dme-mir-2282- Best orthologs

dme-mir-2282	chr3L:3412145-3412251 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 3412166-3412187
   star strand at position 3412203-3412224
   mutations
   read mismatches

Notes: drosim1 ortholog is missing because of a large gap at positions chr3L:2949115-2949968. Apparent that the ortholog is lost in pseudobscura and earlier due to random substitution patterns in these species.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3L:3412130-3412266 -		1	TGGGGC-AGTG------GAGC-----TGCCT----G----------------------------------------C---ATAACG---------CT----------------------GTGGCTTTCCGCTTCTA------------TT----T-------------TTCGTT--------C-------AC----------TGCCTTG-T----------------GCTTCG--TTGG---AAAATCGGTGAGCTAAAAATAGAATTCGGTTGCCACGCTTCAAGGGAAAT---GAGGAAAATTA
droSim1	Unknown		4	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec1	super_2:3404661-3404801 -	LASTZ	4	TGGGGC-AGTG------GAGC-----TGCCT----G----------------------------------------C---ATAAGG---------CT----------------------GTGGCTTTCCGCTTCTA------------TT----T-------------TTCGTT--------C-------AC----------TGCCTTG-TG-------CTT-----GCTTCG--TTGG---AAAAGCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCAAGGGAAAT---GAGGAAAATTA
droYak2	chr3L:3959855-3959989 -	LASTZ	4	TGGGGC-AGTG------GGGC-----TG------------------------------------------------CA-TATAAGG---------CT----------------------GTGGCTTTCCGCTTCTA------------TT----T-------------TGTGCT--------C-------AC----------TGTCTTG-T----------------GCGGCG--TTGG---AAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGTGGAAAAT---GAGGAAAATTA
droEre2	scaffold_4784:6102142-6102274 -	LASTZ	4	TGGGGC-AGTG------GAGC-----TG------------------------------------------------C---ATAAGG---------CT----------------------GTGGCTTTCCGCTTCTA------------TT----T-------------TGTGTT--------C-------AC----------TGTCCTG-C----------------GTTTCG--TTGG---AAAATCGGTGAGCCAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GCGGAAAATTA
droEug1	scf7180000409466:1140592-1140735 -	LASTZ	4	TGGGGC-AGTG------GAGC-----TCTTG----GG----------------------------------ATATGCACTATAAGG---------CT----------------------GTGGCTTTCCGCTTCTA------------TT----TTTCT-------------CTGTTCTT----------------------------G-T----------------TG-TTGTTGTGG---AAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GAGGAAAATTA
droBia1	scf7180000302428:2784843-2785001 -	LASTZ	4	TGGGGC-AGTG------GAGC-----TCTGG----GCAT--GG----------------------------ATATGCACTATGAGG---------CC----------------------GTGGCTTTCCGCTTCTT------------TT----T-------------TTTAC-ATC----------TTTAC----------GGTTTTT-T------GTTGT-----TGTTTG--TTGG---AAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GAGGAAAATTA
droTak1	scf7180000415855:71929-72087 +	LASTZ	4	TGGGGC-AGTG------GAGT-----TCTGT----GCAT--GG----------------------------ATATGCACTATAAGG---------CT--------------------GTGTGGCTTTCCGCTTCTC------------TT----T-------------TTACTT--------TA--CTTTAC-------------T--T-T-TTTT---CGT-----TGTTTG--TTGG---AAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GAGGAAAATTA
droEle1	scf7180000491249:1811852-1812027 +	LASTZ	5	TGGGGT-AGTG------AAGC-----TCTGG----GGATATGGATAT-------------------------TATGCACTACAAGA---------CC----------------------ATGGCTTTCCGCTTCTC------------TT----CTCCT-------------TTTTTCCTTTT-------ATTTTTTTTG------TTGT---TTTTGTTTT-----TGTTCG--TTGG---AAAATCCGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGTGGAAAAT---GAGGAAAATTA
droRho1	scf7180000776556:359-515 +	LASTZ	5	TGGGGC-AGTG------GAGC-----TCTGG----GGATATGGATAT-------------------------TATGCACTGCAAGA---------CT----------------------GTGGCTTTCCGCTTCTT------------TT----TCCCT-------------C-TTCCTTTTT--------------------GTT-------------TTT-----TGTTCG--TTGG---AA-ATCGGCGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GAGGAAAATTA
droFic1	scf7180000454105:1746613-1746784 -	LASTZ	5	TGGGGC-AGTG------GAGC-----CATGG----GGACGTGGGATCGGGGATCGGGGTGCGGGGACTGGGATGTGCACTATAAGA---------CT----------------------GCGGCTTTCCGCCTCCT------------TT----TCCCT-------------TT---------------------------------------------TTT-----CGTTCG--TCGG---AAAAGCGTCGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGGGGAAAAT---GAGGAAAATTA
droKik1	scf7180000302577:903953-904126 +	LASTZ	5	TGGGGC-AGTG------GAGC-----TCCCG----GG----------------------------------ATATGCACTGTGGGGT--------CT----------------------GCGGCTTTCCGCTTCTACTCTATAT----TT----CT--TCATTT----TTTGTT--------C----TTTACTTTTTTTGTTTGCCTTT-GGCT---GTCGC-----TTTTTG--TTGG---AAATTCGGCAAGCTAAAAATAGATTTCGGTTGCCACGCTTCAA------------AGAAAATTA
droAna3	scaffold_13337:10031066-10031241 +	LASTZ	5	TGGGGGCAG-G------TGGT-----GG-CAGGA----GGTGG--CCGGAGGTGGTGGTA------------GGTGGGTGGG---G---------GTGGTGTATGTAGGGGGCCTGTATGTGGCTTTCCGCTTCTA------------CC----------------------------------------AT-------------T--T-T-TTTT---TGTTGGAGGGTTCA--GTGG---AAATTCGGCGAGCTAAAAATATAATTCGGTTGCCACGCTTCGG--AA--------AGAGAATTA
droBip1	scf7180000396569:1328998-1329165 -	LASTZ	5	TGGGGGCAG-GTGGTGGTACC-----TCCCAGGGGGG----------------------------------GTATGTA---GGGGG---------CC-----------------TGTGTGTGGCTTTCCGCTTCTG------------CC----T-------------TTTCTTTTTCTTTCTATA-TATAT-------------T--T-T-TTTTTGGGAG-----GGTTCA--CTGG---AAATTCGGCGAGCTAAAAATAGAATTCGGTTGCCACGCTTCAA------------AGAGAATTA
dp4	chrXR_group8:5510827-5511013 -	LASTZ	0	TGTGTG-TGTG------TGTC-----TGTGT----GTGTGTGTGTGTGTGTGTGTGTGT---------------GGCAGGGTGACAGCACTCTCTCT----------------------AAGGCTTTCCGCTTTTC------------GT----TCTCT-------------T-TTTGTTGTT-------GT----------TGTTCTT-T-CT-----TTC-----GTTTTG--GTGGAAATTTTCGTTGTATCTAAAAATAGACTTT-----TTGGGGTTCAAAGGAAATTTTGTGGGACAAAA
droPer1	super_7263:1394-1409 +	LASTZ	0	TACGGG-TGTG------AGAC-----TG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180955:1135974-1136099 -	LASTZ	0	TATGGC-GATA------TTTTGTAGGTTTTG----G----------------------------------------C----AATGG---------TT----------------------GTGGCTTTCCGCTTCTATTCAGTCGCACGAAAAATTTTCTCGGTTTTT-------------------------------------------------------------------------------TCCCATGTCTAAAAATAGATTTA------CACCCAAAGT--A-------GAAAAACATAA
droVir3	scaffold_13049:19660195-19660299 +	LASTZ	0	GTTC--------------------------------------------------------------------------------------------------------------------------TGCGCTAGCT------------TG----T-------------TCGGTT--------T-------GG----------TAACATG-A----------------GCTTCA--TTAG---TGTATGCAATAATGGCAAACATTTTTTGCCTGCCAGGCCTCGGCGAGGAC---GATGACGACGA
droMoj3	scaffold_6496:15371578-15371721 +	LASTZ	0	TGCAAC-ATTG------ATGA-----AA--------------------------------------------TATGCATAATGAAAATGTGCCCTC-----------------------AGAGTTATCCACGATTT------------TT----CTACT----TTTTTTTTAT------------------------------ACCCTGAAC-------CCA-----TTTTCA--ATGG---GAAATCAGGGTATAA------TGGTTTTGTTGAAATGTATGTAAC----------AGGGAGAAG
droGri2	scaffold_15203:7704730-7704834 +	LASTZ	0	CAGAAT-AATA------GAAT-----G-----------------------------------------------TACTCACTTCAG---------CT----------------------ATGGCATACAGATTTGC------------TT----TATTT-------------G---------C-------TT----------TTCGTTG-T----------------------------------------------------ACTTTCTGTTTTCTCAATGTACATGAAAA---AGACTGAATTT

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	TGGG-GCAG-TGGAGCTG----CCTGC---------------------------------------------------ATAACG-CT-----GTGGCTTTCCGCTTCTATTTTT---------------CGTTCAC----------------------TGCCTTG---T--------G-----CTTCGTTGGAAAATCGGTGAGCTAAAAATAGAATTCGGTTGCCACGCTTCAAGGGAAATGAGGAAAATTA
droSim1	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec1	TGGG-GCAG-TGGAGCTG----CCTGC---------------------------------------------------ATAAGG-CT-----GTGGCTTTCCGCTTCTATTTTT---------------CGTTCAC----------------------TGCCTTG---T--------G-CTTGCTTCGTTGGAAAAGCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCAAGGGAAATGAGGAAAATTA
droYak2	TGGG-GCAG-TGGGGCTG--------------------------------------------------------CA-TATAAGG-CT-----GTGGCTTTCCGCTTCTATTTTG---------------TGCTCAC----------------------TGTCTTG---T--------G-----CGGCGTTGGAAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGTGGAAAATGAGGAAAATTA
droEre2	TGGG-GCAG-TGGAGCTG--------------------------------------------------------C---ATAAGG-CT-----GTGGCTTTCCGCTTCTATTTTG---------------TGTTCAC----------------------TGTCCTG---C--------G-----TTTCGTTGGAAAATCGGTGAGCCAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAATGCGGAAAATTA
droEug1	TGGG-GCAG-TGGAGCTC----TTGG---------------------------------------GAT---ATGCACTATAAGG-CT-----GTGGCTTTCCGCTTCTATTTTT---------------CT----CTGTTCTT---------------------G---T-----TGTT-----GT-T-GTGGAAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAATGAGGAAAATTA
droBia1	TGGG-GCAG-TGGAGCTC----TGGGCAT-----------------------------------GGAT---ATGCACTATGAGG-CC-----GTGGCTTTCCGCTTCTTTTTTT---------------TA----CA-TCTTTAC-------------GGTTTTT---T---GTTGTT-----GTTTGTTGGAAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAATGAGGAAAATTA
droTak1	TGGG-GCAG-TGGAGTTC----TGTGCAT-----------------------------------GGAT---ATGCACTATAAGG-CT---GTGTGGCTTTCCGCTTCTCTTTTT---------------ACTTTAC----TTTAC----------------TTTTTTT------CGTT-----GTTTGTTGGAAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAATGAGGAAAATTA
droEle1	TGGG-GTAG-TGAAGCTC----TGGGGATAT---------------------------------GGATATTATGCACTACAAGA-CC-----ATGGCTTTCCGCTTCTCTTCTC---------------CTTTT----TTCCTTTTATTTTTTTTGT-TG----TTTTT---G---T--TTTTGTTCGTTGGAAAATCCGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGTGGAAAATGAGGAAAATTA
droRho1	TGGG-GCAG-TGGAGCTC----TGGGGATAT---------------------------------GGATATTATGCACTGCAAGA-CT-----GTGGCTTTCCGCTTCTTTTTCC---------------CT----CT-TCCTTTT------------------TG-----------TT-TTTTGTTCGTTGGAA-ATCGGCGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAATGAGGAAAATTA
droFic1	TGGG-GCAG-TGGAGCCA----TGGGGACGTGGGATCGGGGATCGGGGTGCGGGGAC-----TGGGAT---GTGCACTATAAGA-CT-----GCGGCTTTCCGCCTCCTTTTCC---------------CTTTTTT----------------------------------------------CGTTCGTCGGAAAAGCGTCGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGGGGAAAATGAGGAAAATTA
droKik1	TGGG-GCAG-TGGAGCTC----CCGG---------------------------------------GAT---ATGCACTGTGGGGTCT-----GCGGCTTTCCGCTTCTACTCTATATTTCTTCATTTTTTGTTC------TTTAC---TTTTTTTGTTTGCCTTT---GGCTGTCGCT-----TTTTGTTGGAAATTCGGCAAGCTAAAAATAGATTTCGGTTGCCACGCTTCAAA---------GAAAATTA
droAna3	TGGGGGCAGGTGGTGGC-------AGGAGGTGG--CCGGAGGTGGTGGTAGGTGGGTGGGGGTGGTGT---ATGTA---GGGGG-CCTGTATGTGGCTTTCCGCTTCTACCAT------------------------------------------------TTTTTTTT------GTTGGAGGGTTCAGTGGAAATTCGGCGAGCTAAAAATATAATTCGGTTGCCACGCTTCG--GAAA-----GAGAATTA
droBip1	TGGGGGCAGGTGGTGGTACCTCCCAGGGG-----------------------------------GGGT---ATGTA---GGGGG-CCTGTGTGTGGCTTTCCGCTTCTGCCTTT---------------TCTTT----TTCTTTCTATATATAT-------TTTTTTTT---G---G--GAGGGTTCACTGGAAATTCGGCGAGCTAAAAATAGAATTCGGTTGCCACGCTTCAAA---------GAGAATTA

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

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

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

TGGGGC-AGTG------GAGC-----TGCCT----G----------------------------------------C---ATAAGG---------CT----------------------GTGGCTTTCCGCTTCTA------------TT----T-------------TTCGTT--------C-------AC----------TGCCTTG-TG-------CTT-----GCTTCG--TTGG---AAAAGCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCAAGGGAAAT---GAGGAAAATTA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................................................................................................................................................................................................................................AAAAAGAGATTTCGGTTT................................	18	1	2.00	0.00	0.00	2.00

droYak2

TGGGGC-AGTG------GGGC-----TG------------------------------------------------CA-TATAAGG---------CT----------------------GTGGCTTTCCGCTTCTA------------TT----T-------------TGTGCT--------C-------AC----------TGTCTTG-T----------------GCGGCG--TTGG---AAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGTGGAAAAT---GAGGAAAATTA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
TGGGGC-AGTx------AGGC-----TG------------------------------------------------CA-TAT................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................................................................................................CT--------C-------TC----------TGTCTGG-T----------------GCGGC..........................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

TGGGGC-AGTG------GAGC-----TG------------------------------------------------C---ATAAGG---------CT----------------------GTGGCTTTCCGCTTCTA------------TT----T-------------TGTGTT--------C-------AC----------TGTCCTG-C----------------GTTTCG--TTGG---AAAATCGGTGAGCCAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GCGGAAAATTA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................................................................................................................................................................................................................................G---AAAATCGGTGAGCCAAAAATA...........................................	22	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................................................................................................................................GCCAAAAATAGATTTCGG...................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

TGGGGC-AGTG------GAGC-----TCTTG----GG----------------------------------ATATGCACTATAAGG---------CT----------------------GTGGCTTTCCGCTTCTA------------TT----TTTCT-------------CTGTTCTT----------------------------G-T----------------TG-TTGTTGTGG---AAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GAGGAAAATTA

Size

Hit Count

Total Norm

droBia1

TGGGGC-AGTG------GAGC-----TCTGG----GCAT--GG----------------------------ATATGCACTATGAGG---------CC----------------------GTGGCTTTCCGCTTCTT------------TT----T-------------TTTAC-ATC----------TTTAC----------GGTTTTT-T------GTTGT-----TGTTTG--TTGG---AAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GAGGAAAATTA

Size

Hit Count

Total Norm

droTak1

TGGGGC-AGTG------GAGT-----TCTGT----GCAT--GG----------------------------ATATGCACTATAAGG---------CT--------------------GTGTGGCTTTCCGCTTCTC------------TT----T-------------TTACTT--------TA--CTTTAC-------------T--T-T-TTTT---CGT-----TGTTTG--TTGG---AAAATCGGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GAGGAAAATTA

Size

Hit Count

Total Norm

droEle1

TGGGGT-AGTG------AAGC-----TCTGG----GGATATGGATAT-------------------------TATGCACTACAAGA---------CC----------------------ATGGCTTTCCGCTTCTC------------TT----CTCCT-------------TTTTTCCTTTT-------ATTTTTTTTG------TTGT---TTTTGTTTT-----TGTTCG--TTGG---AAAATCCGTGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGTGGAAAAT---GAGGAAAATTA

Size

Hit Count

Total Norm

droRho1

TGGGGC-AGTG------GAGC-----TCTGG----GGATATGGATAT-------------------------TATGCACTGCAAGA---------CT----------------------GTGGCTTTCCGCTTCTT------------TT----TCCCT-------------C-TTCCTTTTT--------------------GTT-------------TTT-----TGTTCG--TTGG---AA-ATCGGCGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGAGGAAAAT---GAGGAAAATTA

Size

Hit Count

Total Norm

droFic1

TGGGGC-AGTG------GAGC-----CATGG----GGACGTGGGATCGGGGATCGGGGTGCGGGGACTGGGATGTGCACTATAAGA---------CT----------------------GCGGCTTTCCGCCTCCT------------TT----TCCCT-------------TT---------------------------------------------TTT-----CGTTCG--TCGG---AAAAGCGTCGAGCTAAAAATAGATTTCGGTTGCCACGCTTCGGGGAAAAT---GAGGAAAATTA

Size

Hit Count

Total Norm

droKik1

TGGGGC-AGTG------GAGC-----TCCCG----GG----------------------------------ATATGCACTGTGGGGT--------CT----------------------GCGGCTTTCCGCTTCTACTCTATAT----TT----CT--TCATTT----TTTGTT--------C----TTTACTTTTTTTGTTTGCCTTT-GGCT---GTCGC-----TTTTTG--TTGG---AAATTCGGCAAGCTAAAAATAGATTTCGGTTGCCACGCTTCAA------------AGAAAATTA

Size

Hit Count

Total Norm

droAna3

TGGGGGCAG-G------TGGT-----GG-CAGGA----GGTGG--CCGGAGGTGGTGGTA------------GGTGGGTGGG---G---------GTGGTGTATGTAGGGGGCCTGTATGTGGCTTTCCGCTTCTA------------CC----------------------------------------AT-------------T--T-T-TTTT---TGTTGGAGGGTTCA--GTGG---AAATTCGGCGAGCTAAAAATATAATTCGGTTGCCACGCTTCGG--AA--------AGAGAATTA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...................................................GTGGTGGTA------------xGTGGGTGGG---.............................................................................................................................................................................................................................	18	1	78.00	6.00	72.00	0.00	0.00
.........................................................GTG------------GGTGGGTGGG---G---------ATGG...............................................................................................................................................................................................................	18	1	78.00	2.00	76.00	0.00	0.00
..................................................GGTGGTGGGT------------GGTGGGTG..................................................................................................................................................................................................................................	18	1	71.00	0.00	70.00	1.00	0.00
...................................................GTGGTGGTA------------xGTGGGTGGG---A---------...................................................................................................................................................................................................................	19	1	65.00	11.00	54.00	0.00	0.00
................................................GTGGTGGTGGTG------------GGTGGG....................................................................................................................................................................................................................................	18	1	62.00	0.00	62.00	0.00	0.00
................................................GTGGTGGTGGTG------------GGTGGGT...................................................................................................................................................................................................................................	19	1	46.00	0.00	46.00	0.00	0.00
...................................................GAGGTGGTA------------GGTGGGTGGG---T---------G..................................................................................................................................................................................................................	21	1	32.00	3.00	29.00	0.00	0.00
...................................................GTGGTGGTx------------GGTGGGCGGG---.............................................................................................................................................................................................................................	18	1	30.00	0.00	30.00	0.00	0.00
...................................................GTGGTGGTx------------GGTGGGCGGG---G---------G..................................................................................................................................................................................................................	20	1	29.00	0.00	29.00	0.00	0.00
...................................................GTGGTGGTx------------GGTGGGTGGG---G---------A..................................................................................................................................................................................................................	20	1	27.00	2.00	25.00	0.00	0.00
...................................................GTGGTGGTx------------GGTGGGTGGG---G---------...................................................................................................................................................................................................................	19	1	16.00	1.00	15.00	0.00	0.00
......................................................GTGGTx------------GGTGGGTGGG---G---------AT.................................................................................................................................................................................................................	18	1	13.00	0.00	13.00	0.00	0.00
...................................................GTGGTGGTx------------GGTGGGCGGG---G---------...................................................................................................................................................................................................................	19	1	10.00	0.00	10.00	0.00	0.00
...................................................GAGGTGGTA------------GGTGGGTGGG---T---------...................................................................................................................................................................................................................	20	1	9.00	0.00	9.00	0.00	0.00
.....................................................GGTGGTG------------GGTGGGTGGT---G---------...................................................................................................................................................................................................................	18	1	8.00	0.00	8.00	0.00	0.00
...................................................GTGGTGGTx------------GGTGGGTGGG---G---------AT.................................................................................................................................................................................................................	21	1	8.00	0.00	8.00	0.00	0.00
......................................................GTGGGA------------GGTGGGTGGG---G---------T..................................................................................................................................................................................................................	18	1	8.00	1.00	7.00	0.00	0.00
...................................................GTGGTGGCA------------xGTGGGTGGG---.............................................................................................................................................................................................................................	18	3	2.67	0.00	2.67	0.00	0.00
...................................................GTGGTGGTG------------GGTGGGTGGA---.............................................................................................................................................................................................................................	19	1	7.00	0.00	7.00	0.00	0.00
...................................................GAGGTGGTA------------GGTGGGTGGG---.............................................................................................................................................................................................................................	19	1	7.00	0.00	7.00	0.00	0.00
......................................................GTGGTG------------GGTGGGTGGT---G---------G..................................................................................................................................................................................................................	18	1	7.00	0.00	7.00	0.00	0.00
...................................................GTGGTGGTA------------xGTGGGTTGG---G---------...................................................................................................................................................................................................................	19	1	6.00	0.00	6.00	0.00	0.00
...................................................GTGGTGGTG------------GGTGGGTGG.................................................................................................................................................................................................................................	18	1	5.00	0.00	5.00	0.00	0.00
.....................................................GGTGGTC------------GGTGGGTGGG---T---------...................................................................................................................................................................................................................	18	1	5.00	0.00	5.00	0.00	0.00
.......................................................TGGGA------------xGTGGGTGGG---G---------GTGG...............................................................................................................................................................................................................	19	2	2.50	0.00	2.50	0.00	0.00
.........................................................GTG------------GGTGGGTGGT---G---------GTGG...............................................................................................................................................................................................................	18	1	5.00	0.00	5.00	0.00	0.00
.........................................................GTG------------GGTGGGTxxG---G---------GTGGTG.............................................................................................................................................................................................................	18	1	5.00	0.00	5.00	0.00	0.00
...................................................GTGGTGGTA------------xGTGGGTGGT---G---------G..................................................................................................................................................................................................................	20	1	5.00	0.00	5.00	0.00	0.00
.....................................................GGTGGTx------------GGTGGGTGGG---G---------A..................................................................................................................................................................................................................	18	1	5.00	1.00	4.00	0.00	0.00
...................................................GTGGTGGTT------------GGTGGGTGGG---T---------...................................................................................................................................................................................................................	20	1	5.00	0.00	5.00	0.00	0.00
......................................................GTGGTA------------GGTGGGTxxG---G---------GTGGTG.............................................................................................................................................................................................................	21	2	2.50	0.50	2.00	0.00	0.00
...............................................GGGGGTGGTGGTx------------GGTGGGT...................................................................................................................................................................................................................................	19	1	4.00	0.00	4.00	0.00	0.00
...................................................GTGGTGGTC------------GGTGGGTGGG---T---------...................................................................................................................................................................................................................	20	1	4.00	1.00	3.00	0.00	0.00
.........................................................................GTGGGTGGT---G---------GTGGTGGAT..........................................................................................................................................................................................................	19	1	4.00	0.00	4.00	0.00	0.00
...................................................GTGGTGGTA------------xGTGGGTGGG---T---------...................................................................................................................................................................................................................	19	1	4.00	0.00	4.00	0.00	0.00
...................................................GTGGTGGTA------------GGTGGGTGGG---G---------G..................................................................................................................................................................................................................	21	1	4.00	0.00	4.00	0.00	0.00
...................................................GTGGTGGTx------------GGTGGGTGGG---A---------...................................................................................................................................................................................................................	19	2	2.00	0.00	2.00	0.00	0.00
.........................................................GTG------------GGTGGGTGGT---G---------GTGGT..............................................................................................................................................................................................................	19	1	3.00	0.00	3.00	0.00	0.00
......................................................GTGGGA------------GGTGGGTGGG---G---------G..................................................................................................................................................................................................................	18	1	3.00	0.00	3.00	0.00	0.00
..........................................................................TGGGxGGG---G---------GTGGTGCATG.........................................................................................................................................................................................................	18	1	3.00	0.00	1.00	2.00	0.00
.....................................................GTTGGTT------------GGTGGGTGGG---G---------...................................................................................................................................................................................................................	18	1	3.00	0.00	3.00	0.00	0.00
...................................................GTGGTGGTx------------GGTGGGTGGT---.............................................................................................................................................................................................................................	18	4	0.75	0.00	0.75	0.00	0.00
..................................................GGTGGTGGGA------------GGTGGGAG..................................................................................................................................................................................................................................	18	1	3.00	0.00	3.00	0.00	0.00
..................................................GGTGGTGGTG------------GGTGGGTG..................................................................................................................................................................................................................................	18	1	3.00	0.00	3.00	0.00	0.00
..................................................AGTGGTGGTA------------xGTGGGTGGG---.............................................................................................................................................................................................................................	19	1	3.00	0.00	3.00	0.00	0.00
...................................................GTGGTGGTG------------GTTGGGTGGG---.............................................................................................................................................................................................................................	19	1	3.00	0.00	3.00	0.00	0.00

droBip1

TGGGGGCAG-GTGGTGGTACC-----TCCCAGGGGGG----------------------------------GTATGTA---GGGGG---------CC-----------------TGTGTGTGGCTTTCCGCTTCTG------------CC----T-------------TTTCTTTTTCTTTCTATA-TATAT-------------T--T-T-TTTTTGGGAG-----GGTTCA--CTGG---AAATTCGGCGAGCTAAAAATAGAATTCGGTTGCCACGCTTCAA------------AGAGAATTA

Size

Hit Count

Total Norm

dp4

TGTGTG-TGTG------TGTC-----TGTGT----GTGTGTGTGTGTGTGTGTGTGTGT---------------GGCAGGGTGACAGCACTCTCTCT----------------------AAGGCTTTCCGCTTTTC------------GT----TCTCT-------------T-TTTGTTGTT-------GT----------TGTTCTT-T-CT-----TTC-----GTTTTG--GTGGAAATTTTCGTTGTATCTAAAAATAGACTTT-----TTGGGGTTCAAAGGAAATTTTGTGGGACAAAA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..TGTG-TGTG------TGTG-----TGTGT----GTGTGTG........................................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
..........................TGTGT----GTGTGTGTGTGTGTGTGTG............................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
...................TG-----TGTGT----GTGTGTGTGTGTGTGTG..............................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
............................TGT----GTGTGTGTGTGTGTGTGTGTG..........................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
.........TG------TGTG-----TGTGT----GTGTGTGTGTGTG..................................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
TGTGTG-TGTG------TGTG-----TGTGT----GTGTG..........................................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
..............................T----GTGTGTGTGTGTGTGTGTGTGTG........................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
....................................TGTGTGTGTGTGTGTGTGTGTGT---------------G.......................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
.................TGTG-----TGTGT----GTGTGTGTGTGTGTG................................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
.......TGTG------TGTG-----TGTGT----GTGTGTGTGTG....................................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
....TG-TGTG------TGTG-----TGTGT----GTGTGTGTG......................................................................................................................................................................................................................................................................	24	35	0.71	0.11	0.00	0.60	0.00
...GTG-TGTG------TGTG-----TGTGT----GTGTGTGTG......................................................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
...........................GTGT----GTGTGTGTGTGTGTGTGTGTG..........................................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
.............................GT----GTGTGTGTGTGTGTGTGTGTGTG........................................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
.GTGTG-TGTG------TGTG-----TGTGT----GTGTGTG........................................................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
.....G-TGTG------TGTG-----TGTGT----GTGTGTGTGTG....................................................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
........GTG------TGTG-----TGTGT----GTGTGTGTGTGTG..................................................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
...................................GTGTGTGTGTGTGTGTGTGTGTGT---------------G.......................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
..................GTG-----TGTGT----GTGTGTGTGTGTGTGTG..............................................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
..........G------TGTG-----TGTGT----GTGTGTGTGTGTGTG................................................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
....................G-----TGTGT----GTGTGTGTGTGTGTGTGTG............................................................................................................................................................................................................................................................	25	28	0.29	0.04	0.00	0.25	0.00
..TGTG-TGTG------TGTG-----TGTGT----GTGTGTGT.......................................................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
.....G-TGTG------TGTG-----TGTGT----GTGTGTGTG......................................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
.........TG------TGTG-----TGTGT----GTGTGTGTGTGTGT.................................................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
.GTGTG-TGTG------TGTG-----TGTGT----GTGTG..........................................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
.....................................GTGTGTGTGTGTGTGTGTGTGT---------------G.......................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
...................................GTGTGTGTGTGTGTGTGTGTGTG........................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
...GTG-TGTG------TGTG-----TGTGT----GTGTGTG........................................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
............................TGT----GTGTGTGTGTGTGTGTGTGTGT.........................................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
...................TG-----TGTGT----GTGTGTGTGTGTGTGTGT.............................................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
.............................GT----GTGTGTGTGTGTGTGTGTGTG..........................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
.................TGTG-----TGTGT----GTGTGTGTGTGTGTGT...............................................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
....................................TGTGTGTGTGTGTGTGTGTGTGT---------------GT......................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
..........................TGTGT----GTGTGTGTGTGTGTGTGTGT...........................................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
....TG-TGTG------TGTG-----TGTGT----GTGTGTGTGT.....................................................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
....................G-----TGTGT----GTGTGTGTGTGTGTGTG..............................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
........GTG------TGTG-----TGTGT----GTGTGTGTGTG....................................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
TGTGTG-TGTG------TGTG-----TGTGT----GTGTGT.........................................................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
..........G------TGTG-----TGTGT----GTGTGTGTGTGTG..................................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
...........................GTGT----GTGTGTGTGTGTGTGTGTG............................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
..............................T----GTGTGTGTGTGTGTGTGTGTGTGT---------------........................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
.......TGTG------TGTG-----TGTGT----GTGTGTGTGTGT...................................................................................................................................................................................................................................................................	25	27	0.22	0.04	0.00	0.19	0.00
..................GTG-----TGTGT----GTGTGTGTGTGTGTG................................................................................................................................................................................................................................................................	23	41	0.15	0.00	0.00	0.15	0.00
.............................GT----ACGTGTGTGTGTGTGTG..............................................................................................................................................................................................................................................................	19	46	0.11	0.04	0.04	0.02	0.00
.......TGTG------TGTG-----TGTGT----GTGTGTGTGTGTG..................................................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
.................TGTG-----TGTGT----GTGTGTGTGTGTGTGTG..............................................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
..............................T----GTGTGTGTGTGTGTGTGTGTGTGT---------------G.......................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
...................................GTACGTGTGTGTGTGTGTG............................................................................................................................................................................................................................................................	19	46	0.11	0.04	0.04	0.02	0.00
.....................................GTACGTGTGTGTGTGTGTG..........................................................................................................................................................................................................................................................	19	46	0.11	0.04	0.04	0.02	0.00
.........................................GTACGTGTGTGTGTGTGT---------------G.......................................................................................................................................................................................................................................	19	46	0.11	0.04	0.04	0.02	0.00
TGTGTG-TGTG------TGTG-----TGTGT----GTGTGTG........................................................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
..........................TGTGT----GTGTGTGTGTGTGTGTGTGTG..........................................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
...........................GTAC----GTGTGTGTGTGTGTG................................................................................................................................................................................................................................................................	19	46	0.11	0.04	0.04	0.02	0.00
..TGTG-TGTG------TGTG-----TGTGT----GTGTGTGTG......................................................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
...................TG-----TGTGT----GTGTGTGTGTGTGTGTGTG............................................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
............................TGT----GTGTGTGTGTGTGTGTGTGTGTG........................................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
.......................................GTACGTGTGTGTGTGTGTG........................................................................................................................................................................................................................................................	19	46	0.11	0.04	0.04	0.02	0.00
..................GTA-----CGTGT----GTGTGTGTGTG....................................................................................................................................................................................................................................................................	19	46	0.11	0.04	0.04	0.02	0.00
....TG-TGTG------TGTG-----TGTGT----GTGTGTGTGTG....................................................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
.........TG------TGTG-----TGTGT----GTGTGTGTGTGTGTG................................................................................................................................................................................................................................................................	26	22	0.23	0.00	0.00	0.23	0.00
....................................TGTGTGTGTGTGTGTGTGTGTGT---------------T.......................................................................................................................................................................................................................................	24	17	0.24	0.00	0.06	0.18	0.00
............................TGT----GTGTGTGTGTGTGTGTGTGTT..........................................................................................................................................................................................................................................................	24	17	0.24	0.00	0.06	0.18	0.00
..............................T----GTGTGTGTGTGTGTGTGTGTGTT........................................................................................................................................................................................................................................................	24	17	0.24	0.00	0.06	0.18	0.00
...................TG-----TGTGT----GTGTGTGTGTGTGTG................................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
.........TG------TGTG-----TGTGT----GTGTGTGTGTG....................................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
........GTC------TGTC-----TGTGT----GTGTATGTG......................................................................................................................................................................................................................................................................	21	4	1.00	0.75	0.00	0.25	0.00
............................TGT----GTGTGTGTGTGTGTGTGTG............................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
......................................TGTGTGTGTGTGTGTGTGTGT---------------G.......................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
..TGTG-TGTG------TGTG-----TGTGT----GTGTG..........................................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
TGTGTG-TGTG------TGTG-----TGTGT----GTG............................................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
..................GTC-----TGTCT----GTGTGTGTATGTG..................................................................................................................................................................................................................................................................	21	4	1.00	0.75	0.00	0.25	0.00
..........................TGTGT----GTGTGTGTGTGTGTGTGTT............................................................................................................................................................................................................................................................	24	17	0.24	0.00	0.06	0.18	0.00
.................TGTG-----TGTGT----GTGTGTGTGTGTG..................................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
..................GTC-----TGTCT----GTGTGTGTATG....................................................................................................................................................................................................................................................................	19	6	0.67	0.67	0.00	0.00	0.00
..............................T----GTGTGTGTGTGTGTGTGTGTG..........................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
..........................TGTGT----GTGTGTGTGTGTGTGTG..............................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
....TG-TGTG------TGTG-----TGTGT----GTGTGTG........................................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
....................................TGTGTGTGTGTGTGTGTGTGTG........................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
.......TGTG------TGTG-----TGTGT----GTGTGTGTG......................................................................................................................................................................................................................................................................	22	49	0.08	0.00	0.00	0.08	0.00
........GTC------TGTC-----TGTGT----GTGTATG........................................................................................................................................................................................................................................................................	19	6	0.67	0.67	0.00	0.00	0.00
...................................GTGTGTGTGTGTGTGTGTGTGTGT---------------GG......................................................................................................................................................................................................................................	26	9	0.33	0.22	0.00	0.11	0.00
..........................................TTTGTGTGTGTGTGTGT---------------G.......................................................................................................................................................................................................................................	18	49	0.06	0.02	0.02	0.02	0.00
...........................GTGT----GTGTGTGTGTGTGTGTGTGTGG.........................................................................................................................................................................................................................................................	26	9	0.33	0.22	0.00	0.11	0.00
........GTC------TGTC-----TGTGT----GTGTATGT.......................................................................................................................................................................................................................................................................	20	4	0.75	0.75	0.00	0.00	0.00
..........................TTTGT----GTGTGTGTGTGTG..................................................................................................................................................................................................................................................................	18	49	0.06	0.02	0.02	0.02	0.00
...................TT-----TGTGT----GTGTGTGTGTG....................................................................................................................................................................................................................................................................	18	49	0.06	0.02	0.02	0.02	0.00
..............................T----TTGTGTGTGTGTGTGTG..............................................................................................................................................................................................................................................................	18	49	0.06	0.02	0.02	0.02	0.00
......................................TTTGTGTGTGTGTGTGTG..........................................................................................................................................................................................................................................................	18	49	0.06	0.02	0.02	0.02	0.00
..........................TGTGT----GTGTGTGTGTGTGT.................................................................................................................................................................................................................................................................	19	35	0.09	0.03	0.00	0.06	0.00
...................TC-----TGTGT----GTGTATGTGTGTT..................................................................................................................................................................................................................................................................	20	6	0.50	0.50	0.00	0.00	0.00
..................GTC-----TGTCT----GTGTGTGTATGT...................................................................................................................................................................................................................................................................	20	4	0.75	0.75	0.00	0.00	0.00
.............................GT----GTGTGTGTGTGTGTGTGTGTGTGG---------------........................................................................................................................................................................................................................................	26	9	0.33	0.22	0.00	0.11	0.00
........................................TGTGTGTGTGTGTGTGTGT---------------........................................................................................................................................................................................................................................	19	35	0.09	0.03	0.00	0.06	0.00
......................................TGTGTGTGTGTGTGTGTGT.........................................................................................................................................................................................................................................................	19	35	0.09	0.03	0.00	0.06	0.00
....................................TGTGTGTGTGTGTGTGTGT...........................................................................................................................................................................................................................................................	19	35	0.09	0.03	0.00	0.06	0.00
............................TTT----GTGTGTGTGTGTGTG................................................................................................................................................................................................................................................................	18	49	0.06	0.02	0.02	0.02	0.00
....................................TTTGTGTGTGTGTGTGTG............................................................................................................................................................................................................................................................	18	49	0.06	0.02	0.02	0.02	0.00
............................TGT----GTGTGTGTGTGTGTGT...............................................................................................................................................................................................................................................................	19	35	0.09	0.03	0.00	0.06	0.00
..............................T----GTGTGTGTGTGTGTGTGT.............................................................................................................................................................................................................................................................	19	35	0.09	0.03	0.00	0.06	0.00
........................................TTTGTGTGTGTGTGTGTG........................................................................................................................................................................................................................................................	18	49	0.06	0.02	0.02	0.02	0.00

droPer1

TACGGG-TGTG------AGAC-----TG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TATGGC-GATA------TTTTGTAGGTTTTG----G----------------------------------------C----AATGG---------TT----------------------GTGGCTTTCCGCTTCTATTCAGTCGCACGAAAAATTTTCTCGGTTTTT-------------------------------------------------------------------------------TCCCATGTCTAAAAATAGATTTA------CACCCAAAGT--A-------GAAAAACATAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................TTTTG----G----------------------------------------C----ATTGG---------CT----------------------GTGGC......................................................................................................................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
............................GTG----G----------------------------------------C----AATGG---------TG----------------------GTGGCT.....................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................ATTTTCTCGGTTTTT-------------------------------------------------------------------------------GCT.........................................................	18	1	1.00	0.00	0.00	0.00	1.00
............................................................................C----AATGG---------TC----------------------GTGGCATTCC.................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................................................................................................................AAAAT--A-------GAAAAACAGAA	18	13	0.08	0.00	0.08	0.00	0.00
...........................TTTG----G----------------------------------------C----ATTGG---------CT----------------------GTGGC......................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droVir3

GTTC--------------------------------------------------------------------------------------------------------------------------TGCGCTAGCT------------TG----T-------------TCGGTT--------T-------GG----------TAACATG-A----------------GCTTCA--TTAG---TGTATGCAATAATGGCAAACATTTTTTGCCTGCCAGGCCTCGGCGAGGAC---GATGACGACGA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.........................................................................................................................................................................................................................................................................................TCGGCGGGGAC---GATGATGAC..	20	1	5.00	2.00	2.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................GATGAC---GACGACGACGA	18	25	0.16	0.00	0.00	0.04	0.12	0.00
..........................................................................................................................................................................................................................................................................................CGGCGGGGAC---GATGATGAC..	19	1	3.00	2.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................................................................................................................TCGGCGGGGAC---GATGATGACG.	21	1	3.00	0.00	3.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................................................................GCGGGGAC---GATGATGACG.	18	1	2.00	0.00	1.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................GGCGGGGAC---GATGATGACG.	19	1	2.00	0.00	1.00	1.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................CGATGAC---GAGGACGACGA	19	5	0.40	0.00	0.00	0.20	0.20	0.00
..........................................................................................................................................................................................................................................................................................CGGCGGGGAC---GATGATGACG.	20	1	2.00	2.00	0.00	0.00	0.00	0.00
....................................................................................................................................AGCT------------TG----T-------------TxGGTG--------T-------GG----------TAA.....................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................GGCGGGGAC---GATGATGAC..	18	1	1.00	0.00	1.00	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................CGGCGAGGAC---GATGATTAC..	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................CGACGATGAC---GATGACGACGA	21	5	0.20	0.20	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................GATGAC---GATGATGACGA	18	15	0.07	0.00	0.00	0.00	0.07	0.00
.........................................................................................................................................................................................................................................................................................TCGGCGGGGAC---GATGATG....	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................CGAGGAC---GAGGAGGACGA	18	4	0.25	0.00	0.00	0.00	0.00	0.25
............................................................................................................................................................................................................................................................................................GCGGGGAC---GATGACGACG.	18	3	0.33	0.00	0.33	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................GACGATGAC---GATGACGACGA	20	9	0.11	0.00	0.00	0.00	0.11	0.00
..TC--------------------------------------------------------------------------------------------------------------------------CGCCCTAGCT------------TG----T-------------TCG.......................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................................................................GCT------------TG----T-------------TxGGTT--------G-------GG----------TAAC....................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................GACGAC---GATGACGACGA	18	22	0.05	0.00	0.00	0.00	0.05	0.00
..............................................................................................................................................................................................................................................................................................GACGAC---GATGATGACGA	18	14	0.07	0.00	0.00	0.00	0.07	0.00
..........................................................................................................................................................................................................................................................................................CGGCGGGGAC---GATGATGA...	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

TGCAAC-ATTG------ATGA-----AA--------------------------------------------TATGCATAATGAAAATGTGCCCTC-----------------------AGAGTTATCCACGATTT------------TT----CTACT----TTTTTTTTAT------------------------------ACCCTGAAC-------CCA-----TTTTCA--ATGG---GAAATCAGGGTATAA------TGGTTTTGTTGAAATGTATGTAAC----------AGGGAGAAG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTTT.....................................	24	7	29.14	15.00	0.00	0.14	14.00
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTT......................................	23	7	6.57	4.86	0.00	0.29	1.43
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTTTT....................................	25	7	5.43	4.00	0.00	0.14	1.29
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGT.......................................	22	7	4.14	3.14	0.00	0.00	1.00
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTTTTG...................................	26	7	3.43	3.14	0.14	0.00	0.14
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGG........................................	21	7	3.14	2.43	0.00	0.00	0.71
.............................................................................................................................................................................................................................A-----TTTTCA--ATGG---GAAATCAGGGT.....................................................	22	5	3.00	2.80	0.20	0.00	0.00
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTC......................................	23	7	2.00	1.86	0.00	0.00	0.14
...........................................................................................................................................................................................................................................ATGG---GAAATCAGGGTATAA------TGGTTT.....................................	25	7	1.86	1.43	0.00	0.00	0.43
.......................................................................................................................................................................................................................................................................................TATGTAAC----------AGGGAGAAG	21	6	2.00	2.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................TGG---GAAATCAGAGTATAA------TGGTTT.....................................	24	7	1.71	1.14	0.00	0.00	0.57
............................................................................................................................................................................................................................................TGG---GAAATCAGTGTATAA------TGGTTT.....................................	24	7	1.57	0.86	0.00	0.00	0.71
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTTC.....................................	24	7	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................................................................................A--ATGG---GAAATCAGGGTATAA------T..........................................	21	8	0.88	0.88	0.00	0.00	0.00
...........................................................................................................................................................................................................................CCA-----TTTTCA--ATGG---GAAATCAGGGT.....................................................	24	4	1.75	1.75	0.00	0.00	0.00
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATTA------TGGTTT.....................................	24	7	1.00	0.71	0.00	0.00	0.29
.....................................................................................................................................................................................................................................TTCA--ATGG---GAAATCAGGGTATAA------TGG........................................	26	4	1.50	1.25	0.00	0.00	0.25
.....................................................................................................................................................................................................................................................................................TGTATGTAAC----------AGGGAGAAG	21	6	0.83	0.67	0.00	0.17	0.00
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTTTTGTC.................................	28	7	0.71	0.71	0.00	0.00	0.00
...........................................................................................................................................................................................................................................ATGG---GAAATCAGGGTATAA------TG.........................................	21	7	0.71	0.43	0.29	0.00	0.00
...............................................................................................................................................................................................................................................................................TTGAAATGTATGTAAC----------AGGGA....	21	4	1.25	1.25	0.00	0.00	0.00
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTGTAA------TGGTTT.....................................	24	7	0.57	0.14	0.00	0.00	0.43
............................................................................................................................................................................................................................................TGG---GAAATCAGAGTATAA------TGGTTTT....................................	25	7	0.57	0.57	0.00	0.00	0.00
...........................................................................................................................................................................................................................................ATGG---GAAATCAGGGTATAA------TGG........................................	22	7	0.57	0.57	0.00	0.00	0.00
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTTTTGC..................................	27	7	0.57	0.57	0.00	0.00	0.00
....................................................................................................................................................................................................................................TTTCA--ATGG---GAAATCAGGGTA....................................................	21	5	0.80	0.60	0.20	0.00	0.00
............................................................................................................................................................................................................................................TGG---GAAATCAGAGTATTA------TGGTTT.....................................	24	6	0.50	0.33	0.00	0.00	0.17
............................................................................................................................................................................................................................................CGG---GAAATCAGGGTATAA------TGGTTT.....................................	24	7	0.43	0.14	0.00	0.00	0.29
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TG.........................................	20	7	0.43	0.29	0.00	0.00	0.14
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTTTC....................................	25	7	0.43	0.43	0.00	0.00	0.00
.....................................................................................................................................................................................................................................TTCA--ATGG---GAAATCAGCGTATAA------TGG........................................	26	4	0.75	0.75	0.00	0.00	0.00
........................................................................................................................................................................................................................................A--ATGG---GAAATCAGGGTATAA------TGGTTT.....................................	26	7	0.43	0.29	0.00	0.14	0.00
...................................................................................................................................................................................................................................TTTTCA--ATGG---GAAATCAGGGT.....................................................	21	5	0.60	0.20	0.20	0.00	0.20
....................................................................................................................................................................................................................................................................................ATGTATGTAAC----------AGGGAGAAG	21	6	0.50	0.50	0.00	0.00	0.00
.............................................................................................................................................................................................................................A-----TTTTCA--ATGG---GAAATCAGGG......................................................	21	5	0.60	0.60	0.00	0.00	0.00
............................................................................................................................................................................................................................CA-----TTTTCA--ATGG---GAAATCAGGGT.....................................................	23	4	0.75	0.75	0.00	0.00	0.00
........................................................................................................................................................................................................................................A--ATGG---GAAATCAGGGTATAA------TGGTTC.....................................	26	7	0.43	0.43	0.00	0.00	0.00
......................................................................................................................................................................................................................................................................................GTATGTAAC----------AGGGAGAAG	21	7	0.43	0.29	0.00	0.14	0.00
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGTTTTA...................................	26	7	0.43	0.14	0.00	0.14	0.14
........................................................................................................................................................................................................................................A--ATGG---GAAATCAGGGTATAA------TG.........................................	22	7	0.43	0.14	0.00	0.14	0.14
.......................................................................................................................................................................................................................................................CAGGGTATAA------TGGTTTTGTTG................................	21	5	0.60	0.40	0.00	0.20	0.00
.............................................................................................................................................................................................................................................................ATAA------TGGTTTTGTTGAAATGT..........................	21	5	0.60	0.60	0.00	0.00	0.00
...........................................................................................................................................................................................................................................ATGG---GAAATCAGGGTATAA------TGGT.......................................	23	7	0.43	0.43	0.00	0.00	0.00
............................................................................................................................................................................................................................................TGG---GAAATCAGGGTATAA------TGGGTTTG...................................	26	7	0.43	0.00	0.00	0.00	0.43
..........................................................................................................................................................................................................................................................................................GTAAC----------AGGGAGAAG	19	6	0.50	0.33	0.17	0.00	0.00

droGri2

CAGAAT-AATA------GAAT-----G-----------------------------------------------TACTCACTTCAG---------CT----------------------ATGGCATACAGATTTGC------------TT----TATTT-------------G---------C-------TT----------TTCGTTG-T----------------------------------------------------ACTTTCTGTTTTCTCAATGTACATGAAAA---AGACTGAATTT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:31:16 EDT

dme-mir-2282

chr3L:3412145-3412251 -

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