dme-mir-4968- Best orthologs

dme-mir-4968	chr3L:11545638-11545793 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 11545724-11545745
   star strand at position 11545684-11545705
   mutations
   read mismatches

Notes: "LASTZ reported many potential orthologs, most of which contain simple repeats hence the reason why many reads map to the reported orthologs."

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3L:11545623-11545808 -		1	AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAACAG-CAGCA---GC--------------------------AGC---AGAAG----------------------------CAACAGCAACT---------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droSim1	chr3L:10929570-10929746 -	LASTZ	4	AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGAA---GC--------------------------A----------------------------------------ACAGCAACT---------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droSec1	super_0:3745423-3745605 -	LASTZ	4	AA--ACTGCATTCGAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGCA---GC--------------------------AGA------AG----------------------------CAACAGCAACT---------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droYak2	chr3L:11579958-11580167 -	LASTZ	5	AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGAA---GC----AGCAG----------------------CAGCAGC------AGTAGAAATAGCAGCAGTAG-CAACAGCAACT---------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droEre2	scaffold_4784:11545792-11545968 -	LASTZ	5	A---ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGAA---GC--------------------------A----------------------------------------ACAGCAACTG--------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droEug1	scf7180000409711:3426755-3426922 -	LASTZ	5	AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AT---TGCTGGC---G------------------GGTTTA-TTGTTGC----TTTTGCAGTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGTAG-CAGCA---GC--------------------------AGC---AGAGG--------------------------------------------------------------AGCAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droBia1	scf7180000302193:27629-27798 +	LASTZ	5	AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----AGCG---CT---CGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCACTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGCA---GC--------------------------AGC--------------------------------------------------------A------ACTGCAGAGGAGCA---------ATAGTAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droTak1	scf7180000415349:71172-71362 +	LASTZ	5	AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AT---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCATTGAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGCA---AC--------------------------AGCAACTGCAGA------AG-------------------CAACAACAGC----------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droEle1	scf7180000490564:2496048-2496253 -	LASTZ	5	AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AT---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGAA---GC----AGCAG----------------------CAGCAGCAAC---------AACAGCAG-------CAACAACAGC----------AGCAGCAACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droRho1	scf7180000779504:19353-19519 +	LASTZ	5	AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AT---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAACA---GC--------------------------A-----------------------------------------------------------------ACTGCAGAGGAGCA---------ATACCAGC-TGAGAGTTCAGTTGTGAAAC-CGGCG
droFic1	scf7180000454113:3152541-3152755 +	LASTZ	5	AA--GCTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---ATTGCTGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGTAG-CAGCAGAAGC----AGCAG----------------------CAGCAGC------AACAACAACAACAGCAACAA-CAACAGCAGC----------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droKik1	scf7180000302391:1285443-1285648 +	LASTZ	5	AAAAACGGCATTCAAGTTTTT-------CCTCGGCAACAACTA------CTAAC---C--ATTGC-----AGTG----T---TGTTGGC---G------------------GGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGAAG-AAGCA---GC--------------------------AGC---AGCAGC----------------------------AAC----------------A------ACAGTAGAGGAGCAATAGCAGCAGCAGCAGC-TGAGAGTTCAGTTGTGAAAC-CGGCG
droAna3	scaffold_13337:5830221-5830437 -	LASTZ	5	AA--ACTGCATTCAAGTTTTGTTTTTGT---T---------------ATTTTTT---CTTT--GC--TTCTGCAACTAT---TGCTGGTTAGC------------------TGC-TAGTTGCTGC----TGCTGCTGCT-G-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGTAG-CAGTA---GC--------------------------AGTGGCAGAGGAGAC---------------AGA-------G---GAGCC--ACTGCAACA------ACTGCAACA---AA---------ACAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
droBip1	scf7180000396371:1156780-1156979 -	LASTZ	5	A---ACTGCATTCAAGTTTTTGTTGT-----T---------------TTTTTCTCGTCTT----CTCTTCTGCAACTAT---TGCTG-------------------------------------------------GTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGAAGGCAGTA---GCTAGTAGCAC----------------------TAGTACT------AGTACTAATACTAGTAGTAGGCAGTAG------------------------GCAGAAGAGG------------AGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG
dp4	chrXR_group6:10126891-10127089 +	LASTZ	0	AA--ACGGCATACAAGTTTTT-------CCTCGCCAAACACAAAGCGTTTTAGC---C--AGAGCTCTTCTGCAACTAT---TGCTGG-------------------------T-TG-TAGTTGT----AGTT-------G-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCGG-TGGCA---GC--------------------------GGTGGCAGCGGTGGC---------------AGC-------G---GTGGC------------------------------A------G--ACGGCAGCCCCCGAGTTCAGTTGCAAAAC-CGGCG
droPer1	super_4:4953737-4953917 +	LASTZ	0	TT--TC-GTTTTC--GTTTTC-------ATT------------------------------TCGC-----TGTA--------AACAAGC-----------------------GA-TT-TTGTTGC----TCTTTCTGCTCG-------TAATTGAG-ATAAATGCATTT---TAAATGCGCAAC--------------CGCAGCTGCAG-CAGCA---GC--------------------------AGC---AGAGGCAGC---AGTTG----------------CAACAGCAGCT---------A------GCTTCAAC----TG---------GTTGCAGT-TGCGTATGCAGATGCGATGCAAGGCG
droWil1	scaffold_180698:2057599-2057768 -	LASTZ	0	AC--ACTGCAGACAAGTTTTAAATGCCT-------------------TTTTTTT---C--GTAGC--------------------TCTC---TTGTTGTTGTTGTTGCTAA-GT----------C----TTCTGCAACTA--------TTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------A---------GCGGCAGC-TTCGAGTTCAGTTGCAAAAC-CGGCG
droVir3	scaffold_12855:885802-885977 -	LASTZ	0	AG--GATATGGGCGATTGTCT-------TATC----------------------------AGTG-------GTG---GT---GCCGGACCAGC------------------TGT-TA-GTGCCGT----TGCTGATGCCAG-------CGGCAACCTTTTGCTCGATCAT-CATCACCATCATCA---------TCAT--CAACAACAG-CAGCA---GC--------------------------AGC---AGCAGCAGCAGCAACAACAA-------------------------------------------CAACAGCAGCA---------ACAGCAGC-AGCTACTGCAG---------------
droMoj3	scaffold_6496:11355914-11356095 -	LASTZ	0	AA--ACGAAATGAAACTTTGT-------GCGC----------------------------ATAGG-------CAACCAA---CAGCGGC--------------------------GG-CAGCAGC----AGCAGCAGC-AG-------CAGCAGCAGCG-CCAGCATCGCTGAGAC-T-TTGACGC---------------G---------------------------TTGGCAAAAGAAGCAGCAGC---AGCAGC------------------------AG-CAACAGCAAC----------A------ACAGC--CGCAGCA---------GCAGCAGC-AGCGACGGCAGCAGCAGAAA-CGTCG
droGri2	scaffold_15110:4649694-4649883 +	LASTZ	0	CA--A----------TTTTCT-------CATC----------------------------AGTTT-----C-------T---TGCCGAT---G--------ATGAAGCAAATGT-CA-TCGCTGCAGAATGTTGCATTTCGCGCCAAGATG-GGTGAGCTGCTGCTGCA---------CACAATGCAACAATCACAAATGCAACAACAG-CAGCA---AC--------------------------AGC---AGCAGCAGC---AGCAAC----------------AACAACA----------------------GC--AACAACA---------ACAGGAGC-CGA---TGCAGCAGCA--A----CCG

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	AA--ACTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCCGCGAC---TGCTGGCGTGT---TA-TTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAACAGCAGCA---G---C-AG---CAGA--------------------------AGCAACAGCAACT-----------------------AACTGCAGAGGAGCA-------------ATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droSim1	AA--ACTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCCGCGAC---TGCTGGCGTGT---TA-TTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGAA---G---C-A--------------------------------------ACAGCAACT-----------------------AACTGCAGAGGAGCA-------------ATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droSec1	AA--ACTGCATTCGAGTTTTT---------------------CCTCAG-----------------AGCCGCGAC---TGCTGGCGTGT---TA-TTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGCA---G---C-AG---A-----------------------------AGCAACAGCAACT-----------------------AACTGCAGAGGAGCA-------------ATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droYak2	AA--ACTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCCGCGAC---TGCTGGCGTGT---TA-TTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGAA---G---C-AG---CAGCAGCAGCAGT--AGAAATAGCAGCAGTAGCAACAGCAACT-----------------------AACTGCAGAGGAGCA-------------ATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droEre2	A---ACTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCCGCGAC---TGCTGGCGTGT---TA-TTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGAA---G---C-A--------------------------------------ACAGCAACTG----------------------AACTGCAGAGGAGCA-------------ATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droEug1	AA--ACTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCCGCGAT---TGCTGGCGGGTT--TA-TTGTTGCTTTTGCAGTTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGTAGCAGCA---G---C-AG--------------------------------------------------------------------------CAGAGGAGCA----------GCAATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droBia1	AA--ACTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCAGCGCT---CGCTGGCGTGT---TA-TTGTTGCTGTTGCACTTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGCA---G---C-AG---C-----------------------------------------------------------------AACTGCAGAGGAGCA-------------ATAGTAGCTGAGAGTTCAGTTGCGAAACCGGCG
droTak1	AA--ACTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCCGCGAT---TGCTGGCGTGT---TA-TTGTTGCTGTTGCATTGAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGCA---A---C-AG---CA--------------------------------------ACTGCAGAAGCAACAAC------AGCAACTGCAGAGGAGCA-------------ATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droEle1	AA--ACTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCCGCGAT---TGCTGGCGTGT---TA-TTGTTGCTGTTGCAGTTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGAA---G---C-AG---CAGCAGCAGCAACAA-----CAGCAGCAA------------------------CAACAGCAGCAGCAACTGCAGAGGAGCA-------------ATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droRho1	AA--ACTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCCGCGAT---TGCTGGCGTGT---TA-TTGTTGCTGTTGCAGTTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAACA---G---C------------------------------------------------------------------------AACTGCAGAGGAGCA-------------ATACCAGCTGAGAGTTCAGTTGTGAAACCGGCG
droFic1	AA--GCTGCATTCAAGTTTTT---------------------CCTCAG-----------------AGCCGCGATTGCTGCTGGCGTGT---TA-TTGTTGCTGTTGCAGTTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGTAGCAGCAGAAG---C-AG---CAGCAGCAGCAAC--AACAACAACAGCAA------------------------CAACAACAGCAGCAACTGCAGAGGAGCA-------------ATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droKik1	AAAAACGGCATTCAAGTTTTT---------------------CCTCGGCAACAACTACTAACCATTGCAGTG-T---TGTTGGCGGGT---TA-TTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGAAGAAGCA---G---C-AG---C---AGCAGCAAC-----------------------------------------------------AACAGTAGAGGAGCAATAG-CA---GCAGCAGCAGCTGAGAGTTCAGTTGTGAAACCGGCG
droAna3	AA--ACTGCATTCAAGTTTTG-TTTTTGTTATTTTTTCTTTGCTTCT-------------------GCAACTAT---TGCTGGTTAGCTGCTAGTTGCTGCTGCTGCTGCT-GCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGTAGCAGTA---G---C-AG---TGGCAGAGGAGACAG-----A-------GGAGCCACTGCAAC------------------------AACTGCAACAA---A-------------ACAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droBip1	A---ACTGCATTCAAGTTTTTGTTGTTTTTTTCTCGTCTTCTCTTCT-------------------GCAACTAT---TGCTG--------------------------GTTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGAAG--GCA---GTAGCTAGTAGCACTAGTACTAGT--ACTAATACTAGTAG---------------------------------TAGGCAGTA----G---------GCAGAA-GAGGAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG

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

AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGAA---GC--------------------------A----------------------------------------ACAGCAACT---------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
............................................................................................G------------------TGT-TA-TTGTTGC----TGTGACA..........................................................................................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
........................................................................................................................................................................................GC---------------AGCAGCAG-CGGAA---GC--------------------------A----------------------------------------AC.................................................................................	20	137	0.01	0.01	0.00	0.00	0.00
....................................................................................................................A-TTGTTGC----TGTTGCAGCTAG-------CC............................................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................CAG-CAGTA---GC--------------------------A----------------------------------------ACAGCAGCT---------A------..........................................................	21	41	0.02	0.02	0.00	0.00	0.00

droSec1

AA--ACTGCATTCGAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGCA---GC--------------------------AGA------AG----------------------------CAACAGCAACT---------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...................................................................................................................................................................................................................AGCA---GC--------------------------GGA------AG----------------------------CAACAGCC.............................................................................	19	10	0.20	0.10	0.10	0.00
..........................................................................................................................................TAG-------CTGCCACGGTTTGTTGCTTCAC........................................................................................................................................................................................................	25	1	2.00	0.00	2.00	0.00
.............................................................................................................................................................................................................GCAG-CAGCA---GC--------------------------GGA------AG----------------------------CAACA................................................................................	21	113	0.02	0.02	0.00	0.00
...................................................................................................................................................................................................................AGCA---GC--------------------------GGA------AG----------------------------CAACAGCCA............................................................................	20	4	0.50	0.50	0.00	0.00
.................................................................................................................................................................................................................................................................................................ATCGACT---------A------ACTGCAGAGG................................................	18	1	1.00	0.00	1.00	0.00
.........................................................................................................................................................................................................AGCAGGAG-CAGGA---GC--------------------------AGA------...................................................................................................................	18	14	0.07	0.00	0.00	0.07
..........................................................................................................................................TAG-------CTGCCACGGTTTGTTGCT............................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
..........................................................................................................................................................................................................GCAGCAG-AAGCA---GG--------------------------AGA------AG----------------------------.....................................................................................	19	17	0.06	0.00	0.06	0.00
...............................................................................................................................................................................................................................................................................................ACAGCAACT---------G------ACTGGAGAG.................................................	19	1	1.00	0.00	1.00	0.00
.............................................................GAGC-----CGCG---TC---TGCTGGT---G------------------...................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CAGCA---GG--------------------------ACA------A..................................................................................................................	19	49	0.02	0.00	0.00	0.02
.............................................................................................................................................................................................................GCAG-CAGCA---GC--------------------------GGA------AG----------------------------CAACAGC..............................................................................	23	61	0.02	0.00	0.02	0.00
.............................................................................................................................................................................................................GCAG-CAGCT---GG--------------------------AGA------AG----------------------------CA...................................................................................	18	28	0.04	0.00	0.04	0.00
............................................................................................................................................................................................................AGCTG-CAGCA---GT--------------------------AGA------AG----------------------------C....................................................................................	18	20	0.05	0.00	0.05	0.00
.......................................................................................GC---G------------------TGT-TA-TTGTTGC----TGTTG............................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00
......TTCATTCGAGTTTTT-------CCTC----------------------------A.....................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00
.......................................................................................................................................................................................TGC---------------AGCAGCAG-CAGCA---GC--------------------------AGA------...................................................................................................................	21	26	0.04	0.00	0.04	0.00
...................................................................................................................................................................................................................................................................................................................................................CAGC-TTGGAGTTCAGTTGC...........	19	1	1.00	0.00	0.00	1.00
........................................................................................................................................................................................GC---------------AGCAGCAG-AAGCA---GG--------------------------AGA------...................................................................................................................	20	17	0.06	0.00	0.06	0.00
...........................................................................................................................................................................................................CAGAAG-CAGCA---CC--------------------------AGA------AG----------------------------CAACA................................................................................	23	5	0.20	0.00	0.00	0.20
.......................................................................................................................................................................................TGC---------------AGCAGCAA-CAGCA---GC--------------------------GGA------...................................................................................................................	21	23	0.04	0.04	0.00	0.00
...........................................................................................................................................................................................................CAGAAG-CAGCA---GC--------------------------AGA------AG----------------------------C....................................................................................	19	499	0.00	0.00	0.00	0.00
.........................................................................................................................................................................................................AGCACCAG-CACCA---GC--------------------------AGA------...................................................................................................................	18	38	0.03	0.00	0.03	0.00
..........................................................................................................................................TAG-------CTGCCACGGTTTGTTGCTT...........................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
..........................................................................................................................................TAG-------CTGCCACGGTTTGTTGCTTCA.........................................................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00
.........................................................................................................................................................................................................AGCAGAAG-CAGAA---GC--------------------------AGA------...................................................................................................................	18	16	0.06	0.00	0.06	0.00
.........................................................................................................................................................................................................AGCAGCAG-GAGCA---GC--------------------------AGA------AG----------------------------.....................................................................................	20	375	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................AGGAGCA---------AxAGCAGA-TGAG......................	18	2	0.50	0.00	0.00	0.50
......................................................................................................................................................................................................................A---GC--------------------------AAA------AG----------------------------CAACAGGAACT---------.................................................................	19	2	0.50	0.00	0.50	0.00
.........................................................................................................................................................................................................AGCAGAGG-CAGCA---GC--------------------------AGA------AG----------------------------.....................................................................................	20	19	0.05	0.00	0.00	0.05
....................................................................................................................A-TTGTTGC----TGTTGCTGCT.......................................................................................................................................................................................................................................	18	25	0.04	0.00	0.04	0.00
...............................................................................................................................................................................................................................................................................................................................................................................TCG	20	19	0.05	0.00	0.00	0.05
...............................................................................................................................................................................................................................................................................................................................................................................GCG	25	14	0.07	0.00	0.07	0.00

droYak2

AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGAA---GC----AGCAG----------------------CAGCAGC------AGTAGAAATAGCAGCAGTAG-CAACAGCAACT---------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................................................................................................................................................C---------------AGCAGCAG-CGGAA---GC----GGCAG----------------------.......................................................................................................................	21	47	0.15	0.00	0.00	0.15	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CGGAA---GC----GGCAG----------------------C......................................................................................................................	21	44	0.05	0.00	0.00	0.05	0.00	0.00
............................................................................................................................................................................................................AGTAC-CAGAA---GC----AGCAG----------------------CAG....................................................................................................................	20	37	0.05	0.00	0.00	0.05	0.00	0.00
.........................................................................................................................................................................................................AGCAGGAG-CAGAA---GC----AGA...............................................................................................................................................	18	28	0.04	0.00	0.00	0.00	0.04	0.00
...................................................................................................................................................................................................................AGAA---GC----AGCAT----------------------CAGCAGC------A.........................................................................................................	19	52	0.02	0.00	0.00	0.00	0.02	0.00
..........................................................................................................................................TAG-------CTGCCACGGTTTGTTGCT............................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................................AGAAGCAG-CGGAA---GC----AGCAG----------------------.......................................................................................................................	20	22	0.05	0.00	0.05	0.00	0.00	0.00
....................................................................................................................................................................................CAATGC---------------AGCAGCAG-CAGGA---GC----AGC...............................................................................................................................................	24	10	0.10	0.10	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................AGCAG-CAGAA---GC----AGGAG----------------------GAGC...................................................................................................................	21	25	0.04	0.00	0.00	0.04	0.00	0.00
...........................................................................................................................................................................................................CACCAG-CAGAA---GC----AGCAG----------------------AA.....................................................................................................................	20	37	0.03	0.00	0.00	0.03	0.00	0.00
............................................................................................................................................................................................................AGCAG-CAGAA---GC----AGCAG----------------------CAGCAG.................................................................................................................	23	372	0.00	0.00	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................AG-AAGAA---GC----AGCAG----------------------CAGCT..................................................................................................................	19	39	0.03	0.00	0.03	0.00	0.00	0.00
...............................................................................................................................................................................................................AG-AGGAA---GC----AGCAG----------------------CAGCAGC------A.........................................................................................................	22	14	0.07	0.00	0.00	0.07	0.00	0.00
...............................................................................................................................................................................................................AG-CAGAC---GC----AGCAG----------------------CAGCAGC------..........................................................................................................	21	17	0.06	0.00	0.06	0.00	0.00	0.00
...........................................................................................................................................................................................................................C----AGCAG----------------------CAGAAGC------AGGAGA....................................................................................................	19	33	0.03	0.00	0.00	0.03	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CAGAA---GC----AGCAG----------------------CAG....................................................................................................................	23	373	0.00	0.00	0.00	0.00	0.00	0.00
.......................................................................................................................................................................................TGC---------------AGCAGCAG-CAGAA---GC----AGCGG----------------------C......................................................................................................................	24	27	0.04	0.00	0.00	0.04	0.00	0.00
....................................................................................................................................................................................................................................G----------------------CAGCAGC------AGTAGAAATC................................................................................................	18	10	0.10	0.00	0.00	0.00	0.00	0.10
...........................................................................................................................................................................................................................C----AGCAG----------------------CAGAAGC------AGGAGAA...................................................................................................	20	28	0.04	0.00	0.04	0.00	0.00	0.00
..........................................................................................................................................................................................................GAAGCAG-CAGAA---GG----AGCAG----------------------CA.....................................................................................................................	21	22	0.05	0.00	0.00	0.05	0.00	0.00
.............................................................................................................................................................................................................GGAG-CAGAA---GC----AGAAG----------------------CAG....................................................................................................................	19	23	0.04	0.00	0.00	0.04	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CGGAA---GC----GGCAG----------------------.......................................................................................................................	20	48	0.02	0.00	0.00	0.02	0.00	0.00
...........................................................................................................................................................................................................CAGCAG-CAGAA---GC----AGGAG----------------------AA.....................................................................................................................	20	28	0.04	0.00	0.04	0.00	0.00	0.00
....................................................................................................................................................................................................................GAA---GC----AGCAG----------------------CAGCAGC------AGTAGA....................................................................................................	23	5	0.20	0.20	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................AGCAG-CAGAA---GC----TGGAG----------------------CAGCAG.................................................................................................................	23	13	0.08	0.00	0.08	0.00	0.00	0.00
...........................................................................................................................................................................................................CAGCAG-CAGAA---GC----AGGAG----------------------A......................................................................................................................	19	33	0.03	0.00	0.00	0.03	0.00	0.00
...................................................................................................................................................................................................................AGAA---GA----AGCAG----------------------CAGCAGC------T.........................................................................................................	19	39	0.03	0.00	0.03	0.00	0.00	0.00
....................................................................................................................................................................................................................GAA---GC----AGCAG----------------------CAGCAGC------AGTAG.....................................................................................................	22	16	0.06	0.06	0.00	0.00	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CGGAA---GC----GGCAG----------------------CA.....................................................................................................................	22	36	0.03	0.00	0.00	0.03	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................A---------ATAGCAGC-TGAGAGTTCA................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................................................AGAA---GC----AGCGG----------------------AAGCAGC------AG........................................................................................................	20	22	0.05	0.00	0.05	0.00	0.00	0.00
............................................................................................................................................................................................................................................................AGCAGC------AGTAGTAGTAGCAGC...........................................................................................	21	31	0.03	0.00	0.00	0.03	0.00	0.00
.............................................................................................................................................................................................................................................................................AAAGAGCAGCAGTAG-CAGCA................................................................................	20	8	0.13	0.00	0.00	0.13	0.00	0.00
..............................................................................................................................................................................................................CAG-CAGAA---GC----AGCAG----------------------CAGTAG.................................................................................................................	21	13	0.08	0.00	0.00	0.08	0.00	0.00
......................................................................................................................TTGTTGC----TGTTTCAGCTAG-------..............................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00	0.00
........................................................................................................................................................................................GG---------------AGCAGAAG-CAGAA---GC----AG................................................................................................................................................	19	23	0.04	0.00	0.00	0.04	0.00	0.00
............................................................................................................................................................................................................AGCAG-CAGAA---GC----AGGAG----------------------GA.....................................................................................................................	19	38	0.03	0.00	0.00	0.03	0.00	0.00
....................................................................................................................................................................................................................GAA---GC----AGCAG----------------------CAGCAGC------AGGAGG....................................................................................................	23	14	0.07	0.07	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................CAG-CAGAA---GC----AGCAG----------------------AACCA..................................................................................................................	20	25	0.04	0.00	0.00	0.00	0.04	0.00
.......................................................................................................................................................................................TGC---------------AGCAGCAG-CAGGA---GC----AGCCG----------------------CA.....................................................................................................................	25	28	0.04	0.04	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................CAGCGG-CAGAA---GC----AGCAG----------------------G......................................................................................................................	19	62	0.02	0.00	0.00	0.02	0.00	0.00
................................................................................................................................................................................................................................AGCAG----------------------CAGCAGC------AGTAGAAATAGCA.............................................................................................	25	2	0.50	0.00	0.00	0.50	0.00	0.00

droEre2

A---ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGAA---GC--------------------------A----------------------------------------ACAGCAACTG--------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................................................................................................................................................................GC---------------AGCAGCAG-CAGAA---GG--------------------------A----------------------------------------...................................................................................	18	31	0.03	0.00	0.00	0.00	0.03
..................................................................................................................................................................................................................................................................................................................................AGCA---------ATAGCAGC-AGAAAG....................	18	2	0.50	0.50	0.00	0.00	0.00
..........................................................................................................................................................................................................................GC--------------------------A----------------------------------------AAAGCAACGG--------A------ACTG......................................................	18	2	0.50	0.00	0.00	0.00	0.50
...........................................................................................................................................................................................................................................................................................................................CGAGAGGAGCA---------ATAGCAGC-T.........................	20	2	0.50	0.00	0.00	0.00	0.50
........................................................................CG---AC---TGCTGGC---G------------------TGT-TA-TTGTTGC----T................................................................................................................................................................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00

droEug1

AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AT---TGCTGGC---G------------------GGTTTA-TTGTTGC----TTTTGCAGTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGTAG-CAGCA---GC--------------------------AGC---AGAGG--------------------------------------------------------------AGCAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG

Size

Hit Count

Total Norm

droBia1

AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----AGCG---CT---CGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCACTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGCA---GC--------------------------AGC--------------------------------------------------------A------ACTGCAGAGGAGCA---------ATAGTAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG

Size

Hit Count

Total Norm

droTak1

AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AT---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCATTGAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGCA---AC--------------------------AGCAACTGCAGA------AG-------------------CAACAACAGC----------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG

Size

Hit Count

Total Norm

droEle1

AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AT---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGAA---GC----AGCAG----------------------CAGCAGCAAC---------AACAGCAG-------CAACAACAGC----------AGCAGCAACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG

Size

Hit Count

Total Norm

droRho1

AA--ACTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---AT---TGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAACA---GC--------------------------A-----------------------------------------------------------------ACTGCAGAGGAGCA---------ATACCAGC-TGAGAGTTCAGTTGTGAAAC-CGGCG

Size

Hit Count

Total Norm

droFic1

AA--GCTGCATTCAAGTTTTT-------CCTC----------------------------AGAGC-----CGCG---ATTGCTGCTGGC---G------------------TGT-TA-TTGTTGC----TGTTGCAGTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGTAG-CAGCAGAAGC----AGCAG----------------------CAGCAGC------AACAACAACAACAGCAACAA-CAACAGCAGC----------A------ACTGCAGAGGAGCA---------ATAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG

Size

Hit Count

Total Norm

droKik1

AAAAACGGCATTCAAGTTTTT-------CCTCGGCAACAACTA------CTAAC---C--ATTGC-----AGTG----T---TGTTGGC---G------------------GGT-TA-TTGTTGC----TGTTGCAGCTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGAAG-AAGCA---GC--------------------------AGC---AGCAGC----------------------------AAC----------------A------ACAGTAGAGGAGCAATAGCAGCAGCAGCAGC-TGAGAGTTCAGTTGTGAAAC-CGGCG

Size

Hit Count

Total Norm

droAna3

AA--ACTGCATTCAAGTTTTGTTTTTGT---T---------------ATTTTTT---CTTT--GC--TTCTGCAACTAT---TGCTGGTTAGC------------------TGC-TAGTTGCTGC----TGCTGCTGCT-G-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGTAG-CAGTA---GC--------------------------AGTGGCAGAGGAGAC---------------AGA-------G---GAGCC--ACTGCAACA------ACTGCAACA---AA---------ACAGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..........................................................................................................................................................................................................GCAGTAG-CAGTG---GC--------------------------AGTGGCA.....................................................................................................................	21	6	0.33	0.17	0.17	0.00	0.00
.........................................................................................................................................................................................................AGCAGTAG-CAGTA---GC--------------------------AGC.........................................................................................................................	18	31	0.03	0.00	0.03	0.00	0.00
...........................................................................................................................................................................................................CAGTAG-CAGTA---GC--------------------------AGTGGCAGA...................................................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
....................................................................................................................AGGAGCTGC----TGCTGCTGCT-G-------C.............................................................................................................................................................................................................................	21	40	0.03	0.00	0.03	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................GC-TGAGAGTTCAGTTGCGA.........	19	2	0.50	0.50	0.00	0.00	0.00
........................................................................................................................................................................................GA---------------AGCAGTAG-CAGTA---GC--------------------------AGA.........................................................................................................................	20	11	0.09	0.00	0.09	0.00	0.00
........................................................................................................................................................................................GA---------------AGCAGTAG-CAGAA---GC--------------------------A...........................................................................................................................	18	38	0.03	0.00	0.00	0.03	0.00
...............................................................................................................................................................................................................AG-CAGxA---GC--------------------------AGTGGCAGTGG.................................................................................................................	19	11	0.09	0.09	0.00	0.00	0.00
............................................................................................................................................................................................................AGTAG-CAGTA---GC--------------------------AGTGGCAGAG..................................................................................................................	22	2	0.50	0.00	0.50	0.00	0.00
.........................................................................................................................................................................................................AGCAGxAG-CAGTG---GC--------------------------AGTGG.......................................................................................................................	19	11	0.09	0.09	0.00	0.00	0.00
......................................................................................................................................................................................AAGC---------------AGCAGTAG-CAATA---GC--------------------------A...........................................................................................................................	20	13	0.08	0.00	0.08	0.00	0.00
................................................................................................................GA-TAGCTGCTGC----TGCTGCTGCT-......................................................................................................................................................................................................................................	22	16	0.06	0.00	0.06	0.00	0.00
.............................................................................................................................................................................................................GAAG-CAGTA---GC--------------------------AGTAGCAGA...................................................................................................................	20	11	0.09	0.00	0.09	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................ACA---AA---------ACAGCAGC-TGAGAGTTCA................	23	2	0.50	0.50	0.00	0.00	0.00
.........................................................................................................................................................................................G---------------AACAGTAG-CAGTA---GC--------------------------AGT.........................................................................................................................	19	6	0.17	0.17	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................A---AA---------ACAGCAGC-CAAGAGTT..................	19	2	0.50	0.00	0.00	0.50	0.00
....................................................................................................................................................................................................................GTA---GC--------------------------AGTGGCAGTGGTG...............................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
...........................................................................................................................................................................................................................................................CAGAGGAGAA---------------AGA-------G---GAGG............................................................................	18	2	0.50	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................CAGAAG-CAGTA---GC--------------------------AGTAGCA.....................................................................................................................	20	37	0.03	0.03	0.00	0.00	0.00
........................................................................................................................................................................................GA---------------AGCAGTAG-CAGTA---GC--------------------------AGC.........................................................................................................................	20	32	0.03	0.00	0.00	0.00	0.03

droBip1

A---ACTGCATTCAAGTTTTTGTTGT-----T---------------TTTTTCTCGTCTT----CTCTTCTGCAACTAT---TGCTG-------------------------------------------------GTTAG-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGAAGGCAGTA---GCTAGTAGCAC----------------------TAGTACT------AGTACTAATACTAGTAGTAGGCAGTAG------------------------GCAGAAGAGG------------AGCAGC-TGAGAGTTCAGTTGCGAAAC-CGGCG

Size

Hit Count

Total Norm

dp4

AA--ACGGCATACAAGTTTTT-------CCTCGCCAAACACAAAGCGTTTTAGC---C--AGAGCTCTTCTGCAACTAT---TGCTGG-------------------------T-TG-TAGTTGT----AGTT-------G-------CTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCGG-TGGCA---GC--------------------------GGTGGCAGCGGTGGC---------------AGC-------G---GTGGC------------------------------A------G--ACGGCAGCCCCCGAGTTCAGTTGCAAAAC-CGGCG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................................................................................................................................................................................GC---------------AGCATCGG-TGGCA---GC--------------------------GGC.........................................................................................................................	20	3	2.67	2.33	0.00	0.33	0.00
......................................................................................................................................................................................ATGC---------------AGCAGCGG-TGGCC---GC--------------------------GGGGGC......................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
..................................................................................TGCTGG-------------------------T-TG-TAGTGGT----ATT..............................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droPer1

TT--TC-GTTTTC--GTTTTC-------ATT------------------------------TCGC-----TGTA--------AACAAGC-----------------------GA-TT-TTGTTGC----TCTTTCTGCTCG-------TAATTGAG-ATAAATGCATTT---TAAATGCGCAAC--------------CGCAGCTGCAG-CAGCA---GC--------------------------AGC---AGAGGCAGC---AGTTG----------------CAACAGCAGCT---------A------GCTTCAAC----TG---------GTTGCAGT-TGCGTATGCAGATGCGATGCAAGGCG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................................................................................................................................................................................CAA-CAGCA---GC--------------------------AGC---AGAGGCAGT---..........................................................................................................	22	17	0.41	0.12	0.00	0.12	0.18	0.00
..............................................................................................................................................................................................................CAA-CAGCA---GC--------------------------AGC---AGAGGCAGA---..........................................................................................................	22	21	0.29	0.00	0.00	0.14	0.14	0.00
................................................................................................................................................................................................................G-CAGCA---GC--------------------------AGC---AGAGTGAG..............................................................................................................	19	10	0.20	0.20	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................G-CAGCA---GC--------------------------AGC---AGAGGAAG..............................................................................................................	19	91	0.02	0.02	0.00	0.00	0.00	0.00
...................................................................................................................................................................................................................AGCA---GC--------------------------AGC---AGAGTGAGC---..........................................................................................................	18	11	0.18	0.18	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................CAA-CAGCA---GC--------------------------AGC---AGAGGCAG..............................................................................................................	21	184	0.01	0.00	0.00	0.00	0.01	0.00
...................................................................................................................................................................................................................................................................................................................................................CAGT-TGCGGATCCAGATGC...........	19	1	2.00	0.00	1.00	0.00	0.00	1.00
................................................................................................................................................................................................................G-CAGCA---GC--------------------------GCC---AGAGGCAGC---A.........................................................................................................	21	16	0.06	0.00	0.06	0.00	0.00	0.00
...............................................................................................................................................................................................................AA-CAGCA---GC--------------------------AGC---AGAGGCAGA---..........................................................................................................	21	21	0.05	0.00	0.00	0.05	0.00	0.00
...................................................................................................................................................................................................................................................................................................................................................CAGT-TGCGGATCCAGATG............	18	1	1.00	0.00	1.00	0.00	0.00	0.00
......................................................................................................................................................................................................................A---GC--------------------------AGC---AGAGGCAGG---GGT.......................................................................................................	18	8	0.13	0.13	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................AG-CAGCA---TC--------------------------AGA---AGAGGC................................................................................................................	18	12	0.08	0.00	0.08	0.00	0.00	0.00
................................................................................................................................................................................................................A-CAGCA---GC--------------------------AGC---AGAGGCAGT---..........................................................................................................	20	22	0.05	0.00	0.00	0.00	0.05	0.00
.............................................................................................................................................................................................................GCAG-CAGCA---GC--------------------------AGC---AGAGTGAGC---..........................................................................................................	23	4	0.25	0.00	0.25	0.00	0.00	0.00
..............................................................................................................................................................................................................CAA-CAGTA---GC--------------------------AGC---AGAGGCA...............................................................................................................	20	10	0.10	0.00	0.00	0.00	0.10	0.00
...............................................................................................................................................................................................................AA-CAGCA---GC--------------------------AGC---AGAGGCAGT---..........................................................................................................	21	19	0.05	0.00	0.00	0.00	0.05	0.00
..............................................................................................................................................................................................................CAA-CAGCA---GC--------------------------AGC---AGAGGCAGT---A.........................................................................................................	23	11	0.09	0.00	0.00	0.00	0.09	0.00
..............................................................................................................................................................................................................CAG-CAGGA---GC--------------------------AGG---AGAGG.................................................................................................................	18	33	0.03	0.00	0.03	0.00	0.00	0.00

droWil1

AC--ACTGCAGACAAGTTTTAAATGCCT-------------------TTTTTTT---C--GTAGC--------------------TCTC---TTGTTGTTGTTGTTGCTAA-GT----------C----TTCTGCAACTA--------TTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGC---------------AGCAGCAG-CAGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------A---------GCGGCAGC-TTCGAGTTCAGTTGCAAAAC-CGGCG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........................................................................................................................................................................................GC---------------AGCAGCAG-CGGCG---GC--------------------------AGC---A.....................................................................................................................	21	36	0.31	0.00	0.31	0.00	0.00
..........................................................................................................................................................................................................GCAGCAG-CAGCG---GC--------------------------GGC---AG-------------------------------------CA--------------------------------.............................................	21	36	0.31	0.00	0.31	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CAGCG---CC--------------------------AGT---A.....................................................................................................................	19	29	0.24	0.00	0.24	0.00	0.00
..........................................................................................................................................................................................................GTAGCAT-CAGCG---GC--------------------------AGC---AG-------------------------------------C..............................................................................	20	41	0.17	0.02	0.15	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CAGCG---GC--------------------------GGC---AG-------------------------------------CA--------------------------------.............................................	22	29	0.21	0.00	0.21	0.00	0.00
........................................................................................................................................................................................GC---------------AGCAGCAG-CGGCG---GC--------------------------AGC---......................................................................................................................	20	50	0.06	0.00	0.06	0.00	0.00
............................................................................................................................................................................................................AGCAT-CAGCG---GC--------------------------AGC---AG-------------------------------------C..............................................................................	18	40	0.08	0.00	0.08	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CAGCG---GC--------------------------GGC---AG-------------------------------------C..............................................................................	21	40	0.08	0.00	0.08	0.00	0.00
..........................................................................................................................................................................................................GCAGCAG-CAGCG---GC--------------------------GGC---AG-------------------------------------C..............................................................................	20	50	0.06	0.00	0.06	0.00	0.00
..........................................................................................................................................................................................................GCAGCAG-CGGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------.............................................	21	31	0.06	0.03	0.03	0.00	0.00
...............................................................................................................................................................................................................AG-CAGCA---GC--------------------------AGC---AG-------------------------------------AA--------------------------------A---------GC.................................	19	19	0.11	0.00	0.00	0.11	0.00
......................................................................................................................................................................................ATAC---------------AGCAACAG-CAGCG---GC--------------------------............................................................................................................................	19	13	0.15	0.00	0.15	0.00	0.00
......................................................................................................................................................................................ATGT---------------AGCAGCAG-CAGAG---G.......................................................................................................................................................	18	1	2.00	0.00	0.00	2.00	0.00
.........................................................................................................................................................................................C---------------AGCAGCAG-CAGCG---CC--------------------------AGT---......................................................................................................................	19	49	0.04	0.00	0.04	0.00	0.00
.........................................................................................................................................................................................................ATTAGCAG-CAGCG---GC--------------------------AGC---AG-------------------------------------C..............................................................................	21	22	0.09	0.00	0.09	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CAGAG---CC--------------------------AGC---......................................................................................................................	18	40	0.05	0.03	0.03	0.00	0.00
........................................................................................................................................................................................GC---------------AGCAGCAG-CAGAG---CC--------------------------AG..........................................................................................................................	19	20	0.05	0.00	0.05	0.00	0.00
.........................................................................................................................................................................................................AGCAGAAG-CAGCG---TC--------------------------AGC---A.....................................................................................................................	19	36	0.03	0.00	0.03	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CAGCG---GT--------------------------AGA---......................................................................................................................	18	49	0.02	0.00	0.02	0.00	0.00
.........................................................................................................................................................................................................AGCAGCGG-GAGCG---GC--------------------------AGC---AG-------------------------------------C..............................................................................	21	28	0.04	0.04	0.00	0.00	0.00
............................................................................................................................................................................................................AGCAT-CAGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------.............................................	19	37	0.03	0.00	0.03	0.00	0.00
.............................................................................................TGTTGTTGTTGTTGATAG-G.................................................................................................................................................................................................................................................................	19	13	0.08	0.00	0.00	0.08	0.00
............................................................................................................................................................................................................AGCAG-CAGCG---GC--------------------------GGC---AG-------------------------------------CA--------------------------------.............................................	19	39	0.03	0.00	0.03	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................G	21	50	0.02	0.02	0.00	0.00	0.00
........................................................................................................................................................................................GC---------------AGCAGCAG-CAGCG---CC--------------------------AGT---......................................................................................................................	20	37	0.03	0.00	0.03	0.00	0.00
.........................................................................................................................................................................................................AGCAATAG-CAGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------A---------...................................	23	39	0.03	0.03	0.00	0.00	0.00
........................................................................................................................................................................................GC---------------AGCAGCAC-CAGCG---GC--------------------------CGC---......................................................................................................................	20	47	0.02	0.00	0.02	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................G	21	12	0.08	0.00	0.08	0.00	0.00
........................................................................................C---ATGTTGTTGTTxTTGCTA....................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CGGCG---GC--------------------------AGC---A.....................................................................................................................	19	39	0.03	0.00	0.03	0.00	0.00
......................................................................................................................................................................................ATAC---------------AGCAACAG-CAGCG---G.......................................................................................................................................................	18	14	0.07	0.00	0.07	0.00	0.00
............................................................................................................................................................................................................AGTAG-CAGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------.............................................	19	18	0.06	0.06	0.00	0.00	0.00
..............................................................................................................................................................................CACGCxAAATGC---------------AGCAGCAG-C...............................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................GA---------------AGTAGCAG-CAGCG---GC--------------------------AGC---......................................................................................................................	20	22	0.05	0.00	0.05	0.00	0.00
.........................................................................................................................................................................................G---------------AGCAGCAG-CAGCG---CC--------------------------AGC---A.....................................................................................................................	20	30	0.03	0.03	0.00	0.00	0.00
............................................................................................................................................................................................................AGTAG-CAGCG---GC--------------------------AGC---AG-------------------------------------C..............................................................................	18	23	0.04	0.00	0.04	0.00	0.00
.............................................................................................................................................................................................................GTAG-CAGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------.............................................	18	23	0.04	0.04	0.00	0.00	0.00
.....................................................................................................................................................................................GATGC---------------GGCAGCAG-CAGCG---GC--------------------------A...........................................................................................................................	21	5	0.20	0.20	0.00	0.00	0.00
..........................................................................................................................................................................................................GCAGTAG-CAGCG---GC--------------------------AGC---AG-------------------------------------C..............................................................................	20	16	0.06	0.06	0.00	0.00	0.00
.........................................................................................................................................................................................................ATTAGCAG-CAGCG---GC--------------------------AGC---A.....................................................................................................................	19	49	0.02	0.00	0.02	0.00	0.00
.............................................................................................................................................................................................................GGAC-CAGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------.............................................	18	42	0.02	0.02	0.00	0.00	0.00
...........................................................................................................................................................................................................................C--------------------------AAC---AG-------------------------------------CA--------------------------------A---------GTGGCAGC-T.........................	18	3	0.33	0.00	0.33	0.00	0.00
..................................................................................................................................................................................................................CAGCA---GC--------------------------AGC---AG-------------------------------------CA--------------------------------A---------GAGGC..............................	20	17	0.06	0.00	0.06	0.00	0.00
............................................................................................................................................................................................................AGCGG-CAGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------.............................................	19	50	0.02	0.00	0.02	0.00	0.00
.......................................................................................TC---TGGTTGTTGTTGTTGC......................................................................................................................................................................................................................................................................	18	127	0.01	0.00	0.01	0.00	0.00
...............................................................................................................................................................................................................AG-CAGCA---GA--------------------------AGC---AG-------------------------------------CA--------------------------------A---------GC.................................	19	16	0.06	0.00	0.06	0.00	0.00
........................................................................................................................................................................................GC---------------ATTAGCAG-CAGCG---GC--------------------------AGC---AG-------------------------------------...............................................................................	22	12	0.08	0.00	0.08	0.00	0.00
.....................................................................................................................................................................................AATAC---------------AGCAACAG-CAGCG---GC--------------------------............................................................................................................................	20	5	0.20	0.00	0.20	0.00	0.00
.....................................................................................................................................................................................AATGC---------------AGCAACAG-AAGCG---GC--------------------------............................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................................................AG-CAGCG---GT--------------------------AGC---AA-------------------------------------CA--------------------------------A---------GCGGC..............................	22	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................CAGCAG-CAGCA---GC--------------------------AGC---AG-------------------------------------AA--------------------------------A---------GC.................................	23	8	0.13	0.00	0.00	0.00	0.13
.........................................................................................................................................................................................C---------------AGCAGCAG-CAGAG---GA--------------------------AGC---A.....................................................................................................................	20	21	0.05	0.05	0.00	0.00	0.00
..............................................................................................................................................................................................................CAG-CAGCG---TC--------------------------AAC---AG-------------------------------------CA--------------------------------A---------GC.................................	20	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................................................GCAGCAG-CAGCG---CC--------------------------AGT---AG-------------------------------------...............................................................................	19	20	0.05	0.00	0.05	0.00	0.00
............................................................................................................................................................................................................AGCAG-CAGCG---GC--------------------------AGA---AG-------------------------------------CA--------------------------------C---------...................................	20	11	0.09	0.00	0.09	0.00	0.00
.........................................................................................................................................................................................................AGCAGCAG-CAGCG---GC--------------------------GGC---A.....................................................................................................................	19	51	0.02	0.00	0.02	0.00	0.00
........................................................................................................................................................................................GC---------------AACAGCAG-CAGCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------.............................................	24	39	0.03	0.03	0.00	0.00	0.00
..........................................................................................................................................................................................................GTAGCAG-CATCG---GC--------------------------AGC---AG-------------------------------------CA--------------------------------.............................................	21	21	0.05	0.05	0.00	0.00	0.00
.........................................................................................................................................................................................................AGAAGAAG-CAGCG---GC--------------------------AGC---AG-------------------------------------C..............................................................................	21	10	0.10	0.10	0.00	0.00	0.00
..................................................................................................................................................................TGCTTCACTGATTACGCGCAATGC---------------.........................................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00

droVir3

AG--GATATGGGCGATTGTCT-------TATC----------------------------AGTG-------GTG---GT---GCCGGACCAGC------------------TGT-TA-GTGCCGT----TGCTGATGCCAG-------CGGCAACCTTTTGCTCGATCAT-CATCACCATCATCA---------TCAT--CAACAACAG-CAGCA---GC--------------------------AGC---AGCAGCAGCAGCAACAACAA-------------------------------------------CAACAGCAGCA---------ACAGCAGC-AGCTACTGCAG---------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.........................................................................................................................................................................................................................................................................ACAACGA-------------------------------------------CAACAGCAGCA---------ACA................................	21	33	0.03	0.00	0.03	0.00	0.00	0.00
................................................................................................................................................................................ACATCATCA---------TCAT--CAACGAC...................................................................................................................................................................	20	4	0.25	0.00	0.25	0.00	0.00	0.00
.....................................................................................................................................................................................ATCA---------GCAT--CAACAACAG-CGGC............................................................................................................................................................	21	17	0.06	0.00	0.00	0.00	0.00	0.06
...................................................................................................................................................................................................CAT--CCACAACAG-CAGCA---TC--------------------------............................................................................................................................	19	34	0.03	0.00	0.00	0.03	0.00	0.00
.......................................................................................................................................................................CAT-CATCACCATCATCG---------GCAT--..........................................................................................................................................................................	21	10	0.10	0.10	0.00	0.00	0.00	0.00
....................................................................................................................................................................................................AT--CAACAACAG-CAGCA---GC--------------------------AGC---A.....................................................................................................................	22	324	0.00	0.00	0.00	0.00	0.00	0.00
.......................................................................GTG---GT---GCCGGCCCGGC------------------TG.................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
....................................................................................................................................................................................CATCG---------TCAG--CAACAACAG-CAGCA---GC--------------------------............................................................................................................................	25	16	0.06	0.00	0.00	0.06	0.00	0.00
........................................................................................................................................................................................A---------TCAT--CAACAACAG-CAGCA---........................................................................................................................................................	19	33	0.03	0.00	0.00	0.03	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................AGAAGCA---------ACAGCAGG-AGCT......................	19	21	0.05	0.00	0.00	0.05	0.00	0.00
...............................................................................................................................................................................ACCGTGATCA---------TCAT--CAAC......................................................................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25	0.00
...................................................................................................................................................................................................................................................................GAAGGAACAACAA-------------------------------------------CAACAGCAGC.............................................	23	50	0.02	0.00	0.00	0.02	0.00	0.00
.................................................................................................................................................................................CATCATCA---------TAAT--CAACGACA..................................................................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.00	0.50
........................................................................................................................................................................................................................................................................AACCACAA-------------------------------------------CAACAGCAGCA---------ACC................................	22	48	0.02	0.02	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................................................ACAA-------------------------------------------CAACAGCAGCA---------ACCGAA.............................	21	40	0.03	0.03	0.00	0.00	0.00	0.00
AG--GATATGGGCGATTGTC..............................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................................................................................................ACAACAA-------------------------------------------GAACAGCAGCA---------AC.................................	20	34	0.03	0.00	0.00	0.00	0.00	0.03
..............................................................................................................................................................................................................................................................................................................................AAGCAGGA---------ACAGCAGC-AGCTA.....................	21	4	0.25	0.25	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................AA-------------------------------------------CAACAGCCGCA---------ACAGCAGC-CGC.......................	24	50	0.02	0.00	0.00	0.02	0.00	0.00

droMoj3

AA--ACGAAATGAAACTTTGT-------GCGC----------------------------ATAGG-------CAACCAA---CAGCGGC--------------------------GG-CAGCAGC----AGCAGCAGC-AG-------CAGCAGCAGCG-CCAGCATCGCTGAGAC-T-TTGACGC---------------G---------------------------TTGGCAAAAGAAGCAGCAGC---AGCAGC------------------------AG-CAACAGCAAC----------A------ACAGC--CGCAGCA---------GCAGCAGC-AGCGACGGCAGCAGCAGAAA-CGTCG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
......................................................................................................................................CAGC-AG-------CAGCGCCAGCG-CCAGC.............................................................................................................................................................................................................	22	32	0.59	0.06	0.13	0.06	0.34
......................................................................................................................................CAGC-AG-------CAGCGCCAGCG-CCAG..............................................................................................................................................................................................................	21	34	0.29	0.03	0.09	0.06	0.12
...........................................................................CCAA---AGGCGGC--------------------------GG-CAGCAGC----A................................................................................................................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
...........................................................................................................................................AG-------CAGCAGCAGAG-CCAGCC............................................................................................................................................................................................................	19	17	0.06	0.06	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................CAACAGC-AGCGACGTCAGC..............	19	47	0.02	0.02	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................CGCAGCA---------GCAGCAGC-AGCGAC....................	21	94	0.01	0.00	0.00	0.00	0.01
......................................................................................................................................CAGC-AC-------CAGCAGCAGCG-CCA...............................................................................................................................................................................................................	20	353	0.00	0.00	0.00	0.00	0.00
....................................................................................GCGGC--------------------------GG-CAGCAGG----AGCAGT...........................................................................................................................................................................................................................................	20	32	0.03	0.03	0.00	0.00	0.00
...................................................................................................................................................................................................................................................................................................CAAC----------A------ACAGC--CGCATCA---------GC.................................	19	8	0.13	0.13	0.00	0.00	0.00
............................................................................................................................................................................................................................................AAGAAGAAGCAGC---AGCAGC------------------------AG-.....................................................................................	21	16	0.06	0.06	0.00	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................................................ACGACGGCAGCAGCAGAGA-CGTC.	23	3	0.33	0.33	0.00	0.00	0.00
..................................................................................CAGAGGC--------------------------GG-CAGCAGC----ATCAG............................................................................................................................................................................................................................................	21	21	0.05	0.05	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................GCAGCAGC-GGCGACGACAGC..............	20	20	0.05	0.05	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................AACAGCAAC----------A------ACAAT--CGCAGCA---------GCAG...............................	26	25	0.04	0.04	0.00	0.00	0.00
.........................................................................................................................................................................................................................................AAAAAGAAGCAGCAGA---AGC...................................................................................................................	19	9	0.11	0.11	0.00	0.00	0.00
...........................................................................................................................................AG-------CAGGAGTAGCG-CCAGCA............................................................................................................................................................................................................	19	49	0.02	0.02	0.00	0.00	0.00

droGri2

CA--A----------TTTTCT-------CATC----------------------------AGTTT-----C-------T---TGCCGAT---G--------ATGAAGCAAATGT-CA-TCGCTGCAGAATGTTGCATTTCGCGCCAAGATG-GGTGAGCTGCTGCTGCA---------CACAATGCAACAATCACAAATGCAACAACAG-CAGCA---AC--------------------------AGC---AGCAGCAGC---AGCAAC----------------AACAACA----------------------GC--AACAACA---------ACAGGAGC-CGA---TGCAGCAGCA--A----CCG	Size	Hit Count	Total Norm	V109 Male body
...............................................................................................................................................................................................................................................................................................................................................ACAGGAGC-GGG---TGCAGCAGC...........	20	1	1.00	1.00
...............................................................................................................................................CCAAGATG-GGTGAGCTGCTGC.............................................................................................................................................................................................................	21	2	0.50	0.50

Generated: 04/20/2012 at 05:21:31 EDT

dme-mir-4968

chr3L:11545638-11545793 -

Known_mirbase

intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup