAGATA--ACACGTTCTAACCAACTGATAT--GAAACTAC-G-A--------------------ATGTTTTTATCGCTGTC---G--------AT----TCGAACGATCTC-----TCATATAACCGTAC--CTATTACAGTGCGCGGTGTCTGTA
droBip1	GTGGCTGGACAAGAGGT-ACG-------AT------------CGAATCT---------------------CTC-----------------------------GTATA----AT----TCAAACGATCTC-----TCATATAACCGTCT--CTCCTACAGTGCCCGGTGTTTGTA
dp4	GTGGCTGGACAAGAGGTGTGTGGG--ATAC------------TGATTTTAGAGAAAAAAAA--------AACC--------------------------ATTAACGT----GA----GGCTTCG-TTTC-----TCACATCATT---TTCCCCTCACAGTGCCCGGTGCCTGTA
droPer1	GTGGCTGGACAAGAGGTGTGTGGG--ATAC------------TGATTTTAGAGAAAAATA----------ACC--------------------------ATTAACGT----GA----GGCTTCG-TTTC-----TCACATCATT---TTCCCCTCACAGTGCCCGGTGCCTGTA
droWil1	ATGGTTGGATAAAAGGT--GGGGT--ACAA------------CAACAACAAAAATAC--G-AATATAATGGTA-----------------------------AACTC----TC------------TCTCTCATCTCTTATCATT---TTCTCCTCACAGTGCGCGTTCACTTTA
droVir3	GTGGCTGGACAAAAGGT-TGGGGC--ACAT------------TGATCTTCAAGAAACTCAC--------AGCC-----------------------------AGCTC----AT----TTACTCACTCTC-----TCTCTCTTCT----CTCCCTCACAGTGCCCGCTGTCTGTA
droMoj3	GTGGCTGGACAAGAGGT-AATTGATCACTC------------CTATCTCTGTCTC-----------------T-----------------------------CTTTCTCTTTC----TG----ACTCTC-----TCCCA-CTCT---T--TATTTGTAGTGCTCGCTGCCTGTA
droGri2	GTGGCTGGACAAAAGGT-AGGAGAGCACAT------------TGATCTTGAAGAAACTTGC--------AGAAAACTCTCTAATACTCTCAC-----------TCCATTTCTCTAACTCTCCCTCTCTC-----TTATTTAACT---T--C-ATTTTAGTGCGCGCTGTTTATA

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAG...............	22	1	1133.00	26.00	994.00	20.00	93.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	728.00	16.00	444.00	55.00	213.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	132.00	3.00	107.00	18.00	4.00
...............GT-TGGGGG--ACAT------------TGATCTCGGA..........................................................................................................................	22	1	122.00	0.00	92.00	22.00	8.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACA................	21	1	101.00	1.00	97.00	2.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGG........................................................................................................................	24	1	91.00	0.00	46.00	9.00	36.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAA--------------.........................................................................................................	25	1	25.00	1.00	21.00	2.00	1.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAC...............	22	1	20.00	0.00	19.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGA..............	22	1	16.00	0.00	14.00	1.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCGGG..........................................................................................................................	22	1	11.00	0.00	10.00	1.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGT..............	22	1	10.00	3.00	6.00	1.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAG...............	21	1	10.00	0.00	10.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCAC.................	20	1	9.00	0.00	9.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGC........................................................................................................................	24	1	9.00	0.00	5.00	1.00	3.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAA.........................................................................................................................	23	1	8.00	0.00	6.00	2.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------G........................................................................................................	26	1	7.00	0.00	3.00	0.00	4.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------.........................................................................................................	25	1	7.00	0.00	4.00	3.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAAA........................................................................................................................	24	1	6.00	0.00	6.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAC.........................................................................................................................	23	1	6.00	0.00	5.00	1.00	0.00
................G-TTGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	23	1	6.00	0.00	2.00	0.00	4.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCA..................	19	1	5.00	0.00	5.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCCCACAG...............	22	1	4.00	0.00	4.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTC.............................................................................................................................	19	1	4.00	0.00	4.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACGG...............	22	1	4.00	0.00	2.00	2.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGC..............	22	1	4.00	0.00	4.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCGCAG...............	22	1	3.00	0.00	3.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGG...........................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGG..............	22	1	3.00	0.00	3.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAGA..............	23	1	3.00	0.00	3.00	0.00	0.00
...............GT-TGGGTG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	3.00	0.00	2.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAT--------------.........................................................................................................	25	1	2.00	0.00	2.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGT........................................................................................................................	24	1	2.00	0.00	2.00	0.00	0.00
...............GT-TGGTGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	2.00	0.00	1.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATTTCGGAGA........................................................................................................................	24	1	2.00	0.00	0.00	0.00	2.00
...............................................................................................................................TC-----TCACATCACT---C--CCCTCACAG...............	22	1	2.00	0.00	1.00	0.00	1.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAGT..............	23	1	2.00	0.00	2.00	0.00	0.00
...............................................................................................................................TC-----CCACATCACT---T--CCCTCACAG...............	22	1	2.00	0.00	2.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGGTCTCGGA..........................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............CT-TGGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................TC-----TCACATCACT---T--CACTCACAG...............	22	1	1.00	0.00	1.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGCTCTCGGAGA........................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...............GT-TGAGGG--ACAT------------TGATCTCGGAGAC--------------G........................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCGGTGA........................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TC-----CCACATCACT---T--CCCTCTCAG...............	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................TC-----TCACTTCACT---T--CCCTCACAG...............	22	1	1.00	0.00	1.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTAGGAGA........................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
................G-TTGGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACATTACT---T--CCCTCACAG...............	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACACCACT---T--CCCTCACAC...............	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................C----TGATCCATTxTC-----TCACACC.................................	19	1	1.00	0.00	0.00	0.00	1.00
...............GT-TGGGGT--ACAT------------TGATCTCGGG..........................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
................T-TGGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...............GT-TGTTGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAA--------------A........................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00
................G-TTGGGG--ACAT------------TGATCTCGGAGAC--------------G........................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................TCACATAACT---T--CCCTCACAGT..............	21	1	1.00	0.00	1.00	0.00	0.00
................G-TTGGGG--ACAT------------TGATCTCGG...........................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...............GT-TGGGCG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTGACAG...............	22	1	1.00	0.00	0.00	0.00	1.00
...............GT-TGTGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAGAA.............	24	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACACCACT---T--CCCTCACAG...............	22	1	1.00	0.00	0.00	0.00	1.00
.....................GGG--ACAT------------TGATCTCGGAGG........................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............GT-TCGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................GC-----TCACATCACT---T--CCCTCACAG...............	22	1	1.00	0.00	1.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAAT........................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACTG...............	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCTTCACAG...............	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TA-----TCACATCACT---T--CCCTCACAG...............	22	1	1.00	1.00	0.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGC..........................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............GC-TGGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGGTCTCGGAG.........................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CACTCAC.................	20	1	1.00	0.00	1.00	0.00	0.00
................T-TGGGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CGCTCACAG...............	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACGTCACT---T--CCCTCACAG...............	22	1	1.00	0.00	1.00	0.00	0.00
...............GT-TGGGGG--CCAT------------TGATCTCGGAGA........................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................TCACATCACT---T--CCCTCACAGT..............	21	1	1.00	0.00	1.00	0.00	0.00
...............GT-TGGGGT--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00

droSec1

GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCTGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............GT-TGGGGG--ACAT------------TGATCTCTGAG.........................................................................................................................	23	1	120.00	10.00	36.00	74.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAG...............	22	1	84.00	2.00	16.00	66.00
...............GT-TGGGGG--ACAT------------TGATCTCTGAGA........................................................................................................................	24	1	53.00	1.00	25.00	27.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGT..............	22	1	23.00	0.00	12.00	11.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACA................	21	1	19.00	0.00	1.00	18.00
......................................................................................................................................TCACATCACT---T--CCCTCACAGT..............	21	1	18.00	0.00	2.00	16.00
...............GT-TGGGGG--ACAT------------TGATCTCTGA..........................................................................................................................	22	1	7.00	0.00	2.00	5.00
...............GT-TGGGGG--ACAT------------TGATCTCTG...........................................................................................................................	21	1	4.00	0.00	0.00	4.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAGT..............	23	1	4.00	0.00	0.00	4.00
...............GT-TGGGGG--ACAT------------TGATCTCTGAGAC--------------G........................................................................................................	26	1	4.00	0.00	3.00	1.00
.............AGGT-TGGGGG--AxAT------------TGATG...............................................................................................................................	18	1	3.00	1.00	0.00	2.00
...............GT-TGGGGG--ACAT------------TGATCTCT............................................................................................................................	20	1	2.00	0.00	0.00	2.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCAC.................	20	1	2.00	0.00	0.00	2.00
...............GT-TGGGGG--ACAT------------TGATCTCTGAGAA--------------.........................................................................................................	25	1	2.00	0.00	0.00	2.00
.............AGGT-TGGGGG--xCAT------------TGATG...............................................................................................................................	18	1	1.00	1.00	0.00	0.00
...............GT-TGGTGG--ACAT------------TGATCTCTGAG.........................................................................................................................	23	1	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCTTAGA........................................................................................................................	24	1	1.00	0.00	1.00	0.00
...............................................................................................................................TC-----TCACATCACT---C--CCCTCACA................	21	1	1.00	0.00	0.00	1.00
...............................................................................................................................TC-----TCAAATCACT---T--CCCTCACAG...............	22	1	1.00	0.00	1.00	0.00
.....................................................AC--------------GGCG-----------------------------GTTTA----AC----TGACCCCTTCT..............................................	24	1	1.00	0.00	0.00	1.00
......................................................................................................................................TCACATCACT---T--TCCTCACAGT..............	21	1	1.00	0.00	1.00	0.00
................T-TGGGGG--ACAT------------TGATCTCTGAGA........................................................................................................................	23	1	1.00	1.00	0.00	0.00
...............GT-TGGGGG--CCAT------------TGATCTCTGAG.........................................................................................................................	23	1	1.00	0.00	0.00	1.00
........................................................................................................................................ACATCACT---T--CCCTCACAGT..............	19	1	1.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTTACAGT..............	22	1	1.00	0.00	0.00	1.00
...............................................................................................................................TC-----TCACATCACT---T--CCCCCACAG...............	22	1	1.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACA................	20	1	1.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTCGCAGT..............	22	1	1.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGACCTCTG...........................................................................................................................	21	1	1.00	0.00	1.00	0.00
......................................................................................................................................TCTCATCACT---T--CCCTCACA................	19	1	1.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGTTCTCTGAG.........................................................................................................................	23	1	1.00	0.00	0.00	1.00
.....................................................AC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCT..............................................	24	1	1.00	0.00	0.00	1.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCAAAG...............	22	1	1.00	0.00	0.00	1.00
................................................................................................................................C-----TCACGTCACT---T--CCCTCACAGT..............	22	1	1.00	0.00	1.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGA..............	22	1	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCTAAG.........................................................................................................................	23	1	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTC.............................................................................................................................	19	1	1.00	0.00	0.00	1.00
.......................................................................................................................................CACATCACT---T--CCCTCACAG...............	19	1	1.00	0.00	0.00	1.00
......................................................................................................................................TCAAATCACT---T--CCCTCACAGT..............	21	1	1.00	0.00	0.00	1.00
...............................................................................................................................AC-----TCACATCACT---T--CCCTCACAG...............	22	1	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACCT------------TGATCTCTGAG.........................................................................................................................	23	1	1.00	0.00	1.00	0.00
...............GT-CGGGGG--ACAT------------TGATCTCTGAGA........................................................................................................................	24	1	1.00	0.00	1.00	0.00
...............................................................................................................................TC-----TCACATCACT---C--CCCTCACAG...............	22	1	1.00	1.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCCCTGAG.........................................................................................................................	23	1	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------CGATCTCTGAGA........................................................................................................................	24	1	1.00	0.00	1.00	0.00
...............GT-TCGGGG--ACAT------------TGATCTCTGAG.........................................................................................................................	23	1	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCTGAGAT--------------T........................................................................................................	26	1	1.00	0.00	0.00	1.00
......................................................................................................................................TCACATCACT---T--CCCTCACAGA..............	21	1	1.00	1.00	0.00	0.00
...............................................................................................................................TC-----CCACATCACT---T--CCCTCACAG...............	22	1	1.00	0.00	0.00	1.00
......................GG--ACAT------------TGATCTCTGAGAC--------------GGC......................................................................................................	22	1	1.00	1.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCTGAGAC--------------.........................................................................................................	25	1	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAC------------TGATCTCTGAG.........................................................................................................................	23	1	1.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCTGAGC........................................................................................................................	24	1	1.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGC..............	22	1	1.00	0.00	0.00	1.00

droYak2

GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGATGTTTGTA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAG...............	22	1	454.00	36.00	26.00	3.00	37.00	352.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	373.00	11.00	8.00	8.00	15.00	331.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	98.00	0.00	24.00	10.00	38.00	26.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACA................	21	1	56.00	0.00	11.00	1.00	6.00	38.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGG........................................................................................................................	24	1	35.00	0.00	0.00	0.00	0.00	35.00
...............GT-TGGGGG--ACAT------------TGATCTCGGA..........................................................................................................................	22	1	25.00	1.00	3.00	5.00	8.00	8.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGT..............	22	1	25.00	2.00	8.00	1.00	12.00	2.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAA--------------.........................................................................................................	25	1	16.00	1.00	1.00	0.00	0.00	14.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCAC.................	20	1	14.00	0.00	3.00	0.00	3.00	8.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGC........................................................................................................................	24	1	10.00	0.00	0.00	0.00	1.00	9.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAC...............	22	1	7.00	0.00	0.00	0.00	0.00	7.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------G........................................................................................................	26	1	7.00	0.00	0.00	0.00	1.00	6.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCCCAG...............	22	1	5.00	0.00	0.00	0.00	2.00	3.00
...............GT-TGGGGG--CCAT------------TGATCTCGGAGA........................................................................................................................	24	1	5.00	0.00	0.00	0.00	0.00	5.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACCG...............	22	1	4.00	0.00	1.00	0.00	2.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCGGCG.........................................................................................................................	23	1	4.00	0.00	0.00	1.00	3.00	0.00
......................................................................................................................................TCACATCACT---T--CCCTCACAGT..............	21	1	4.00	0.00	2.00	0.00	2.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------.........................................................................................................	25	1	3.00	1.00	0.00	0.00	0.00	2.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCA..................	19	1	3.00	0.00	0.00	0.00	0.00	3.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAGT..............	23	1	3.00	1.00	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCTGAG.........................................................................................................................	23	1	2.00	0.00	0.00	0.00	2.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAAA........................................................................................................................	24	1	2.00	0.00	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCGG...........................................................................................................................	21	1	2.00	0.00	2.00	0.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGCGA........................................................................................................................	24	1	2.00	0.00	1.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGG..........................................................................................................................	22	1	2.00	0.00	0.00	0.00	0.00	2.00
...............................................................................................................................TC-----TCACATCACT---T--CCCCCACAG...............	22	1	2.00	0.00	1.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTC.............................................................................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
...............GT-TGGGGG--ACAT------------TGATCTCGGTG.........................................................................................................................	23	1	2.00	0.00	0.00	0.00	2.00	0.00
...............................................................................................................................TC-----TCACATCAGT---T--CCCTCACAC...............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TGGGGA--ACAT------------TGATCTCGGA..........................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCT..............................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
......................................................................................................................................TCACATCACT---T--CCCTCACAG...............	20	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAA...............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TGGGGG--GCAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................................C-----TGACATCACT---G--CCCTCACAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGT........................................................................................................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TAGGGG--ACAT------------TGATCCCGGAGA........................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00	0.00
...............GT-CGGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGG..............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACA................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
................T-TGGGGG--ACAT------------TGATCTCGGAGG........................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
..............CGT-TGGGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................GGG--ACAT------------TGATCTCGGAG.........................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAT.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAGA..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGGG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGACA........................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--TCAT------------TGATCTCGGAGG........................................................................................................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTCCCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--ACCTCACAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TC-----TCACATCACT---C--CCCTCACAG...............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................................................................GC-----TCACATCACT---T--CCCTCACAG...............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TCGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................................................................TC-----TCACATCACT---A--CCCTCACAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGAGGG--ACAT------------CGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAAT..............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACATT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACCGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACGG...............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TGGGGG--ACAT------------TGATCTGGGTG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGA--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TAGGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCTAACTGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------GGATCACGGAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ATAT------------TGATCTCGGAGA........................................................................................................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACCGG..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................C-----CCACATCACT---T--CCCTCCCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TC-----TTACGTCACT---T--CCCTCACAG...............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGAAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACC................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TGGAGG--ACAT------------TGATCTCGCAGA........................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TA-----TCACATCACT---T--CCCTCTCAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................CC-----TCACATCACT---T--CCCTCACA................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................ATCTCGGAGxC--------------GGTG-----------------------------GTT.....................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................C-----TCACATCACT---T--CCCCCACAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TC-----TTACATCACT---T--CCCTCACAG...............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...............GA-TGGGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAA--------------AG.......................................................................................................	27	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TGGGGG--AAAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCG............................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCAGA..........................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAC.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................................C-----TCACATCACT---T--CACTCACAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............GT-TGGGTG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TGGGGG--ACGT------------TGATCTCGGAGC........................................................................................................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TGGGGT--ACAT------------TGCTCTCGG...........................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
....................GGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GT-TGGGGG--CCAT------------TGATCTCGGAG.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................TC-----TCACCTCTCT---T--CCCTCACAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................A-----TCACATCACT---T--CCCTCACAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................................................................TA-----TCGCATCACT---T--CCCTCACAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GT-TGGGGG--ACAT------------TGCTCTCGG...........................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
................G-TTGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................................................................TC-----TCACATCACT---T--CCCCCACA................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................................................................................TCACATCACT---T--CCCTCACA................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

GTGGCTGGACAAGAGGT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------GGCG-----------------------------GTTTA----AC----TGATCCAATCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAG...............	22	1	506.00	35.00	66.00	0.00	405.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	248.00	14.00	13.00	0.00	221.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	146.00	2.00	17.00	0.00	127.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGT..............	22	1	82.00	1.00	10.00	0.00	71.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACA................	21	1	76.00	1.00	13.00	0.00	62.00
...............GT-TGGGGG--ACAT------------TGATCTCGG...........................................................................................................................	21	1	20.00	0.00	2.00	0.00	18.00
...............GT-TGGGGG--ACAT------------TGATCTCGGA..........................................................................................................................	22	1	19.00	0.00	1.00	0.00	18.00
...............................................................................................................................TC-----TCACATCACT---T--CCATCACAG...............	22	1	11.00	0.00	0.00	0.00	11.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCAC.................	20	1	7.00	0.00	0.00	0.00	7.00
...............GT-TGTGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	7.00	0.00	0.00	0.00	7.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACAGT..............	23	1	6.00	0.00	0.00	0.00	6.00
...............GT-TGGGGG--ACAT------------TGATCTCTGAGA........................................................................................................................	24	1	5.00	0.00	0.00	0.00	5.00
......................................................................................................................................TCACATCACT---T--CCCTCACAGT..............	21	1	5.00	0.00	1.00	0.00	4.00
...............GT-TTGGGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	5.00	0.00	0.00	0.00	5.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGAC--------------G........................................................................................................	26	1	5.00	0.00	0.00	0.00	5.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAGA..............	22	1	5.00	0.00	0.00	0.00	5.00
...............GT-TTGGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
......................................................................................................................................TCACATCACT---T--CCCTCACAG...............	20	1	4.00	1.00	1.00	0.00	2.00
................................................................................................................................C-----TCACATCACT---T--CCCTCACAG...............	21	1	4.00	0.00	0.00	0.00	4.00
...............................................................................................................................TA-----TCACATCACT---T--CCCTCACAG...............	22	1	4.00	0.00	0.00	0.00	4.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAA.........................................................................................................................	23	1	4.00	0.00	1.00	0.00	3.00
...............................................................................................................................TC-----TCACATCACT---T--CACTCACAG...............	22	1	4.00	0.00	0.00	0.00	4.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTAACAG...............	22	1	4.00	0.00	0.00	0.00	4.00
...............................................................................................................................TC-----TCGCATCACT---T--CCCTCACAG...............	22	1	4.00	1.00	0.00	0.00	3.00
...............GT-TGGGGG--ACAT------------TGATCTCGGATA........................................................................................................................	24	1	4.00	0.00	0.00	0.00	4.00
...............GT-TGGTGG--ACAT------------TGATCTCGGAGA........................................................................................................................	24	1	3.00	0.00	0.00	0.00	3.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAT.........................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
...............GT-TGGGGG--ACAT------------TGATCTCGGACA........................................................................................................................	24	1	3.00	0.00	0.00	0.00	3.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCACCG...............	22	1	3.00	2.00	1.00	0.00	0.00
...............................................................................................................................TC-----TCACATAACT---T--CCCTCACAG...............	22	1	3.00	0.00	0.00	0.00	3.00
...............GT-TGGTGG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
...............................................................................................................................TC-----TCACATCACT---T--CCCTCA..................	19	1	3.00	0.00	0.00	0.00	3.00
...............GT-TGTGGG--ACAT------------TGATCTCGGAG.........................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
...............GT-TGGGGG--ACAT------------TGATCTCGGAGC........................................................................................................................	24	1	3.00	0.00	1.00	0.00	2.00

droEug1

GTGGCTGGACAAAAGGT-TGGGGG--ACAC------------TGATCTCGGAGATCGCTGA---------TCC-----------------------------GATTT----AC----TGATCTATTCTC-----TCACATCACT---T--CCCTCACAGCGCGCGGTGCCTGTA

Size

Hit Count

Total Norm

droBia1

GTGGCTGGACAAGAGGT-TGGGGG--ACAC------------TGATCTCGGAGACTGATCC--------ATT-------------------------------CCTT----AC----TGATCCACTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA

Size

Hit Count

Total Norm

droTak1

GTGGCTGGACAAAAGGT-TGGGGG--ACAC------------TGATCTCGGAGACTGATCC----------CG-----------------------------ATCT---TTAC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGTGCGCGGTGCTTGTA

Size

Hit Count

Total Norm

droEle1

GTGGCTGGACAAAAGGT-GCGGTT--TCAT------------TGATCTTGGAGACCTTTTC--------GACT-----------------------------ATCCT----AG----TGATCCATTCTC-----TCACATCACT---T--CCCTTATAGCGCGAGGTGCCTGTA

Size

Hit Count

Total Norm

droRho1

GTGGCTGGACAAAAGGT-TGGGGG--ACAT------------TGATCTTGGAGAC--------------GGCT-----------------------------GGCTT----AC----TGATCCATTCTC-----TCACATCACT---T--CCCTCACAGCGCGCGGTGCCTGTA

Size

Hit Count

Total Norm

droFic1

GTGGCTGGACAAGAGGT-TGGGGG--ACAC------------TGATCTCGGAGAATCGCTC--------ATT------------------------------CGCTC----AC----TGATCCATTCTC-----TCACATCTCT---T--CCCTCACAGCGCGCGGGGCCTGTA

Size

Hit Count

Total Norm

droKik1

GTGGCTCGACAAGAGGT--GAAGG--ACAC------------TGATCTTAGAGAAAGGCAA-------CAGCA-----------------------------AATTA----TA----TG--TAATTCTC-----TCACATCACT---T--CCTTCACAGTGCGAGGTGCTTGTA

Size

Hit Count

Total Norm

droAna3

GTGGCTGGACAAGAGGT-GAGATA--ACACGTTCTAACCAACTGATAT--GAAACTAC-G-A--------------------ATGTTTTTATCGCTGTC---G--------AT----TCGAACGATCTC-----TCATATAACCGTAC--CTATTACAGTGCGCGGTGTCTGTA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.............................................................................................GCTGTC---G--------AT----TCGAACGATC...............................................	19	1	6.00	1.00	4.00	1.00	0.00
..........................................................................................ATCGCTGTC---G--------AT----TCGAACGATC...............................................	22	1	3.00	0.00	3.00	0.00	0.00
....................................................................................GTTTTTATCGCTGTC---G--------AT----TCGA.....................................................	22	1	3.00	0.00	3.00	0.00	0.00
.............................CGTTCTAACCAACTGATAT--GAAACT......................................................................................................................	25	1	2.00	0.00	2.00	0.00	0.00
.......................................AACTGATAT--GAAACTAC-G-A--------------------AT..........................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................................................TTATCGCTGTC---G--------AT----TCGAACGATC...............................................	24	1	1.00	1.00	0.00	0.00	0.00
..........................................TGATAT--GAAACTAC-G-A--------------------ATGT........................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................GCTGTC---G--------AT----TCGAACGATCT..............................................	20	1	1.00	1.00	0.00	0.00	0.00
GTGGCTGGTCAAGAAGT-G...........................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...........................................GATAT--GAAACTAC-G-A--------------------ATGTTTT.....................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................................AACTAC-G-A--------------------ATGTTTTTATCGC...............................................................................	21	1	1.00	0.00	1.00	0.00	0.00

droBip1

GTGGCTGGACAAGAGGT-ACG-------AT------------CGAATCT---------------------CTC-----------------------------GTATA----AT----TCAAACGATCTC-----TCATATAACCGTCT--CTCCTACAGTGCCCGGTGTTTGTA

Size

Hit Count

Total Norm

dp4

GTGGCTGGACAAGAGGTGTGTGGG--ATAC------------TGATTTTAGAGAAAAAAAA--------AACC--------------------------ATTAACGT----GA----GGCTTCG-TTTC-----TCACATCATT---TTCCCCTCACAGTGCCCGGTGCCTGTA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
......................................................................................................................................TCACATCATT---TTCCCCTCACAGT..............	23	1	42.00	4.00	2.00	36.00	0.00
......................................................................................................................................TCACATCATT---TTCCCCTCACAG...............	22	1	17.00	1.00	2.00	14.00	0.00
...............GTGTGTGGG--ATAC------------TGATTTTAGAGA........................................................................................................................	25	1	3.00	2.00	1.00	0.00	0.00
......................................................................................................................................TCACATCATT---TTCCCCTCACA................	21	1	2.00	0.00	0.00	2.00	0.00
........................................................................................................................................ACATCATT---TTCCCCTCACAGT..............	21	1	2.00	0.00	0.00	2.00	0.00
......................................................................................................................................TCACATCAxT---TTCCCCTCACAGT..............	22	1	1.00	1.00	0.00	0.00	0.00
...........AGTGGTGTTTGGG--ATAC------------TG..................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................TCACATCATT---TTCCACTCACAGT..............	23	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACATCATT---TTCCCCTCACGG...............	22	1	1.00	0.00	1.00	0.00	0.00
.TGGCTTGATAAGAGGTGTGTGG.......................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................CACATCATT---TTCCCCTCACAGT..............	22	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACATCATG---TTCCCCTCACA................	21	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACAACATT---TACCCCTCACAGT..............	23	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................TCACATCATT---TTAACCTCACAGT..............	23	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACATCATT---CTCCCCTCACAGT..............	23	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACATCATT---TTCCCCTCACAA...............	22	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACATCATT---TTCCCCTCACAGA..............	23	1	1.00	0.00	0.00	1.00	0.00

droPer1

GTGGCTGGACAAGAGGTGTGTGGG--ATAC------------TGATTTTAGAGAAAAATA----------ACC--------------------------ATTAACGT----GA----GGCTTCG-TTTC-----TCACATCATT---TTCCCCTCACAGTGCCCGGTGCCTGTA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................................................................................................TCACATCATT---TTCCCCTCACAGT..............	23	1	45.00	1.00	0.00	18.00	25.00	1.00
......................................................................................................................................TCACATCATT---TTCCCCTCACAG...............	22	1	20.00	0.00	3.00	8.00	9.00	0.00
...............GTGTGTGGG--ATAC------------TGATTTTAGAGA........................................................................................................................	25	1	11.00	6.00	0.00	1.00	2.00	2.00
......................................................................................................................................TCACATCATT---TTCCCCTCACA................	21	1	10.00	0.00	0.00	4.00	6.00	0.00
.......................................................................................................................................CACATCATT---TTCCCCTCACAGT..............	22	1	3.00	0.00	0.00	3.00	0.00	0.00
......................................................................................................................................TCACATCATT---TTCCCCTCAAAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACACCATT---TTCCCCTCACAGT..............	23	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................TAACATCATC---TTCCCCTCACAGT..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACATCATT---TTCCCCTCACAGC..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................................................................................CACATCATT---TTCACCTCACAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGTGTGGG--ATAC------------GGATTTTAGAGA........................................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACATCATT---TTCCCCTCGCT................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTGGG--ATAC------------TGATTTTAGAGA........................................................................................................................	25	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................................................................CACATCATT---TTCCCCTCACAG...............	21	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................TCACATCATT---TGCCCCTCACAGT..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................................................................................CACATCATT---TTCCCCTCACA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................................................................................CACATCATT---TCCCCCTCACA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACATCATT---TTCCGCTCACCGT..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................................................................TCACATCATT---TTCACCTCACAG...............	22	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................TCACATCATT---TTCCCCTCAGAGT..............	23	1	1.00	0.00	0.00	1.00	0.00	0.00
...............GTGTGTGGG--ATAC------------TGATTTTAGAGAA.......................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

ATGGTTGGATAAAAGGT--GGGGT--ACAA------------CAACAACAAAAATAC--G-AATATAATGGTA-----------------------------AACTC----TC------------TCTCTCATCTCTTATCATT---TTCTCCTCACAGTGCGCGTTCACTTTA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
......................GT--ACAA------------CAACAATAAGAA........................................................................................................................	18	7	0.29	0.00	0.29	0.00	0.00
.............................A------------CAACAACAAAAATAC--C-AAC..............................................................................................................	20	30	0.03	0.00	0.03	0.00	0.00
......................GT--ACAA------------CAACAACAAGAAGA......................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
....................GGGT--AGAA------------CAAAAACAAAA.........................................................................................................................	19	7	0.14	0.00	0.14	0.00	0.00
............................AA------------CAACAACGAAAATAC--G-T................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................ACAA------------CAACAACAAAATAAC--G-A................................................................................................................	21	6	0.17	0.17	0.00	0.00	0.00

droVir3

GTGGCTGGACAAAAGGT-TGGGGC--ACAT------------TGATCTTCAAGAAACTCAC--------AGCC-----------------------------AGCTC----AT----TTACTCACTCTC-----TCTCTCTTCT----CTCCCTCACAGTGCCCGCTGTCTGTA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.........................................................................................................................TCAGTCTC-----TCTCTCTCCT----..........................	18	7	0.71	0.00	0.00	0.00	0.00	0.71
...........................CAT------------TGAACTTCAAGAACC.....................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00

droMoj3

GTGGCTGGACAAGAGGT-AATTGATCACTC------------CTATCTCTGTCTC-----------------T-----------------------------CTTTCTCTTTC----TG----ACTCTC-----TCCCA-CTCT---T--TATTTGTAGTGCTCGCTGCCTGTA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....................TGATTACTx------------CTATCTCTGTCTC-----------------T-----------------------------C.......................................................................	23	1	1.00	0.00	0.00	1.00	0.00

droGri2

GTGGCTGGACAAAAGGT-AGGAGAGCACAT------------TGATCTTGAAGAAACTTGC--------AGAAAACTCTCTAATACTCTCAC-----------TCCATTTCTCTAACTCTCCCTCTCTC-----TTATTTAACT---T--C-ATTTTAGTGCGCGCTGTTTATA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:22:03 EDT

dme-mir-1004

chr2L:3767621-3767688 +

Known_mirbase

mirtron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup