sblock26534- Best orthologs

sblock26534	chr2L:12284769-12284877 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 12284832-12284853
   star strand at position 12284794-12284816
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:12284754-12284892 +		1	AAA----------AGTTCCTTGCGC-CAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGATTGGTTTTCTT-TTTGAT-------------T---------TTCGTTCGCCATAG--GTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTCTA
droSim1	chr2L:12084763-12084872 +	LASTZ	4	AAA----------AGTTCCTTGCGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGAT----------------------------------------------------AG--ATATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTGTA
droSec1	super_16:474625-474734 +	LASTZ	5	AAA----------AGTTCCTTGCGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTGTGAT----------------------------------------------------AG--ATATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TGGA------------------------------CT-GCGGTGTA
droYak2	chr2L:8714891-8715022 +	LASTZ	3	AAA----------AGTTCTTTTCGC-AAAAGTG--TTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCAGATTGGTTTACTT-TTC----------------T-----CCTTTG------CCATAG--GTTTTGTTATTCTC---------GATTCT-------------------------------------------------------------------------TCGA------------------------------CT-GCCTTGTA
droEre2	scaffold_4929:13133063-13133194 -	LASTZ	3	AAC----------AGTTCTTTTCGC-AAAAGTG--TTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGAACAA-------CCCTCAGATTGGTTTTCTT-TTG----------------C-----CCCTTG------CCATAG--GTATAGTTATTCTC---------GATTCC-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTGTA
droEug1	scf7180000409122:667028-667164 +	LASTZ	4	AAA----------GTTTTCTTTTGC-GAAAGTG--TTGCATACTTTTCGGCTGGCGGAAA------------------TCGCTA-AAGAGAACAA--C----CCCTCTGATTGGTTTTCTT-TCT----------------T-TGTTCTTTTG------CCATTG--CTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TAGA------------------------------CT-GGTTTTTT
droBia1	scf7180000302422:707901-708031 -	LASTZ	4	AAA----------AGTTG--TTCGC-AAAAGTG--TTGCATACTTT-TGGGAGGCGGAAA------------------TCGCTA-AAGAGAACAA-------CCCTCTGATTGGTTTTCTT-TTC----------------CCT---ACTTTT------CTACTG--CTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TAGA------------------------------CT-GGGCTGTA
droTak1	scf7180000415865:331344-331479 -	LASTZ	4	CAA----------AGTTTTTTCCAC-AAAAGTG--TTGCATACTTTTTGGGAGGCGGAAA------------------TCGCTA-AAGAGGACAG--CAA--CCCCCTGATTGGTTTCCCTTTTC----------------T-----CTTTTC------CTATTG--CTATTGTTATTTTT---------GATTCT-------------------------------------------------------------------------TCAA------------------------------CT-GGGCTGTA
droEle1	scf7180000491028:2849763-2849871 -	LASTZ	4	AAA----------AGTTTC-ATTGC-AAAAGAG--TGGCAT---TTTAGGCAGGCGGATA------------------TCGCTA-GAGAGGAAAA-------A------ATTGTTTTTCTT-TT-------------------------TTTG------CTATAA--CTATTGTTTTTCTT---------GATTCT-------------------------------------------------------------------------TATA------------------------------T----------
droRho1	scf7180000780043:108180-108289 +	LASTZ	4	AAA----------AGTTGT-TTCGC-AAAAGTG--TTGCATATTTTTTGGCAGGCGGATA------------------TCGATA-AAGAGGACAA-------CCTTCTT---------C---TTC----------------T-----CTTTTG------CTATTG--CTAATGATATTCT--------------------------------------------------------------------------------------------A------------------------------CT-GTAATTTA
droFic1	scf7180000454015:137236-137368 +	LASTZ	4	AAA----------GTTTTCCTTCGC-AAAAGTG--TTGCATACTT-TTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGATTGGTTTTCTT-TTT----------------C-----TTTTTG------CTGTTCCTCTATTCTTATTTTC---------GATTCG-------------------------------------------------------------------------TCGT------------------------------CT-GTGGTGTA
droKik1	scf7180000301476:370791-370905 +	LASTZ	4	CGT----------TTTACCACCCAC-CAAAGTG--TTGCATACTTTTTGG-------------------------------CTA-AGAAGGACAA-------ACCTCTGATTGGTTTTCTT-TGG----------------CCT---CGT------------TCG--ACATTGTTATTCCT---------GATTCT-------------------------------------------------------------------------TCGA------------------------------CT-GGGGTGTA
droAna3	scaffold_12916:13110146-13110270 -	LASTZ	5	ACC----------CGTTTG-CCTGC-AAAAGTG--TTGCATACTTTTTGGCAGGCTAAC-------------------G--------GGGGACAG--ACCTCCCCTGCGATTGGTTTTCTT-CTC----------------T---------TT------CATCCG--CCATTGTTATTCCT---------GATTCG-------------------------------------------------------------------------GAGA------------------------------GTCGCATTCGA
droBip1	scf7180000396580:411008-411118 +	LASTZ	4	ACC----------CGTTTT-CCGGC-AAAAGTG--TTGCATACTTTTTGGCAGGC---------------------------TA-ACG-GGACAG-------ACCTCCGATTGGTTTTCTT-TTC----------------T---------TT------CATCCG--CCATTGTTATTCCT---------GATTCG-------------------------------------------------------------------------GGGA------------------------------AT-------CA
dp4	chr4_group3:5836352-5836516 -	LASTZ	1	GAG----------TGT------CGC-AAAAGTG--TTGCATACTTTTTGGCAGGCAGCAA------------------T-GCTA-AAGAGGGCAG--A----GCCTTTGATTGGTTTTTCT-TTGGGCTCGGGGCTCCCAC---GT-TCTGTG------GCATTG--CTATTGTTATTCCTGGCAGACCG------AGAGAGAG--AGAG--AGC-------------------------------------------------AGGCTTGGC------------------------------CT--TCTTCTT
droPer1	super_1:7324752-7324918 -	LASTZ	1	GAG----------TGT------CGC-AAAAGTG--TTGCATACTTTTTGGCAGGCAGCAA------------------T-GCTA-AAGAGGACAG--A----GCCTTTGATTGGTTTTTCC-TTGGGCTCGGGGCTCCCAC---GT-TCTTTG------GCATTG--CTATTGTTATTCCTGGCAGACCG------AGAGAGAG--AGAGACAGC-------------------------------------------------AGGCATGGC------------------------------CT--TCTTCTT
droWil1	scaffold_180708:9979069-9979243 +	LASTZ	5	A---------------------------AAGTG--TAGCATACTTACTGGCAGGCAAAAG---------CA-------GTGCAG-AAGAAGCTGCCACAT--TTTTTAGATTGGTTTTACG-AGT----------------TT----TGTG--------TCCTTG--C--TTGTTATTGTT---TGACTG------AAT-------------------------------------------GGTTTATTTTGTATCCCGTTTT-----GAAAGGGTTCTTTTTTTTTTGGCTCTCGTCGCCCCC-GTGTTTGC
droVir3	scaffold_12963:17362502-17362582 +	LASTZ	5	CAG------------------------AAAGTG--TAGCATACTTTTTGGCAGTCG----TTGCCAAAGCAGCAGGCGGCGGCA-AGCAGAAGCA-------ACCTTTGATTGGTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:22410643-22410826 +	LASTZ	3	CTGCTCCTGCCGCTGCTGCTGTCGCAGAAAGTG--TAGCATACTTTTTGGCAGTCG----TCGCAAAAGCAGCAGGC---GGCAAGGCAGCAGCA-------ACCTTTGATTGGTTTTTGG-GTT----------------T-----TGTATG------CAGTGC--TTGTTGTTATTTTC---------AGTTTGGGCAAGGGCTAAGG--------------------------------GCTCCATT-----GAAG-----A-GCTTTG-------------------------------CA--GTTTCAA
droGri2	scaffold_15252:14795099-14795283 +	LASTZ	4	ACT----------GTTTCTCTGCTC-CTTGTCC--TTAGATACTTTTTGGCAGAGTTGCGTCGCC--------A----G-GCAA-AAGCAAAAGC--A----ACCTTTGATTGGTTTTTGG-GGT----------------T-----TCT-GT------CTGTCT--------CTCTGTCC---------GACTGT-CCGACTG--TCTC--CTCTGGTGTGGCTCTGTCTGCAATTGTGTTGTTTCATGTCGTTTAAGGGCTT-----CAAA------------------------------C----------

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	AAA----------AGTTCCTTGCGC-CAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGATTGGTTTTCTT-TTTGAT-------------T---------TTCGTTCGCCATAG--GTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTCTA
droSim1	AAA----------AGTTCCTTGCGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGAT----------------------------------------------------AG--ATATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTGTA
droSec1	AAA----------AGTTCCTTGCGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTGTGAT----------------------------------------------------AG--ATATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TGGA------------------------------CT-GCGGTGTA
droYak2	AAA----------AGTTCTTTTCGC-AAAAGTG--TTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCAGATTGGTTTACTT-TTC----------------T-----CCTTTG------CCATAG--GTTTTGTTATTCTC---------GATTCT-------------------------------------------------------------------------TCGA------------------------------CT-GCCTTGTA
droEre2	AAC----------AGTTCTTTTCGC-AAAAGTG--TTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGAACAA-------CCCTCAGATTGGTTTTCTT-TTG----------------C-----CCCTTG------CCATAG--GTATAGTTATTCTC---------GATTCC-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTGTA
droEug1	AAA----------GTTTTCTTTTGC-GAAAGTG--TTGCATACTTTTCGGCTGGCGGAAA------------------TCGCTA-AAGAGAACAA--C----CCCTCTGATTGGTTTTCTT-TCT----------------T-TGTTCTTTTG------CCATTG--CTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TAGA------------------------------CT-GGTTTTTT
droBia1	AAA----------AGTTG--TTCGC-AAAAGTG--TTGCATACTTT-TGGGAGGCGGAAA------------------TCGCTA-AAGAGAACAA-------CCCTCTGATTGGTTTTCTT-TTC----------------CCT---ACTTTT------CTACTG--CTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TAGA------------------------------CT-GGGCTGTA
droTak1	CAA----------AGTTTTTTCCAC-AAAAGTG--TTGCATACTTTTTGGGAGGCGGAAA------------------TCGCTA-AAGAGGACAG--CAA--CCCCCTGATTGGTTTCCCTTTTC----------------T-----CTTTTC------CTATTG--CTATTGTTATTTTT---------GATTCT-------------------------------------------------------------------------TCAA------------------------------CT-GGGCTGTA
droEle1	AAA----------AGTTTC-ATTGC-AAAAGAG--TGGCAT---TTTAGGCAGGCGGATA------------------TCGCTA-GAGAGGAAAA-------A------ATTGTTTTTCTT-TT-------------------------TTTG------CTATAA--CTATTGTTTTTCTT---------GATTCT-------------------------------------------------------------------------TATA------------------------------T----------
droRho1	AAA----------AGTTGT-TTCGC-AAAAGTG--TTGCATATTTTTTGGCAGGCGGATA------------------TCGATA-AAGAGGACAA-------CCTTCTT---------C---TTC----------------T-----CTTTTG------CTATTG--CTAATGATATTCT--------------------------------------------------------------------------------------------A------------------------------CT-GTAATTTA
droFic1	AAA----------GTTTTCCTTCGC-AAAAGTG--TTGCATACTT-TTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGATTGGTTTTCTT-TTT----------------C-----TTTTTG------CTGTTCCTCTATTCTTATTTTC---------GATTCG-------------------------------------------------------------------------TCGT------------------------------CT-GTGGTGTA
droKik1	CGT----------TTTACCACCCAC-CAAAGTG--TTGCATACTTTTTGG-------------------------------CTA-AGAAGGACAA-------ACCTCTGATTGGTTTTCTT-TGG----------------CCT---CGT------------TCG--ACATTGTTATTCCT---------GATTCT-------------------------------------------------------------------------TCGA------------------------------CT-GGGGTGTA
droAna3	ACC----------CGTTTG-CCTGC-AAAAGTG--TTGCATACTTTTTGGCAGGCTAAC-------------------G--------GGGGACAG--ACCTCCCCTGCGATTGGTTTTCTT-CTC----------------T---------TT------CATCCG--CCATTGTTATTCCT---------GATTCG-------------------------------------------------------------------------GAGA------------------------------GTCGCATTCGA
droBip1	ACC----------CGTTTT-CCGGC-AAAAGTG--TTGCATACTTTTTGGCAGGC---------------------------TA-ACG-GGACAG-------ACCTCCGATTGGTTTTCTT-TTC----------------T---------TT------CATCCG--CCATTGTTATTCCT---------GATTCG-------------------------------------------------------------------------GGGA------------------------------AT-------CA
dp4	GAG----------TGT------CGC-AAAAGTG--TTGCATACTTTTTGGCAGGCAGCAA------------------T-GCTA-AAGAGGGCAG--A----GCCTTTGATTGGTTTTTCT-TTGGGCTCGGGGCTCCCAC---GT-TCTGTG------GCATTG--CTATTGTTATTCCTGGCAGACCG------AGAGAGAG--AGAG--AGC-------------------------------------------------AGGCTTGGC------------------------------CT--TCTTCTT
droPer1	GAG----------TGT------CGC-AAAAGTG--TTGCATACTTTTTGGCAGGCAGCAA------------------T-GCTA-AAGAGGACAG--A----GCCTTTGATTGGTTTTTCC-TTGGGCTCGGGGCTCCCAC---GT-TCTTTG------GCATTG--CTATTGTTATTCCTGGCAGACCG------AGAGAGAG--AGAGACAGC-------------------------------------------------AGGCATGGC------------------------------CT--TCTTCTT
droWil1	A---------------------------AAGTG--TAGCATACTTACTGGCAGGCAAAAG---------CA-------GTGCAG-AAGAAGCTGCCACAT--TTTTTAGATTGGTTTTACG-AGT----------------TT----TGTG--------TCCTTG--C--TTGTTATTGTT---TGACTG------AAT-------------------------------------------GGTTTATTTTGTATCCCGTTTT-----GAAAGGGTTCTTTTTTTTTTGGCTCTCGTCGCCCCC-GTGTTTGC
droVir3	CAG------------------------AAAGTG--TAGCATACTTTTTGGCAGTCG----TTGCCAAAGCAGCAGGCGGCGGCA-AGCAGAAGCA-------ACCTTTGATTGGTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	CTGCTCCTGCCGCTGCTGCTGTCGCAGAAAGTG--TAGCATACTTTTTGGCAGTCG----TCGCAAAAGCAGCAGGC---GGCAAGGCAGCAGCA-------ACCTTTGATTGGTTTTTGG-GTT----------------T-----TGTATG------CAGTGC--TTGTTGTTATTTTC---------AGTTTGGGCAAGGGCTAAGG--------------------------------GCTCCATT-----GAAG-----A-GCTTTG-------------------------------CA--GTTTCAA
droGri2	ACT----------GTTTCTCTGCTC-CTTGTCC--TTAGATACTTTTTGGCAGAGTTGCGTCGCC--------A----G-GCAA-AAGCAAAAGC--A----ACCTTTGATTGGTTTTTGG-GGT----------------T-----TCT-GT------CTGTCT--------CTCTGTCC---------GACTGT-CCGACTG--TCTC--CTCTGGTGTGGCTCTGTCTGCAATTGTGTTGTTTCATGTCGTTTAAGGGCTT-----CAAA------------------------------C----------

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

AAA----------AGTTCCTTGCGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGAT----------------------------------------------------AG--ATATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTGTA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

AAA----------AGTTCCTTGCGC-AAAAGTGTGTTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTGTGAT----------------------------------------------------AG--ATATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TGGA------------------------------CT-GCGGTGTA

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

AAA----------AGTTCTTTTCGC-AAAAGTG--TTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCAGATTGGTTTACTT-TTC----------------T-----CCTTTG------CCATAG--GTTTTGTTATTCTC---------GATTCT-------------------------------------------------------------------------TCGA------------------------------CT-GCCTTGTA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................TTGCATACTTTTTGGCGCGC...................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

AAC----------AGTTCTTTTCGC-AAAAGTG--TTGCATACTTTTTGGCAGGCGGAAA------------------TCGCTA-AAGAGAACAA-------CCCTCAGATTGGTTTTCTT-TTG----------------C-----CCCTTG------CCATAG--GTATAGTTATTCTC---------GATTCC-------------------------------------------------------------------------TTGA------------------------------CT-GCGTTGTA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.............................................TTTGGCAGGCGGAAC------------------TGGC........................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droEug1

AAA----------GTTTTCTTTTGC-GAAAGTG--TTGCATACTTTTCGGCTGGCGGAAA------------------TCGCTA-AAGAGAACAA--C----CCCTCTGATTGGTTTTCTT-TCT----------------T-TGTTCTTTTG------CCATTG--CTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TAGA------------------------------CT-GGTTTTTT

Size

Hit Count

Total Norm

droBia1

AAA----------AGTTG--TTCGC-AAAAGTG--TTGCATACTTT-TGGGAGGCGGAAA------------------TCGCTA-AAGAGAACAA-------CCCTCTGATTGGTTTTCTT-TTC----------------CCT---ACTTTT------CTACTG--CTATTGTTATTCTT---------GATTCT-------------------------------------------------------------------------TAGA------------------------------CT-GGGCTGTA

Size

Hit Count

Total Norm

droTak1

CAA----------AGTTTTTTCCAC-AAAAGTG--TTGCATACTTTTTGGGAGGCGGAAA------------------TCGCTA-AAGAGGACAG--CAA--CCCCCTGATTGGTTTCCCTTTTC----------------T-----CTTTTC------CTATTG--CTATTGTTATTTTT---------GATTCT-------------------------------------------------------------------------TCAA------------------------------CT-GGGCTGTA

Size

Hit Count

Total Norm

droEle1

AAA----------AGTTTC-ATTGC-AAAAGAG--TGGCAT---TTTAGGCAGGCGGATA------------------TCGCTA-GAGAGGAAAA-------A------ATTGTTTTTCTT-TT-------------------------TTTG------CTATAA--CTATTGTTTTTCTT---------GATTCT-------------------------------------------------------------------------TATA------------------------------T----------

Size

Hit Count

Total Norm

droRho1

AAA----------AGTTGT-TTCGC-AAAAGTG--TTGCATATTTTTTGGCAGGCGGATA------------------TCGATA-AAGAGGACAA-------CCTTCTT---------C---TTC----------------T-----CTTTTG------CTATTG--CTAATGATATTCT--------------------------------------------------------------------------------------------A------------------------------CT-GTAATTTA

Size

Hit Count

Total Norm

droFic1

AAA----------GTTTTCCTTCGC-AAAAGTG--TTGCATACTT-TTGGCAGGCGGAAA------------------TCGCTA-AAGAGGACAA-------CCCTCTGATTGGTTTTCTT-TTT----------------C-----TTTTTG------CTGTTCCTCTATTCTTATTTTC---------GATTCG-------------------------------------------------------------------------TCGT------------------------------CT-GTGGTGTA

Size

Hit Count

Total Norm

droKik1

CGT----------TTTACCACCCAC-CAAAGTG--TTGCATACTTTTTGG-------------------------------CTA-AGAAGGACAA-------ACCTCTGATTGGTTTTCTT-TGG----------------CCT---CGT------------TCG--ACATTGTTATTCCT---------GATTCT-------------------------------------------------------------------------TCGA------------------------------CT-GGGGTGTA

Size

Hit Count

Total Norm

droAna3

ACC----------CGTTTG-CCTGC-AAAAGTG--TTGCATACTTTTTGGCAGGCTAAC-------------------G--------GGGGACAG--ACCTCCCCTGCGATTGGTTTTCTT-CTC----------------T---------TT------CATCCG--CCATTGTTATTCCT---------GATTCG-------------------------------------------------------------------------GAGA------------------------------GTCGCATTCGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................................................................GGTACAG--ACCTCCCCGGC..............................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droBip1

ACC----------CGTTTT-CCGGC-AAAAGTG--TTGCATACTTTTTGGCAGGC---------------------------TA-ACG-GGACAG-------ACCTCCGATTGGTTTTCTT-TTC----------------T---------TT------CATCCG--CCATTGTTATTCCT---------GATTCG-------------------------------------------------------------------------GGGA------------------------------AT-------CA

Size

Hit Count

Total Norm

dp4

GAG----------TGT------CGC-AAAAGTG--TTGCATACTTTTTGGCAGGCAGCAA------------------T-GCTA-AAGAGGGCAG--A----GCCTTTGATTGGTTTTTCT-TTGGGCTCGGGGCTCCCAC---GT-TCTGTG------GCATTG--CTATTGTTATTCCTGGCAGACCG------AGAGAGAG--AGAG--AGC-------------------------------------------------AGGCTTGGC------------------------------CT--TCTTCTT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.............................................................................................................................................................................................G------AGAGAGAG--AGAT--AGC-------------------------------------------------AGGC..............................................	20	2	0.50	0.50	0.00	0.00	0.00
.............................................................................................................................................................................................G------AGAGAGAG--AGAT--AGC-------------------------------------------------AGGCC.............................................	21	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................................AGACGG------AGAGAGAG--AGAG--A.....................................................................................................	19	13	0.08	0.08	0.00	0.00	0.00
.............................................................................................................................................................................................G------AGAGAGAG--AGAT--AGC-------------------------------------------------CGGC..............................................	20	2	0.50	0.50	0.00	0.00	0.00
.............................................................................................................................................................................................G------AGTGAGAG--AGAG--AGC-------------------------------------------------AGG...............................................	19	7	0.14	0.00	0.00	0.14	0.00
................................................................................................................................................GT-TCTGCG------GCATTG--CTGTTG.............................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................G------AGAGAGAG--AGAT--AGC-------------------------------------------------AGG...............................................	19	6	0.17	0.17	0.00	0.00	0.00
...........................................................................................................................................................................................ACG------AGAGAGAG--TGAG--AGC-------------------------------------------------..................................................	18	3	0.33	0.00	0.33	0.00	0.00
..................................................................................................................................AGGGCTCCCAC---xT-TCTGTG------GC.........................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................AGAGAGAG--AGAG--AGG-------------------------------------------------ATGC..............................................	19	6	0.17	0.00	0.00	0.17	0.00
......................................................................................................................................................................................GCAGAAAG------AGAGAGAG--AGAG--A.....................................................................................................	21	25	0.04	0.00	0.04	0.00	0.00
....................................................................................................................................................................................................AGCGAGAG--AGAG--GGC-------------------------------------------------AGGC..............................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................................................................AGAGAGAG--AGAG--AGT-------------------------------------------------AGA...............................................	18	20	0.05	0.00	0.05	0.00	0.00

droPer1

GAG----------TGT------CGC-AAAAGTG--TTGCATACTTTTTGGCAGGCAGCAA------------------T-GCTA-AAGAGGACAG--A----GCCTTTGATTGGTTTTTCC-TTGGGCTCGGGGCTCCCAC---GT-TCTTTG------GCATTG--CTATTGTTATTCCTGGCAGACCG------AGAGAGAG--AGAGACAGC-------------------------------------------------AGGCATGGC------------------------------CT--TCTTCTT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................................................................................................................GTTTTTAT-TTGGGCTCGG......................................................................................................................................................................................	18	1	4.00	0.00	0.00	0.00	0.00	4.00
.......................................................................................................................................................................................CAAAGCG------AGAGAGAG--AGAGA.......................................................................................................	20	24	0.04	0.04	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................G------AGAGAGAG--AGAGATAGC-------------------------------------------------AGGCC.............................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................................................................................................................................................................GACGG------AGATAGAG--AGAGA.......................................................................................................	18	19	0.05	0.05	0.00	0.00	0.00	0.00
............................................................................................................................................................................................CG------AGAGAGAG--AGAGAGAGC-------------------------------------------------..................................................	19	16	0.06	0.00	0.00	0.00	0.00	0.06
.............................................................................................................................................................................................G------AGAGAGAG--AGAGATAGC-------------------------------------------------A.................................................	19	27	0.04	0.04	0.00	0.00	0.00	0.00
.....................................................................................................................................................................................TGCAGACAG------AGAGAGAG--AGA.........................................................................................................	20	7	0.14	0.14	0.00	0.00	0.00	0.00
...............................................................................................................TTGTTTTTCT-TTGGGCTC........................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................................AGCG------AGAGAGAG--AGAGAC......................................................................................................	18	13	0.08	0.00	0.00	0.00	0.00	0.08
.......................................................................................................................................................................................CAAAGCG------AGAGAGAG--AGA.........................................................................................................	18	31	0.03	0.03	0.00	0.00	0.00	0.00

droWil1

A---------------------------AAGTG--TAGCATACTTACTGGCAGGCAAAAG---------CA-------GTGCAG-AAGAAGCTGCCACAT--TTTTTAGATTGGTTTTACG-AGT----------------TT----TGTG--------TCCTTG--C--TTGTTATTGTT---TGACTG------AAT-------------------------------------------GGTTTATTTTGTATCCCGTTTT-----GAAAGGGTTCTTTTTTTTTTGGCTCTCGTCGCCCCC-GTGTTTGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.............................................................................................................................................................................TTATTATT---TGACTG------AAT-------------------------------------------A.......................................................................	18	4	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................................................................................TTTGGCTGTCGTCGCCGC..........	18	1	2.00	0.00	0.00	0.00	2.00
.............................................................................................................................................TT----TGTG--------ATCTTG--C--TTGTTATTGT......................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................TGGT---TGACTG------AGT-------------------------------------------GGTTTA..................................................................	19	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................AGCGTTCATTTTTTTTTG........................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................GAAG---------Cx-------GTGCAG-AAGAAGCT.............................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................................................GGT---TGACTG------AGT-------------------------------------------GGTTTA..................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................AG-AAGATGCGGCCACAT--T...................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................................................................TCTTTGGCTGTCGTCGCC............	18	1	1.00	0.00	0.00	0.00	1.00

droVir3

CAG------------------------AAAGTG--TAGCATACTTTTTGGCAGTCG----TTGCCAAAGCAGCAGGCGGCGGCA-AGCAGAAGCA-------ACCTTTGATTGGTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.............................GGTG--TAGCATACTTTTCGG........................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................G----TTGGCAAAGCAGCAGCC.............................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

CTGCTCCTGCCGCTGCTGCTGTCGCAGAAAGTG--TAGCATACTTTTTGGCAGTCG----TCGCAAAAGCAGCAGGC---GGCAAGGCAGCAGCA-------ACCTTTGATTGGTTTTTGG-GTT----------------T-----TGTATG------CAGTGC--TTGTTGTTATTTTC---------AGTTTGGGCAAGGGCTAAGG--------------------------------GCTCCATT-----GAAG-----A-GCTTTG-------------------------------CA--GTTTCAA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....................................................................................................................TTGG-GTT----------------T-----TGxATG------CAGG.......................................................................................................................................................	17	1	1.00	0.00	1.00	0.00	0.00

droGri2

ACT----------GTTTCTCTGCTC-CTTGTCC--TTAGATACTTTTTGGCAGAGTTGCGTCGCC--------A----G-GCAA-AAGCAAAAGC--A----ACCTTTGATTGGTTTTTGG-GGT----------------T-----TCT-GT------CTGTCT--------CTCTGTCC---------GACTGT-CCGACTG--TCTC--CTCTGGTGTGGCTCTGTCTGCAATTGTGTTGTTTCATGTCGTTTAAGGGCTT-----CAAA------------------------------C----------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:31:58 EDT

sblock26534

chr2L:12284769-12284877 +

Candidate

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