dme-mir-4951- Best orthologs

dme-mir-4951	chr3R:17142437-17142587 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 17142468-17142488
   star strand at position 17142541-17142563
   mutations
   read mismatches

Notes: miR is perfectly conserved in the melanogaster group

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3R:17142422-17142602 +		1	TTT--GAAA--A-TCC-------------CTTCCTTTTCGTACGTAC----A--A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTTCCTA-------A-CAATTA-----------------------------------AA---------------CCCTATGTCGGTATTACG--AATACC-AT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-CAAC------G-
droSim1	chr3R:4327111-4327287 -	LASTZ	1	TTT--CAAA--AATCC-------------CTTCCTTTTCGTACGTAC----A--A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTCCCTA-------A-AAATAA-----------------------------------GA---------------CCCTATGTCGGTATTTCG--AATACC-AT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-------------
droSec1	super_6:4348795-4348971 -	LASTZ	1	TTT--CAAA--AATCC-------------CTTCCTTTTCGTACGTAC----A--A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTCCCTA-------A-CAATTA-----------------------------------GA---------------CCCTATGTCGGTATTTCG--AATACC-AT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-------------
droYak2	chr3R:5943432-5943618 +	LASTZ	1	TTA--AAAA--AATTCA------------TTTACTTTACGTGCGTAC----A--AAAAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTTCCTA-------A-CAACTA-----------------------------------GT---------------CCCTATGTTGGTACTACG--AATACC-AAAT----CAAAAAACCTCACCCACCAAAAGTATGAACAGAGAGATAAAAA-T-TTCAATATAAAAAC------A-
droEre2	scaffold_4770:4529493-4529670 -	LASTZ	3	TAT-----------------------------------TGTACGTAAGCATT--A-TTAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--CG-TCTCTTAAGT-------TTTCCATA-------A-CAATTG-----------------------------------GT---------------CCCTATGTTGGTATTACA--AATACC-ATAC----CAAAAAACCTCACCCACCAAATGTATGAACAGAGAGATAAAAA-T-TTCAATAAAAAAATGTTGTCGA
droEug1	scf7180000409760:1269937-1270134 -	LASTZ	5	TCC--TAAAAAGCTTCAAACCCCTTTTCTAATCCCTTTCGTACGAAA-------A-AAAGGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTTTTA-GTTT----C-GCGCCTT-------T-TTATAA-----------------------------------AC---------------CCCTTTGTCGGTATTGCA--AATACC-AT------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGATACAAA-T-TTCAATCAATTAAC------T-
droBia1	scf7180000302155:521238-521435 +	LASTZ	5	CTT--AAGA--ACTTCACACCC--TTTCACGTCCTTTTCGTACGAAT----A--AATAAAGCGTCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTACCT-TTTTAC-ATCCCTT-------T-ACATGA-----------------------------------AT-C-------------CCCCATCTTGGTATTGCA--AATACC-A-------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGAA-AAAA-T-TTCAATAAG-TACT------G-
droTak1	scf7180000415417:230044-230222 -	LASTZ	4	ACT--AAAA--ACTTCAAACCC--TTTCACAT-ATTTTCGTACGAAC----A----AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCCCTTA----------------------------CATGA-----------------------------------AT---------------TCCTATATCGGTATTGAA--AATGCC-AC------CTAAAAACCTCACCCACCAAATGTATATTCAAAGAGAATAAAA-T-TTCAATAAACTAAC------G-
droEle1	scf7180000491104:1675814-1676010 +	LASTZ	4	TAT--TAAA--ACTTCACTCCC-CTTTCACATTCTTATCGTTCGAAC----G--AATTCAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTA--TG-TCTTTGTACC-------TTCTCCAA-------A-AAATGA-----------------------------------AT---------------CCCTACCTTGGTATTGCA--AATACC-CTA-----TAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATATAAA-T-TTCAATAAACTAAC------A-
droRho1	scf7180000767410:75272-75464 -	LASTZ	5	CAT--AAAA---CTTCTGGCCC-CATTTACTT-CTTATCGTACGACC----G--AAAACAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCCTTTTACA-------TTCTCCAA-------T-AAAAT------------------------------------AT---------------CCCTATTTCGGTATTTCA--AATACT-TT------AAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAA-T-TTCAATAAAGTAAA------A-
droFic1	scf7180000454096:426559-426742 +	LASTZ	5	CTT--CA----------GACCC-TTTTCATTTCCCTATCGTACGAA--------A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTCGACT-------TTACCCCT-------T-ATACTA-----------------------------------TC---------------CCCTG-TTTGGCATTCCA--AATGCC-AC------CTAAAAACCTCACCCACCAAATGTATGAACAAAGAGAAAAACA-T-TTCAATAAGGTATT------G-
droKik1	scf7180000302461:267813-268013 +	LASTZ	5	TCT--AAAA--GCTTCAAACCC-TTTTCCAAT-ACCATCGTACGAAC----A--TTAAAAGCATCAGAT-TTTCGGGTGAGGTTA--CTGATGCTCTTTG-TCTCTAAAAT----------------------------ATGTTTTTTTTTTCTAAAAAAAAAATAAA---------------------------------AGGAA-AACA--TACACC-ACCT---TAAAATAACCTCACCCACCAAATGTATGAACAAAGAGAACAAAA-T-TTCAATACA--AAC------C-
droAna3	scaffold_13340:3794779-3794949 +	MAF	1	TCT--C------------------------TACATTAATATTATCAT----G--G-AAAAGCATCAGTTTTTTCGGGTGAGGTTATACTGATGCTT--AG-TCATTTCAAT-------TGCCCAAA-------A-TAATTG-----------------------------------AA---------------TTTT-AATTGGTATTTTT-CAATACC-CA------AGACTAACCTCACCCACCAAATATATGAACAAAGAGATATAAA-T-TTCAATAAA-------------
droBip1	scf7180000396395:545263-545439 -	LASTZ	5	TTTCTTATA--A-TTA-------------CAATAATTTTA---TAAT----A--G-ATAAGCATCAGTTTTTTCGGGTGAGGTCAA-CTGTTGCGA--AA-TCATTTCAAT-------TGCCCAAA--A----A-CAATTG-----------------------------------AA---------------TTTT-AATTGGTATTTTT-CAATGCC-CA------AAACTAACCTCACCCACCAAATATATGAAAAAAGAGATACAAA-T-TTCAATAA--------------
dp4	chr2:5640393-5640558 +	MAF	5	CCC--------------------------CGTCAATATTGTAATTAA----A--ATAAAAGCATCCGAG-CTTCGGGTGAGGTTA--TGGATGCATTTTGATCTCTGCACT-------TATCTCCA-------A------------------------------------------AA--------------CCCC--CTTTTGTATGGAAA-CATACC-ACC-----CAAATAACCTCACCCACCAAAT-TATGAACAAAGAGAAAAAAA-T-TTCAATAAA-------------
droPer1	super_19:1368761-1368939 +	LASTZ	5	CCC--------------------------CGTCAATATTGTAATTAA----A--ATAAAAGCATCCGAG-CTTCGGGTGAGGTTA--TGGATGCATTTTGATCTCTGCACT-------TATCTCCA-------A------------------------------------------AA--------------CCCC--TTTTTGTATGGAAA-CATACC-ACC-----CAAATAACCTCACCCACCAAAT-TATGAACAAAGAGAAAAAAA-T-TTCAATAAACACAAAACCACG-
droWil1	scaffold_181130:16134997-16135163 +	LASTZ	5	TAA--A--------------------------TCTTACTGTTATCC--------A-AAAATCATCACGG-TTTCGGGTGAGGTTA--GTGATGACT--TT-TCCTTT--------------TTCAAACA-------ACTAA-----------------------------------AATTTTAATTCCAAAAACCC--TTTCGGTATAGAC--AATACC-AA------AAAAAAACCTCACCCACCAAATATATGAACAAAGAGAAACAAA-TTTTCA------------------
droVir3	scaffold_12822:1191963-1192168 -	LASTZ	5	CTT--AA----------------------------TGTCGTACGACT----TATG-AGAAGCATCTAGT--TTCGGGTGAGGTTTT-ATGATGCAATTCTCGCTCT--------------ATCCC---ATCTTGAACATACGT--------TCCAAAATAAATACATAATAAAAAAAT-C-------------CCCTGCTTTGGTATTTAA--GCTACC-AACC---AAAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAAATTTTCAATACACC-AT------G-
droMoj3	scaffold_6540:33813435-33813629 -	LASTZ	5	CCT--C-----------------------CTCCCAAGTTGTACAGCT----TGTG-AGATGCATCAGAT-TTTCGGGTGAGGTTTT-ATGATGCAGTAC--TCCAT---GT-------CC----C---ACTCCGAATACTA--------------------AAATAAA----AAGAAT-C-------C-TT-CTCCC-ATTTGGTATTAAA--GCCACCCAC-C----AAAAAAACCTCACCCACCAAACATATGAACAAAGAGATACAAAATATTCAATACAACAAC--------
droGri2	scaffold_15074:2653282-2653451 +	LASTZ	5	TG-----------------------------------TCGTACGACT----AATG-AAATGCATCTAGT-TTTCGGGTGAGGTTT--TAGATGCGT--T--------------------TCCCCCA-------GAAAATAA--------------------------A----AC--AC---------------TCCT-TTTTGGTATTTAA--ACTACA-AAAAAAAAAAAAAAACCTCACCCACCAAATATATGAACAAAGAGATAAAAT-A-TTCAATAAACCAACAAACCCG-

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	TTT--GAAA--A-TCC-------------CTTCCTTTTCGTACGTAC----A--A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTTCCTA-------A-CAATTA-----------------------------------AA---------------CCCTATGTCGGTATTACG--AATACC-AT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-CAAC------G-
droSim1	TTT--CAAA--AATCC-------------CTTCCTTTTCGTACGTAC----A--A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTCCCTA-------A-AAATAA-----------------------------------GA---------------CCCTATGTCGGTATTTCG--AATACC-AT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-------------
droSec1	TTT--CAAA--AATCC-------------CTTCCTTTTCGTACGTAC----A--A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTCCCTA-------A-CAATTA-----------------------------------GA---------------CCCTATGTCGGTATTTCG--AATACC-AT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-------------
droYak2	TTA--AAAA--AATTCA------------TTTACTTTACGTGCGTAC----A--AAAAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTTCCTA-------A-CAACTA-----------------------------------GT---------------CCCTATGTTGGTACTACG--AATACC-AAAT----CAAAAAACCTCACCCACCAAAAGTATGAACAGAGAGATAAAAA-T-TTCAATATAAAAAC------A-
droEre2	TAT-----------------------------------TGTACGTAAGCATT--A-TTAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--CG-TCTCTTAAGT-------TTTCCATA-------A-CAATTG-----------------------------------GT---------------CCCTATGTTGGTATTACA--AATACC-ATAC----CAAAAAACCTCACCCACCAAATGTATGAACAGAGAGATAAAAA-T-TTCAATAAAAAAATGTTGTCGA
droEug1	TCC--TAAAAAGCTTCAAACCCCTTTTCTAATCCCTTTCGTACGAAA-------A-AAAGGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTTTTA-GTTT----C-GCGCCTT-------T-TTATAA-----------------------------------AC---------------CCCTTTGTCGGTATTGCA--AATACC-AT------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGATACAAA-T-TTCAATCAATTAAC------T-
droBia1	CTT--AAGA--ACTTCACACCC--TTTCACGTCCTTTTCGTACGAAT----A--AATAAAGCGTCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTACCT-TTTTAC-ATCCCTT-------T-ACATGA-----------------------------------AT-C-------------CCCCATCTTGGTATTGCA--AATACC-A-------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGAA-AAAA-T-TTCAATAAG-TACT------G-
droTak1	ACT--AAAA--ACTTCAAACCC--TTTCACAT-ATTTTCGTACGAAC----A----AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCCCTTA----------------------------CATGA-----------------------------------AT---------------TCCTATATCGGTATTGAA--AATGCC-AC------CTAAAAACCTCACCCACCAAATGTATATTCAAAGAGAATAAAA-T-TTCAATAAACTAAC------G-
droEle1	TAT--TAAA--ACTTCACTCCC-CTTTCACATTCTTATCGTTCGAAC----G--AATTCAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTA--TG-TCTTTGTACC-------TTCTCCAA-------A-AAATGA-----------------------------------AT---------------CCCTACCTTGGTATTGCA--AATACC-CTA-----TAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATATAAA-T-TTCAATAAACTAAC------A-
droRho1	CAT--AAAA---CTTCTGGCCC-CATTTACTT-CTTATCGTACGACC----G--AAAACAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCCTTTTACA-------TTCTCCAA-------T-AAAAT------------------------------------AT---------------CCCTATTTCGGTATTTCA--AATACT-TT------AAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAA-T-TTCAATAAAGTAAA------A-
droFic1	CTT--CA----------GACCC-TTTTCATTTCCCTATCGTACGAA--------A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTCGACT-------TTACCCCT-------T-ATACTA-----------------------------------TC---------------CCCTG-TTTGGCATTCCA--AATGCC-AC------CTAAAAACCTCACCCACCAAATGTATGAACAAAGAGAAAAACA-T-TTCAATAAGGTATT------G-
droKik1	TCT--AAAA--GCTTCAAACCC-TTTTCCAAT-ACCATCGTACGAAC----A--TTAAAAGCATCAGAT-TTTCGGGTGAGGTTA--CTGATGCTCTTTG-TCTCTAAAAT----------------------------ATGTTTTTTTTTTCTAAAAAAAAAATAAA---------------------------------AGGAA-AACA--TACACC-ACCT---TAAAATAACCTCACCCACCAAATGTATGAACAAAGAGAACAAAA-T-TTCAATACA--AAC------C-
droAna3	TCT--C------------------------TACATTAATATTATCAT----G--G-AAAAGCATCAGTTTTTTCGGGTGAGGTTATACTGATGCTT--AG-TCATTTCAAT-------TGCCCAAA-------A-TAATTG-----------------------------------AA---------------TTTT-AATTGGTATTTTT-CAATACC-CA------AGACTAACCTCACCCACCAAATATATGAACAAAGAGATATAAA-T-TTCAATAAA-------------
droBip1	TTTCTTATA--A-TTA-------------CAATAATTTTA---TAAT----A--G-ATAAGCATCAGTTTTTTCGGGTGAGGTCAA-CTGTTGCGA--AA-TCATTTCAAT-------TGCCCAAA--A----A-CAATTG-----------------------------------AA---------------TTTT-AATTGGTATTTTT-CAATGCC-CA------AAACTAACCTCACCCACCAAATATATGAAAAAAGAGATACAAA-T-TTCAATAA--------------
dp4	CCC--------------------------CGTCAATATTGTAATTAA----A--ATAAAAGCATCCGAG-CTTCGGGTGAGGTTA--TGGATGCATTTTGATCTCTGCACT-------TATCTCCA-------A------------------------------------------AA--------------CCCC--CTTTTGTATGGAAA-CATACC-ACC-----CAAATAACCTCACCCACCAAAT-TATGAACAAAGAGAAAAAAA-T-TTCAATAAA-------------
droPer1	CCC--------------------------CGTCAATATTGTAATTAA----A--ATAAAAGCATCCGAG-CTTCGGGTGAGGTTA--TGGATGCATTTTGATCTCTGCACT-------TATCTCCA-------A------------------------------------------AA--------------CCCC--TTTTTGTATGGAAA-CATACC-ACC-----CAAATAACCTCACCCACCAAAT-TATGAACAAAGAGAAAAAAA-T-TTCAATAAACACAAAACCACG-
droWil1	TAA--A--------------------------TCTTACTGTTATCC--------A-AAAATCATCACGG-TTTCGGGTGAGGTTA--GTGATGACT--TT-TCCTTT--------------TTCAAACA-------ACTAA-----------------------------------AATTTTAATTCCAAAAACCC--TTTCGGTATAGAC--AATACC-AA------AAAAAAACCTCACCCACCAAATATATGAACAAAGAGAAACAAA-TTTTCA------------------
droVir3	CTT--AA----------------------------TGTCGTACGACT----TATG-AGAAGCATCTAGT--TTCGGGTGAGGTTTT-ATGATGCAATTCTCGCTCT--------------ATCCC---ATCTTGAACATACGT--------TCCAAAATAAATACATAATAAAAAAAT-C-------------CCCTGCTTTGGTATTTAA--GCTACC-AACC---AAAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAAATTTTCAATACACC-AT------G-
droMoj3	CCT--C-----------------------CTCCCAAGTTGTACAGCT----TGTG-AGATGCATCAGAT-TTTCGGGTGAGGTTTT-ATGATGCAGTAC--TCCAT---GT-------CC----C---ACTCCGAATACTA--------------------AAATAAA----AAGAAT-C-------C-TT-CTCCC-ATTTGGTATTAAA--GCCACCCAC-C----AAAAAAACCTCACCCACCAAACATATGAACAAAGAGATACAAAATATTCAATACAACAAC--------
droGri2	TG-----------------------------------TCGTACGACT----AATG-AAATGCATCTAGT-TTTCGGGTGAGGTTT--TAGATGCGT--T--------------------TCCCCCA-------GAAAATAA--------------------------A----AC--AC---------------TCCT-TTTTGGTATTTAA--ACTACA-AAAAAAAAAAAAAAACCTCACCCACCAAATATATGAACAAAGAGATAAAAT-A-TTCAATAAACCAACAAACCCG-

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

TTT--CAAA--AATCC-------------CTTCCTTTTCGTACGTAC----A--A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTCCCTA-------A-AAATAA-----------------------------------GA---------------CCCTATGTCGGTATTTCG--AATACC-AT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-------------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................TCGGGTGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	21	1	63.00	0.00	47.00	12.00	4.00
.......................................................................TTCGGGTGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	22	1	50.00	0.00	34.00	11.00	5.00
.........................................................................................................................................................................................................................CC-AT------CAAAAAACCTCACCCACC..................................................	22	1	19.00	0.00	13.00	2.00	4.00
.......................................................................TTCGGGTGAGGTTT--CTGATG...........................................................................................................................................................................................................	20	1	17.00	0.00	14.00	1.00	2.00
........................................................................TCGGGTGAGGTTT--CTGATGCTT--......................................................................................................................................................................................................	22	1	13.00	0.00	7.00	4.00	2.00
.......................................................................TTCGGGTGAGGTTT--CTGATGCC.........................................................................................................................................................................................................	22	1	8.00	0.00	7.00	0.00	1.00
........................................................................TCGGGTGAGGTTT--CTGATGCC.........................................................................................................................................................................................................	21	1	7.00	0.00	5.00	2.00	0.00
........................................................................TCGGGTGAGGTTT--CTGATGCG.........................................................................................................................................................................................................	21	1	4.00	0.00	2.00	0.00	2.00
........................................................................TCGGGTGAGGTTT--CTGATGCTT--TG-TC.................................................................................................................................................................................................	26	1	4.00	0.00	4.00	0.00	0.00
.......................................................................TTCGGGTGAGGTTT--CTGATGC..........................................................................................................................................................................................................	21	1	4.00	0.00	4.00	0.00	0.00
.........................................................................CGGGTGAGGTTT--CTGATGCTT--TG-TCT................................................................................................................................................................................................	26	1	3.00	0.00	2.00	1.00	0.00
.........................................................AAAGCATCAGGT-TTTCGGGT..........................................................................................................................................................................................................................	20	1	3.00	0.00	2.00	1.00	0.00
.........................................................................................................................................................................................................................CC-AT------CAAAAAACCTCACCCAC...................................................	21	1	3.00	0.00	2.00	1.00	0.00
.......................................................................TTCGGGTGAGTTTT--CTGATGCT.........................................................................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
.............................................................................................................................A-------A-AAATAA-----------------------------------GA---------------CCCTATGTCGGT...........................................................................................	22	1	2.00	2.00	0.00	0.00	0.00
.........................................................................CGGGTGAGGTTT--CTGATGCTT--......................................................................................................................................................................................................	21	1	2.00	0.00	2.00	0.00	0.00
.............................................AC----A--A-AAAAGCATCAGGT-TTTCGGGT..........................................................................................................................................................................................................................	25	1	2.00	0.00	2.00	0.00	0.00
.......................................................................TTCGGGTGAGGTTT--CTGAT............................................................................................................................................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
.......................................................................................................................................AAATAA-----------------------------------GA---------------CCCTATGTCGGT...........................................................................................	20	1	2.00	0.00	0.00	0.00	2.00
........................................................................TCGGGTGAGGTTT--CTGATGC..........................................................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
......................................................................TTTCGGGTGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	23	1	2.00	0.00	0.00	0.00	2.00
..................................................................GGT-TTTCGGGTGAGGTTT--CTGATGC..........................................................................................................................................................................................................	25	1	2.00	0.00	1.00	0.00	1.00
........................................................................TCGGGGGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	21	1	2.00	0.00	1.00	1.00	0.00
........................................................................TCGGGTGAGGTTT--CTGATGCTT--TG-T..................................................................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
.........................................................................CGGGTGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..........................................................AAGCATCAGGT-TTTCGGGG..........................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.......................................................................TTCGGGAGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................TTCCCTA-------A-AAATAA-----------------------------------GA---------------CCCTATGTCGGT...........................................................................................	28	1	1.00	0.00	0.00	0.00	1.00
.......................................................................TTCGGGGGAGGTTT--CTGATT...........................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.......................................................................TTCGGGTGAGGTTT--CTGATGCTT--TG-TC.................................................................................................................................................................................................	27	1	1.00	0.00	1.00	0.00	0.00
..............................................................ATCAGGT-TTTCGGGTGAGGTTT--CTGA.............................................................................................................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
.......................................................................TTCGGGGGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................................................T-TTTCGGGTGAGGTTT--CTGATGCC.........................................................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.......................................................................TTCGGGTAAGGTTT--CTGATGCT.........................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.............................CTTCCTTTTCGTACGTAC----A--A-AAAAG...........................................................................................................................................................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00
........................................................................TCGGGTGAGGTTT--CTGATGG..........................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
......................................................A-AAAAGCATCAGGT-TTTCGGGTGA........................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................................CCCTATGTCGGTATTTCG--AAT................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................................................................GT-TTTCGGGTGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................TTTCG--AATACC-AT------CAAAAAACCTC.........................................................	24	1	1.00	0.00	1.00	0.00	0.00
........A--AATCC-------------CTTCCTTTTCGTACGTAC----.....................................................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
...............C-------------CTTCCTTTTCGTACGTAC----.....................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................CTATGTCGGTATTTCG--AATACC-AT------C...................................................................	25	1	1.00	0.00	0.00	0.00	1.00
..................................................................GGT-TTTCGGGTGAGGTTT--CTGA.............................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..........................................................AAGCATCAGGT-TTTCGGGTGA........................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................CGGGTGAGGTTT--CTGATGCTT--T.....................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................................................TTCGGGTGAGGTTT--CTGATGCTT--......................................................................................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.......................................................................TTCGGGTGAGGTTT--CTGATGCTT--TG-T..................................................................................................................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................C-AT------CAAAAAACCTCACCCACCA.................................................	22	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................................................CCCTATGTCGGTATTTCG--AATACC-............................................................................	24	1	1.00	0.00	0.00	0.00	1.00
.................................................................................GTTT--CTGATGCTT--TG-TCTCTTAAGT-------T.................................................................................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................GTCGGTATTTCG--AATACC-............................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................TTCGGGTGAGGTTT--CTGATGCG.........................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
........................................................................TCGGGTGAGGTTT--CTGATGCTT--TG-TCTC...............................................................................................................................................................................................	28	1	1.00	0.00	0.00	1.00	0.00

droSec1

TTT--CAAA--AATCC-------------CTTCCTTTTCGTACGTAC----A--A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTCCCTA-------A-CAATTA-----------------------------------GA---------------CCCTATGTCGGTATTTCG--AATACC-AT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................................TCGGGTGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	21	1	4.00	2.00	0.00	2.00
.......................................................................TTCGGGTGAGGTTT--CTGATGC..........................................................................................................................................................................................................	21	1	3.00	3.00	0.00	0.00
........................................................................TCGGGTGAGGTTT--CTGATGC..........................................................................................................................................................................................................	20	1	2.00	0.00	0.00	2.00
.......................................................................TTCGGGTGAGGTTT--CTGATGCT.........................................................................................................................................................................................................	22	1	2.00	1.00	0.00	1.00
.........................................................AAAGCATCAGGT-TTTCGGGT..........................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00
.......................................................................TTCGGGTGAGGTTT--CTGATGCTT--TG-T..................................................................................................................................................................................................	26	1	1.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................C-AT------CAAAAAACCTCACCCACCA.................................................	22	1	1.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................................................GACCAGAGAGACAATAA-T-......................	18	1	1.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................C-AT------CAAAAAACCTCACCCACC..................................................	21	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................................................CCTATGTCGGTATTTCG--AA.................................................................................	19	1	1.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................CC-AT------CAAAAAACCTCACCCACC..................................................	22	1	1.00	0.00	0.00	1.00
........................................................................TAGGGTGAGGTTT--CTGATGCTT--......................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................................ATGACCAGAGAGATAAAAA-T-TTCAATA...............	27	1	1.00	0.00	0.00	1.00
.........................................................................................................................................................................................................................CC-AT------CAAAAAACCTCACCCACCA.................................................	23	1	1.00	0.00	0.00	1.00
.........................................................................................................................................................................................................................CC-AT------CAAAAAACCTCACCCAC...................................................	21	1	1.00	0.00	0.00	1.00
..........................................................AAGCATCAGGT-TTTAGGGTGAGG......................................................................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00
.......................................................................................................................................................................................................................................................AATGTATGACCAGAGAGATAAAA..........................	23	1	1.00	1.00	0.00	0.00
..............................................................ATCAGGT-TTTCGGGTGAGG......................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
........................................................................................................................................AATTA-----------------------------------GA---------------CCCTATGTCGGT...........................................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

TTA--AAAA--AATTCA------------TTTACTTTACGTGCGTAC----A--AAAAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTAAGT-------TTTTCCTA-------A-CAACTA-----------------------------------GT---------------CCCTATGTTGGTACTACG--AATACC-AAAT----CAAAAAACCTCACCCACCAAAAGTATGAACAGAGAGATAAAAA-T-TTCAATATAAAAAC------A-	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................................................TCGGGTGAGGTTT--CTGATGCTT--......................................................................................................................................................................................................	22	2	2.50	0.00	0.00	0.00	0.00	2.50
..........................................................................................................................................................................................................................C-AAAT----CAAAAAACCTCACCCAC...................................................	22	2	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................................................................C-AAAT----CAAAAAACCTCACCCACC..................................................	23	2	1.00	0.00	0.00	0.50	0.50	0.00
........................................................................TCGGGTGAGGTTT--CTGATGCTT--TG-...................................................................................................................................................................................................	24	2	0.50	0.00	0.00	0.50	0.00	0.00
................................................................................GGTTT--CTGATGCTT--TG-TCTCTTAAGT-------..................................................................................................................................................................................	26	2	0.50	0.00	0.00	0.50	0.00	0.00
..........................................................................................................................................................................................................................C-AAAT----CAAAAAACCTCGCCCA....................................................	21	2	0.50	0.00	0.00	0.00	0.00	0.50
..........................................................................................................................................................................................................................C-AAAT----CAAAAAACCTCACCCACT..................................................	23	2	0.50	0.00	0.00	0.00	0.00	0.50
.............................................................CATCAGGT-TTTCGGGTGAG.......................................................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
.............................................................CATCAGGT-TTTCGGGTGAGG......................................................................................................................................................................................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00
........................................................................TCGGGTGGGGTTT--CTGATGCTT--C.....................................................................................................................................................................................................	23	2	0.50	0.00	0.00	0.00	0.50	0.00
.........................................................................CGGGTGAGGTTT--CTGATGCTT--TG-A..................................................................................................................................................................................................	24	2	0.50	0.00	0.00	0.00	0.00	0.50
........................................................................TCGGGTGAGGTTT--CTGATGCTT--TG-TC.................................................................................................................................................................................................	26	2	0.50	0.00	0.00	0.00	0.00	0.50
........................................................................TCGGGTGAGGTTT--CTGATGCTT--T.....................................................................................................................................................................................................	23	2	0.50	0.00	0.00	0.00	0.00	0.50
.............................................................CATCAGGT-TTTAGGGTGAGGTTT--CTGA.............................................................................................................................................................................................................	27	2	0.50	0.00	0.00	0.50	0.00	0.00

droEre2

TAT-----------------------------------TGTACGTAAGCATT--A-TTAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--CG-TCTCTTAAGT-------TTTCCATA-------A-CAATTG-----------------------------------GT---------------CCCTATGTTGGTATTACA--AATACC-ATAC----CAAAAAACCTCACCCACCAAATGTATGAACAGAGAGATAAAAA-T-TTCAATAAAAAAATGTTGTCGA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................................................T--A-TTAAGCATCAGGT-TTTCGGG...........................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.............................................................CATCAGGx-TTTCGGGTGAG.......................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.............................................................CATCAGGT-TTTCGGGTGAG.......................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................................................................ATACC-ATAC----CAAAAAACCTCACCCACC..................................................	27	1	1.00	0.00	0.00	0.00	1.00
........................................................................TCGGGTGAGGTTT--CTGATGCTT--CG-...................................................................................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
........................................................................................TGATGCTT--CG-TCTCTTACG..........................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................TATGAACAGAGAGATAAA...........................	18	1	1.00	0.00	0.00	0.00	1.00
..............................................................ATCAGGT-TTTCTGGTGAG.......................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droEug1

TCC--TAAAAAGCTTCAAACCCCTTTTCTAATCCCTTTCGTACGAAA-------A-AAAGGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTTTTA-GTTT----C-GCGCCTT-------T-TTATAA-----------------------------------AC---------------CCCTTTGTCGGTATTGCA--AATACC-AT------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGATACAAA-T-TTCAATCAATTAAC------T-

Size

Hit Count

Total Norm

droBia1

CTT--AAGA--ACTTCACACCC--TTTCACGTCCTTTTCGTACGAAT----A--AATAAAGCGTCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTTACCT-TTTTAC-ATCCCTT-------T-ACATGA-----------------------------------AT-C-------------CCCCATCTTGGTATTGCA--AATACC-A-------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGAA-AAAA-T-TTCAATAAG-TACT------G-

Size

Hit Count

Total Norm

droTak1

ACT--AAAA--ACTTCAAACCC--TTTCACAT-ATTTTCGTACGAAC----A----AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCCCTTA----------------------------CATGA-----------------------------------AT---------------TCCTATATCGGTATTGAA--AATGCC-AC------CTAAAAACCTCACCCACCAAATGTATATTCAAAGAGAATAAAA-T-TTCAATAAACTAAC------G-

Size

Hit Count

Total Norm

droEle1

TAT--TAAA--ACTTCACTCCC-CTTTCACATTCTTATCGTTCGAAC----G--AATTCAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTA--TG-TCTTTGTACC-------TTCTCCAA-------A-AAATGA-----------------------------------AT---------------CCCTACCTTGGTATTGCA--AATACC-CTA-----TAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATATAAA-T-TTCAATAAACTAAC------A-

Size

Hit Count

Total Norm

droRho1

CAT--AAAA---CTTCTGGCCC-CATTTACTT-CTTATCGTACGACC----G--AAAACAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCCTTTTACA-------TTCTCCAA-------T-AAAAT------------------------------------AT---------------CCCTATTTCGGTATTTCA--AATACT-TT------AAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAA-T-TTCAATAAAGTAAA------A-

Size

Hit Count

Total Norm

droFic1

CTT--CA----------GACCC-TTTTCATTTCCCTATCGTACGAA--------A-AAAAGCATCAGGT-TTTCGGGTGAGGTTT--CTGATGCTT--TG-TCTCTCGACT-------TTACCCCT-------T-ATACTA-----------------------------------TC---------------CCCTG-TTTGGCATTCCA--AATGCC-AC------CTAAAAACCTCACCCACCAAATGTATGAACAAAGAGAAAAACA-T-TTCAATAAGGTATT------G-

Size

Hit Count

Total Norm

droKik1

TCT--AAAA--GCTTCAAACCC-TTTTCCAAT-ACCATCGTACGAAC----A--TTAAAAGCATCAGAT-TTTCGGGTGAGGTTA--CTGATGCTCTTTG-TCTCTAAAAT----------------------------ATGTTTTTTTTTTCTAAAAAAAAAATAAA---------------------------------AGGAA-AACA--TACACC-ACCT---TAAAATAACCTCACCCACCAAATGTATGAACAAAGAGAACAAAA-T-TTCAATACA--AAC------C-

Size

Hit Count

Total Norm

droAna3

TCT--C------------------------TACATTAATATTATCAT----G--G-AAAAGCATCAGTTTTTTCGGGTGAGGTTATACTGATGCTT--AG-TCATTTCAAT-------TGCCCAAA-------A-TAATTG-----------------------------------AA---------------TTTT-AATTGGTATTTTT-CAATACC-CA------AGACTAACCTCACCCACCAAATATATGAACAAAGAGATATAAA-T-TTCAATAAA-------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................................................TCGGGTGAGGTTATACTGATGC..........................................................................................................................................................................................................	22	1	8.00	2.00	5.00	1.00	0.00
.........................................................................................................................................................................................................................CC-CA------AGACTAACCTCACCCACC..................................................	22	1	8.00	0.00	7.00	0.00	1.00
........................................................................TCGGGTGAGGTTATACTGATGCT.........................................................................................................................................................................................................	23	1	5.00	1.00	4.00	0.00	0.00
..........................................................................................................................................................................................................................C-CA------AGACTAACCTCACCCACCA.................................................	22	1	5.00	0.00	3.00	1.00	1.00
........................................................................TCGGGTGAGGTTATACTGATG...........................................................................................................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
.........................................................................................................................................................................................................................CC-CA------AGACTAACCTCACCCACCA.................................................	23	1	3.00	0.00	1.00	1.00	1.00
.........................................................................................................................................................................................................................CC-CA------AGACTAACCTCACCCAC...................................................	21	1	3.00	1.00	2.00	0.00	0.00
............................................................................................................................................................................................................................CA------AGACTAACCTCACCCACC..................................................	20	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................................................................ACC-CA------AGGCTAACCTCACCCACCA.................................................	24	1	1.00	0.00	0.00	0.00	1.00
..................................................................GTTTTTTCGGGTGAGGTTATACTGA.............................................................................................................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
.........................................................................CGGGTGAGGTTATACTGATTCT.........................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.........................................................................CGGGTGAGGTTATACTGATGCT.........................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................GAACAAAxAGATATAAA-A-T.....................	18	1	1.00	0.00	0.00	0.00	1.00
..............................................................ATCAGTTTTTTCGGGTGAGGTTATACT...............................................................................................................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................................CA------AGACTGACCTCACCCACC..................................................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................................A------AGACTAACCTCACCCACCA.................................................	20	1	1.00	0.00	1.00	0.00	0.00
............................................................GCATCAGTTTTTTCGGGTGAGGT.....................................................................................................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................................................................................................................................................C-CA------AGACTAACCTCACCCACT..................................................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................CA------AGACTAACCTCACCCACCA.................................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................................CGGGTGAGGTTATACTGATGAT.........................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................ATTTTT-CAATACC-CA------AGACTAACCTCACC......................................................	29	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................................................TTTT-CAATACC-CA------AGACTAACCTCACC......................................................	27	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................................TT-AATTGGTATTTTT-CAATAC..............................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................................................CC-CA------AGACTAACATCACCCACCA.................................................	23	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................CC-CA------AGACTAACCTCATCCACC..................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................AATCTTATCxT----G--G-AAAAGC..........................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
......................................TATTATCAT----G--G-AAAAGCATC.......................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
......................................................................TTTAGGGTGAGGTTACAC................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....................................AATATTATCxT----G--G-TAAAGC..........................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................................TTTCGGGTGAGGTTATACTG..............................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
........................................................................TCGGGTGAGGTTATACTTATGCC.........................................................................................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................CC-CA------AAACTAACCTCACCCAGC..................................................	22	1	1.00	0.00	0.00	1.00	0.00
...................................TAATATTATCxT----G--G-TAAAGC..........................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
..........................................ATCGT----G--G-AAAAGCATCGGTTT..................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................AT----G--G-AAAAGCATCAGTTTTTT...............................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................TGTT-AATTGGTATTTTT-TA..................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................................................TCGGGAGCGGTTATACTGATG...........................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00

droBip1

TTTCTTATA--A-TTA-------------CAATAATTTTA---TAAT----A--G-ATAAGCATCAGTTTTTTCGGGTGAGGTCAA-CTGTTGCGA--AA-TCATTTCAAT-------TGCCCAAA--A----A-CAATTG-----------------------------------AA---------------TTTT-AATTGGTATTTTT-CAATGCC-CA------AAACTAACCTCACCCACCAAATATATGAAAAAAGAGATACAAA-T-TTCAATAA--------------

Size

Hit Count

Total Norm

dp4

CCC--------------------------CGTCAATATTGTAATTAA----A--ATAAAAGCATCCGAG-CTTCGGGTGAGGTTA--TGGATGCATTTTGATCTCTGCACT-------TATCTCCA-------A------------------------------------------AA--------------CCCC--CTTTTGTATGGAAA-CATACC-ACC-----CAAATAACCTCACCCACCAAAT-TATGAACAAAGAGAAAAAAA-T-TTCAATAAA-------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..................................................................................................TGATCTCTGCACT-------TATCTC............................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.....................................TTGTAATTAA----A--ATAAAAGG..........................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droPer1

CCC--------------------------CGTCAATATTGTAATTAA----A--ATAAAAGCATCCGAG-CTTCGGGTGAGGTTA--TGGATGCATTTTGATCTCTGCACT-------TATCTCCA-------A------------------------------------------AA--------------CCCC--TTTTTGTATGGAAA-CATACC-ACC-----CAAATAACCTCACCCACCAAAT-TATGAACAAAGAGAAAAAAA-T-TTCAATAAACACAAAACCACG-	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................................................................................TCTGCACT-------TATCTCCA-------A------------------------------------------AA--------------CCCC--TTT...............................................................................................	26	1	3.00	0.00	0.00	0.00	0.00	3.00
....................................................................................A--TGGATGCATTTTGATCT................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................................................CGGGTGAGGTTA--TGGATGCA.........................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................................................CGGGTGAGGTTA--TGGATGC..........................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...................................................A--ATAAAAGCATCCGAG-CTTCGGGT..........................................................................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

TAA--A--------------------------TCTTACTGTTATCC--------A-AAAATCATCACGG-TTTCGGGTGAGGTTA--GTGATGACT--TT-TCCTTT--------------TTCAAACA-------ACTAA-----------------------------------AATTTTAATTCCAAAAACCC--TTTCGGTATAGAC--AATACC-AA------AAAAAAACCTCACCCACCAAATATATGAACAAAGAGAAACAAA-TTTTCA------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...............................................................TCACGG-TTTCGGGTGAGGTTA--GTGA.............................................................................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
.........................................................................CGGGTGAGGTTA--GTGATGACT--TT-...................................................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................C-AT------CAAAAAACCTCACCCAC...................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................................................................................ATATATGAAAAAAAAGAA..............................	18	10	0.10	0.00	0.10	0.00	0.00
........................................................................TCGGGTGAGGTTA--GTGATGACT--TT-T..................................................................................................................................................................................................	25	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................................................................ACC-AA------AAAAAAACCTCACCCA....................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................................................................................................................AACAAAGAGCAACAAA-GT......................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

CTT--AA----------------------------TGTCGTACGACT----TATG-AGAAGCATCTAGT--TTCGGGTGAGGTTTT-ATGATGCAATTCTCGCTCT--------------ATCCC---ATCTTGAACATACGT--------TCCAAAATAAATACATAATAAAAAAAT-C-------------CCCTGCTTTGGTATTTAA--GCTACC-AACC---AAAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAAATTTTCAATACACC-AT------G-	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.....AA----------------------------TGTCGTACGACT----TATG-AGAAGC..........................................................................................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
..T--AA----------------------------TGTCGTACGACT----TATG-AGAAGCATCT......................................................................................................................................................................................................................................	29	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................GCATCTAGT--TTCGGGTGAGGTTTT-ATG..............................................................................................................................................................................................................	27	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................................ATGAACAAAGAGATAAAAAAT.......................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................GCATCTAGT--TTCGGGTGA........................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................ATCTAGT--TTCGGGTGAGGTTTT-ATGATGC..........................................................................................................................................................................................................	29	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................CTAGT--TTCGGGTGAGGTTTT-ATGATGC..........................................................................................................................................................................................................	27	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................................................................ATCCC---ATCTTGAACATACGT--------T................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................ATCTAGT--TTCGGGTGAGGTTTT-ATGAT............................................................................................................................................................................................................	27	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................GCC---ATGTTGAACATACGT--------.................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................TCGGGTGAGGTTTT-ATGATGC..........................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................TATGAACAAAGAGATAAAAAAT.......................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................TACGACT----TATG-AGAAGCATCTAGT--.................................................................................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................ATCTAGT--TTCGGGTTAGG......................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................ATCTAGT--TTCGGGTGAGGT.....................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................T--TTCGGGTGAGGTTTT-ATGATG...........................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

CCT--C-----------------------CTCCCAAGTTGTACAGCT----TGTG-AGATGCATCAGAT-TTTCGGGTGAGGTTTT-ATGATGCAGTAC--TCCAT---GT-------CC----C---ACTCCGAATACTA--------------------AAATAAA----AAGAAT-C-------C-TT-CTCCC-ATTTGGTATTAAA--GCCACCCAC-C----AAAAAAACCTCACCCACCAAACATATGAACAAAGAGATACAAAATATTCAATACAACAAC--------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
........................................................................TCGGGTGAGGTTTT-ATGATGC..........................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
........................................................................TCGGGTGATGTTTT-ATGATG...........................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..........................................................ATGCATCAGAT-TTTCGGGT..........................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droGri2

TG-----------------------------------TCGTACGACT----AATG-AAATGCATCTAGT-TTTCGGGTGAGGTTT--TAGATGCGT--T--------------------TCCCCCA-------GAAAATAA--------------------------A----AC--AC---------------TCCT-TTTTGGTATTTAA--ACTACA-AAAAAAAAAAAAAAACCTCACCCACCAAATATATGAACAAAGAGATAAAAT-A-TTCAATAAACCAACAAACCCG-	Size	Hit Count	Total Norm	V109 Male body
......................................CGTACGACT----AATG-AAATGCATC.......................................................................................................................................................................................................................................	22	1	1.00	1.00
....................................................................................T--TAGATGCGT--T--------------------TCCCCCA-------GAA................................................................................................................................................................	21	1	1.00	1.00

Generated: 04/20/2012 at 05:18:10 EDT

dme-mir-4951

chr3R:17142437-17142587 +

Known_mirbase

intergenic

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup