sblock216052- Best orthologs

sblock216052	chr2L:12421882-12421990 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 12421952-12421972
   mutations
   read mismatches

Notes: TODO: Could not infer star position

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:12421867-12422005 -		1	CCATTTGGA--------ATATTTATAAGCCCAG----CGGCTAATTGAGTGAGAGGGAG------------------AGCAAGAGAGC----------GGTCA-GCTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTCTCACTCGCT----CACTCACTCA---------------------------------------------------------------------------------GCCG--GCCGCCGTTTATTTGCCGCTTCCTCAAATCAT
droSim1	chr2L:12227297-12227427 -	LASTZ	1	CCATTTGGA--------ATATTTATAAGCCCAG----CGGCTAATTGAGTGAGAGGGAG------------------AGCAGGAGAGC----------GGTCA-GCTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCA---------------------------------------------------------------------------------GCCG--GCGGCCGTTTATTTGCCGCTTCCTCAAATCAT
droSec1	super_16:612338-612468 -	LASTZ	1	CCATTTGGA--------ATATTTATAAGCCCGG----CGGCTAATTGAGTGAGAGGGAG------------------AGCAAGAGAGC----------GGTCA-GCTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCA---------------------------------------------------------------------------------GCCG--GCGGCCGTTTATTTGCCGCTTCCTCAAATCAT
droYak2	chr2L:8858070-8858199 -	LASTZ	1	CCATTTGGA--------ATATTTATAAACCCAG----CGACTAATTGAGTGAGAGGGAG------------------AGCGAGAGAGC----------GGTCA-GCTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCA---------------------------------------------------------------------------------CCCG--ACCGCCGTTTAT-TGCCGCTTCCTCAAATCAT
droEre2	scaffold_4929:12994744-12994878 +	LASTZ	1	CCATTCGGA--------ATATTTATAAAAGCAG----CGACTAATTGAGTGAGAGGGAG------------------AGCGAGAGAGC----------GGTCA-GCTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCACT-----------------------------------------------------------------CG------------ACCG--CCCGCCGTTTATTTGCCGCTTCCTCAAATCAT
droEug1	scf7180000409122:808456-808586 -	LASTZ	4	CCATCTAGA--------ATATTTATAAAACCAG----CGACTAATTGAGTGAGAGGGAG------------------AGTGAGAGAGC----------GGTCA-TTTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCG---------------------------------------------------------------------------------CTTG--CTTTCCGTTTATTTGCCGCTTCCTCAAATCAT
droBia1	scf7180000302422:556733-556867 +	LASTZ	4	CCATTTAGAGTACGTGTATATTTATAAACACAG----CGACTAATTGAGTGAGAGGGAG------------------AGTGCGAGAGT----------GGCCC-GCGACTC-----ACT------CAG-------------------TCGGT---------------------------TTC--------C----CACTCACTC-------------------------------------------------------------------------------------G--CCTGCCGCTTATTTGCCGCTTCCTCAAATCAT
droTak1	scf7180000415865:175521-175648 +	LASTZ	4	CCATTTAGAATACATGTATATTTATAAACCCAC----CGACTAATTGAGTGAGAGGGAG------------------AGTGAGAGAGC----------AAT--------TC-----ACT------CAC-------------------TCGGC---------------------------TTC--------T----CAGTCACTC-------------------------------------------------------------------------------------G--CTTGCCGTTTATTTGCCGCTTCCTCAAATCAT
droEle1	scf7180000491028:2693496-2693615 +	LASTZ	4	CCATTTAGA--------ATATTTATAAGCCCAG----CGACTAATTGAGTGAG------------------------AGTGAGAGAGC----------GGTCA-G-TATTC-----ACT------CAC-------------------TCGGC---------------------------TGC--------T----CACTCACTC-------------------------------------------------------------------------------------G--CTTGCCGTTTATTTGCCGCTTCCTCAAATCAT
droRho1	scf7180000780043:277013-277139 -	LASTZ	4	CCATTTAGA--------ATATTTATAAACCCAG----CGACTAATTGAGTGAGAGGGAG------------------AGTGAGAGAGC----------GGTCA-GTTGTTC-----ACT------CAC-------------------TCGGC---------------------------TAC--------T----CACTCACTC-------------------------------------------------------------------------------------G--CTTGCCGTTTATTTGCCGCTTCCTCAAATTAT
droFic1	scf7180000454015:306275-306419 -	LASTZ	4	CCATTTGGA--------ATATTTATAAACCCAG----CGAATAATTGAGTGAGAGGGATAGGGAGTGTAAGAGCAAGAGCGAGAGAGC----------GGTCA-GCTATTC-----ACT------CAC-------------------TCATT---------------------------TAG--------C----CACTCATTC-------------------------------------------------------------------------------------G--CTTGCCGTTTATTTGCCGCTTCCTCAAATCAT
droKik1	scf7180000301476:521809-522009 -	LASTZ	4	CTATTTAGA--------ATATTTTTAAACCCAG----CGACTAATTGAGAGAGCGAGAG------------------TGTCA----CTCATTGAGGCCCCTCA-GT-------------------CACTCATTTA-------C----TCACTCACTCCCTCTCTTTTCCCCCAG------T--------CGCACCCTCT----CTTTCTCTGCTATAGCACTCTCTCTTTCTGAT------------------TCC-A---------TAGCCGGGTCTC----------G--TTCGCCGCTTATTTACCGCTTCCTCAAATCAT
droAna3	scaffold_12916:12976682-12976854 +	LASTZ	5	CCATTTAAA--------ATATTTATAAACACAG----CGACTAATTGAATGAGCGGGTG------------------AGTGAGAGTGT----------CGGCA-GTTGCTCGTTGTACTCACAAGTAC-------------------TCACT---------------------------TTC--------A----CACTCATTG-----------------------------------------G-----------AAGCGGTTCCCAGCTCGGTTTCGTTTGCGGCCGCCGTTGCCGTTTATTTGCCGCTTCCTCAAATCAT
droBip1	scf7180000396580:543946-544113 -	LASTZ	5	CCATTTAAA--------ATATTAATAAACACAG----CGACTAATTGAATGAGCGGGTG------------------AGTGAGAGTGT----------CGCCAAGTTGCTCGTTGTACTCGCAAGTAC-------------------TCACT---------------------------TTC--------A----CACTCATTG-----------------------------------------G-----------CAGCGGTTCCCAGCTCGGTTTCGTGTG----CT--GCCGCCGTTTATTTGCCGTTTCCTCAAATCAT
dp4	chr4_group3:5666738-5666907 +	LASTZ	3	CCGTTTAAT--------TTAGTCGAAGG--GAG----AGCCATATTCATTGAGAGGGAG------------------AGTGTGAGAGCAAGCGAGC--GGTCA-GC-GT---CAAC-GT------CAGCGTCAGGCTAGCCACTCACTCAATCGCTCTCCC-------------------T--------CACGCCCTCT----CATT-----------------------------------------------------------------CGGTTTC----------G--TTTGCCGTTTATTTGCCGTTTCCTCAAATCAT
droPer1	super_1:7158003-7158172 +	LASTZ	3	CCGTTTAAT--------TTAGTCGAAGG--GAG----AGCCATATTCATTGAGAGGGAG------------------AGTGTGAGAGCAAGCGAGC--GGTCA-GC-GT---CAAC-GT------CAGCGTCAGGCTAGCCACTCACTCAATCGCTCTCCC-------------------T--------CACGCCCTCT----CATT-----------------------------------------------------------------CGGTTTC----------G--TTTGCCGTTTATTTGCCGTTTCCTCAAATCAT
droWil1	scaffold_180708:10168062-10168287 -	LASTZ	3	AAATGAAAT--------GTATTTATTTT--TAACGCTCGACTAATTGAGTGACGAAAAG------------------GGGGG---CAGATGGCAAA--GAGCT-AC-AG---TTGA-GT------GAATGAGTGATTCTTCTCTCCCTCTCTTTTTGTCTT-------------------T--------CTCTTTCTCT----CTGTCTCTGTTAGT-CACTCAATTTAGGTGAGAGACTCAATGTTGTCCCCTCCAA---------CAAGTAGGTTTCA---------G--TTTG--CTTTATTTGCCGTTTCCTCAAATCAT
droVir3	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:22602044-22602122 -	LASTZ	0	G------------------------------------------------------------------------------------------------------------TC-----GCT------CAA-------------------TCTGT----TGCGCTCATTTCACTCAGTGATTT----------C----TGTTCGTT-----------------------------------------------------------------------------------------CATTCTGTTTATTTGCCGTTTCCTCGACGCAT
droGri2	scaffold_15252:14983982-14984007 -	LASTZ	0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTATTTGTTCTTTCCTCAACACAT

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	CCATTTGGA--------ATATTTATAAGCCCAG----CGGCTAATTGAGTGAGAGGGAGA------------------GCAAGAGAGC----------GGTCA-GC-------------------TAGTC---ACTCACTCGGTTTCT--------CACTCGCTC-------------------------ACTCACT-----------------------------------------------------------------CA------------GCCGG--CCGCCGTTTATTTGCCGCTTCCTCAAATCAT
droSim1	CCATTTGGA--------ATATTTATAAGCCCAG----CGGCTAATTGAGTGAGAGGGAGA------------------GCAGGAGAGC----------GGTCA-GC-------------------TAGTC---ACTCACTCGGTTTCT--------CACTCACTC-----------------------------A---------------------------------------------------------------------------------GCCGG--CGGCCGTTTATTTGCCGCTTCCTCAAATCAT
droSec1	CCATTTGGA--------ATATTTATAAGCCCGG----CGGCTAATTGAGTGAGAGGGAGA------------------GCAAGAGAGC----------GGTCA-GC-------------------TAGTC---ACTCACTCGGTTTCT--------CACTCACTC-----------------------------A---------------------------------------------------------------------------------GCCGG--CGGCCGTTTATTTGCCGCTTCCTCAAATCAT
droYak2	CCATTTGGA--------ATATTTATAAACCCAG----CGACTAATTGAGTGAGAGGGAGA------------------GCGAGAGAGC----------GGTCA-GC-------------------TAGTC---ACTCACTCGGTTTCT--------CACTCACTC-----------------------------A---------------------------------------------------------------------------------CCCGA--CCGCCGTTTAT-TGCCGCTTCCTCAAATCAT
droEre2	CCATTCGGA--------ATATTTATAAAAGCAG----CGACTAATTGAGTGAGAGGGAGA------------------GCGAGAGAGC----------GGTCA-GC-------------------TAGTC---ACTCACTCGGTTTCT--------CACTCACTC-----------------------------ACT-----------------------------------------------------------------CG------------ACCGC--CCGCCGTTTATTTGCCGCTTCCTCAAATCAT
droEug1	CCATCTAGA--------ATATTTATAAAACCAG----CGACTAATTGAGTGAGAGGGAGA------------------GTGAGAGAGC----------GGTCA-TT-------------------TAGTC---ACTCACTCGGTTTCT--------CACTCACTC-----------------------------G---------------------------------------------------------------------------------CTTGC--TTTCCGTTTATTTGCCGCTTCCTCAAATCAT
droBia1	CCATTTAGAGTACGTGTATATTTATAAACACAG----CGACTAATTGAGTGAGAGGGAGA------------------GTGCGAGAGT----------GGCCC-GC-------------------GACTC---ACTCAGTCGGTTTCC--------CACTCACTC------------------------------------------------------------------------------------------------------------------GC--CTGCCGCTTATTTGCCGCTTCCTCAAATCAT
droTak1	CCATTTAGAATACATGTATATTTATAAACCCAC----CGACTAATTGAGTGAGAGGGAGA------------------GTGAGAGAGC----------AAT---------------------------TC---ACTCACTCGGCTTCT--------CAGTCACTC------------------------------------------------------------------------------------------------------------------GC--TTGCCGTTTATTTGCCGCTTCCTCAAATCAT
droEle1	CCATTTAGA--------ATATTTATAAGCCCAG----CGACTAATTGAGTGAGA------------------------GTGAGAGAGC----------GGTCA-G--------------------TATTC---ACTCACTCGGCTGCT--------CACTCACTC------------------------------------------------------------------------------------------------------------------GC--TTGCCGTTTATTTGCCGCTTCCTCAAATCAT
droRho1	CCATTTAGA--------ATATTTATAAACCCAG----CGACTAATTGAGTGAGAGGGAGA------------------GTGAGAGAGC----------GGTCA-GT-------------------TGTTC---ACTCACTCGGCTACT--------CACTCACTC------------------------------------------------------------------------------------------------------------------GC--TTGCCGTTTATTTGCCGCTTCCTCAAATTAT
droFic1	CCATTTGGA--------ATATTTATAAACCCAG----CGAATAATTGAGTGAGAGGGATAGGGAGTGTAAGAGCAAGAGCGAGAGAGC----------GGTCA-GC-------------------TATTC---ACTCACTCATTTAGC--------CACTCATTC------------------------------------------------------------------------------------------------------------------GC--TTGCCGTTTATTTGCCGCTTCCTCAAATCAT
droKik1	CTATTTAGA--------ATATTTTTAAACCCAG----CGACTAATTGAGAGAGCGAGAGT------------------GTCA----CTCATTGAGGCCCCTCA-GT-------------------CACTC---A--------TTTACT--------CACTCACTCCCTCTCTTTTCCCCCAGTCGCACCCTCTCTTTCTCTGCTATAGCACTCTCTCTTTCTGAT------------------TCC-A---------TAGCCGGGTCTC----------GT--TCGCCGCTTATTTACCGCTTCCTCAAATCAT
droAna3	CCATTTAAA--------ATATTTATAAACACAG----CGACTAATTGAATGAGCGGGTGA------------------GTGAGAGTGT----------CGGCA-GT-------------------TGCTCGTTGTACTCACAAGTACTCACTTTCACACTCATTG----------------------------------------------------------------------G-----------AAGCGGTTCCCAGCTCGGTTTCGTTTGCGGCCGCCGTTGCCGTTTATTTGCCGCTTCCTCAAATCAT
droBip1	CCATTTAAA--------ATATTAATAAACACAG----CGACTAATTGAATGAGCGGGTGA------------------GTGAGAGTGT----------CGCCAAGT----------------TGCTCGTT---GTACTCGCAAGTACTCACTTTCACACTCATTG----------------------------------------------------------------------G-----------CAGCGGTTCCCAGCTCGGTTTCGTGTG----CTG--CCGCCGTTTATTTGCCGTTTCCTCAAATCAT
dp4	CCGTTTAAT--------TTAGTCGAAGG--GAG----AGCCATATTCATTGAGAGGGAGA------------------GTGTGAGAGCAAGCGAGC--GGTCA-GCGTCAACGTCAGCGTCAGGCTAGCC---ACTCACTCAATCGCTCTCCCTC-----------------------------ACGCCCTCTCATT-----------------------------------------------------------------CGGTTTC----------GT--TTGCCGTTTATTTGCCGTTTCCTCAAATCAT
droPer1	CCGTTTAAT--------TTAGTCGAAGG--GAG----AGCCATATTCATTGAGAGGGAGA------------------GTGTGAGAGCAAGCGAGC--GGTCA-GCGTCAACGTCAGCGTCAGGCTAGCC---ACTCACTCAATCGCTCTCCCTC-----------------------------ACGCCCTCTCATT-----------------------------------------------------------------CGGTTTC----------GT--TTGCCGTTTATTTGCCGTTTCCTCAAATCAT
droWil1	AAATGAAAT--------GTATTTATTTT--TAACGCTCGACTAATTGAGTGACGAAAAGG------------------GGGG---CAGATGGCAAA--GAGCT-ACAGTTGAGTGAATGAGTGATTCTTC---TCTCCCTCTCTTTTTGTCTTTC-----------------------------TCTTTCTCTCTGTCTCTGTTAGT-CACTCAATTTAGGTGAGAGACTCAATGTTGTCCCCTCCAA---------CAAGTAGGTTTCA---------GT--TTG--CTTTATTTGCCGTTTCCTCAAATCAT

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
UNAFold Image																		None

Small RNA-seq read pileup

Species

Alignment

droSim1

CCATTTGGA--------ATATTTATAAGCCCAG----CGGCTAATTGAGTGAGAGGGAG------------------AGCAGGAGAGC----------GGTCA-GCTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCA---------------------------------------------------------------------------------GCCG--GCGGCCGTTTATTTGCCGCTTCCTCAAATCAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................G------------------AGCAGGAGATC----------CGTCA-GCT.........................................................................................................................................................................................................................	20	1	3.00	1.00	0.00	0.00	2.00
..............................................................................GCAGGAGATC----------CGTCA-GCT.........................................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
......................................................................................................................................................GT---------------------------TTC--------G----GACTCACTCA---------------------------------------------------------------------------------GC....................................	18	1	2.00	0.00	0.00	0.00	2.00
.....................................................................................................................................................................................................CTCAAGCA---------------------------------------------------------------------------------GCCG--GCGGCC..........................	18	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................CAC-------------------TCGGT---------------------------TTC--------T----CACTCACT.........................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..........................................................G------------------AGCAGGAGATC----------CGTCA-GC..........................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droSec1

CCATTTGGA--------ATATTTATAAGCCCGG----CGGCTAATTGAGTGAGAGGGAG------------------AGCAAGAGAGC----------GGTCA-GCTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCA---------------------------------------------------------------------------------GCCG--GCGGCCGTTTATTTGCCGCTTCCTCAAATCAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...................................................AGAGTGAG------------------AGGAAGAGAGC----------..................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
..................................................GAGTGGGAG------------------AGCAAGAAA..............................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
...........................................ATTGAGTGAGAGGGAG------------------AG.....................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
.............................................................................AGCAAGAGAGC----------GGTCA-GCTAGTC-----ACT------C......................................................................................................................................................................................................	27	1	1.00	0.00	1.00	0.00
...........................................ATTGAGTGAGxGGGAG------------------AGA....................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
..........................................AATTGAGTGAGAGGGAG------------------AGT....................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00
..........................................AATTGAGTGAGAGGGAG------------------AGCA...................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00
.........................................................AG------------------AGCAAGAGAGC----------GGAGA-GCTA........................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00

droYak2

CCATTTGGA--------ATATTTATAAACCCAG----CGACTAATTGAGTGAGAGGGAG------------------AGCGAGAGAGC----------GGTCA-GCTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCA---------------------------------------------------------------------------------CCCG--ACCGCCGTTTAT-TGCCGCTTCCTCAAATCAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.................................................TGTGTGGGAG------------------AGCGAGAGAGC----------..................................................................................................................................................................................................................................	21	1	9.00	9.00	0.00	0.00	0.00	0.00
...............................................ATTGAGAGGGAG------------------AGAGAGAGA..............................................................................................................................................................................................................................................	21	4	0.50	0.25	0.00	0.25	0.00	0.00
.................................................TGTGTGGGAG------------------AGCGAGAGA..............................................................................................................................................................................................................................................	19	2	1.00	1.00	0.00	0.00	0.00	0.00
...................................................AGAGGAAG------------------AGGGAGAGA..............................................................................................................................................................................................................................................	17	14	0.07	0.00	0.00	0.00	0.07	0.00
..................................................GAGAGGGAG------------------AGCGAGAGA..............................................................................................................................................................................................................................................	18	5	0.20	0.00	0.00	0.20	0.00	0.00
..........................................................................................................TAGTC-----ATT------CxC-------------------TCGGT---------------------------TTC--------T----.................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
...................................................TGTGGGAG------------------AGCGAGAGAGC----------G.................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................TGTGTGGGAG------------------AGCGAGAGAG.............................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
...................................................TGTGGGAG------------------AGCGAGAGAG.............................................................................................................................................................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00	0.00
.................................................TGTGTGGGAG------------------AGCGAGAGAGC----------G.................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................ATTGAGAGGGAG------------------AGAGAGAGAG.............................................................................................................................................................................................................................................	22	4	0.25	0.00	0.00	0.25	0.00	0.00
................................................AAGAGAGGGAG------------------AGCGAGAGAGC----------..................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................GATTGAGAGGGAG------------------AGAGAGA................................................................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.33	0.00	0.00
...................................................AGAAAGAG------------------AGCGAGAGAGC----------..................................................................................................................................................................................................................................	19	13	0.08	0.00	0.00	0.00	0.08	0.00
..................................................GAGAGAGAG------------------AACGAGAGAGC----------..................................................................................................................................................................................................................................	20	7	0.14	0.00	0.00	0.14	0.00	0.00
......................................GACAAATTGAGTTAGAGGGA..........................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................GTGGGAG------------------AGTGAGAGAGC----------..................................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droEre2

CCATTCGGA--------ATATTTATAAAAGCAG----CGACTAATTGAGTGAGAGGGAG------------------AGCGAGAGAGC----------GGTCA-GCTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCACT-----------------------------------------------------------------CG------------ACCG--CCCGCCGTTTATTTGCCGCTTCCTCAAATCAT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................................................AGAGGCAG------------------AGAGAGAGAG.............................................................................................................................................................................................................................................	18	38	0.03	0.00	0.00	0.00	0.03
...............................................................................................................................C-------------------TCGGC---------------------------TTC--------T----CACTCACTCACT-----------------------------------------------------------------....................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................GAGGGAGCGGGAG------------------AGCGA..................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
..............................................GAGTGAGCGGGAG------------------AGAGAG.................................................................................................................................................................................................................................................	19	5	0.20	0.00	0.00	0.00	0.20
...................................................ACAGGGAG------------------AGCGAAAGAG.............................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................GAGAGAGAG------------------AGCGAGAGA..............................................................................................................................................................................................................................................	18	29	0.03	0.00	0.00	0.00	0.03

droEug1

CCATCTAGA--------ATATTTATAAAACCAG----CGACTAATTGAGTGAGAGGGAG------------------AGTGAGAGAGC----------GGTCA-TTTAGTC-----ACT------CAC-------------------TCGGT---------------------------TTC--------T----CACTCACTCG---------------------------------------------------------------------------------CTTG--CTTTCCGTTTATTTGCCGCTTCCTCAAATCAT

Size

Hit Count

Total Norm

droBia1

CCATTTAGAGTACGTGTATATTTATAAACACAG----CGACTAATTGAGTGAGAGGGAG------------------AGTGCGAGAGT----------GGCCC-GCGACTC-----ACT------CAG-------------------TCGGT---------------------------TTC--------C----CACTCACTC-------------------------------------------------------------------------------------G--CCTGCCGCTTATTTGCCGCTTCCTCAAATCAT

Size

Hit Count

Total Norm

droTak1

CCATTTAGAATACATGTATATTTATAAACCCAC----CGACTAATTGAGTGAGAGGGAG------------------AGTGAGAGAGC----------AAT--------TC-----ACT------CAC-------------------TCGGC---------------------------TTC--------T----CAGTCACTC-------------------------------------------------------------------------------------G--CTTGCCGTTTATTTGCCGCTTCCTCAAATCAT

Size

Hit Count

Total Norm

droEle1

CCATTTAGA--------ATATTTATAAGCCCAG----CGACTAATTGAGTGAG------------------------AGTGAGAGAGC----------GGTCA-G-TATTC-----ACT------CAC-------------------TCGGC---------------------------TGC--------T----CACTCACTC-------------------------------------------------------------------------------------G--CTTGCCGTTTATTTGCCGCTTCCTCAAATCAT

Size

Hit Count

Total Norm

droRho1

CCATTTAGA--------ATATTTATAAACCCAG----CGACTAATTGAGTGAGAGGGAG------------------AGTGAGAGAGC----------GGTCA-GTTGTTC-----ACT------CAC-------------------TCGGC---------------------------TAC--------T----CACTCACTC-------------------------------------------------------------------------------------G--CTTGCCGTTTATTTGCCGCTTCCTCAAATTAT

Size

Hit Count

Total Norm

droFic1

CCATTTGGA--------ATATTTATAAACCCAG----CGAATAATTGAGTGAGAGGGATAGGGAGTGTAAGAGCAAGAGCGAGAGAGC----------GGTCA-GCTATTC-----ACT------CAC-------------------TCATT---------------------------TAG--------C----CACTCATTC-------------------------------------------------------------------------------------G--CTTGCCGTTTATTTGCCGCTTCCTCAAATCAT

Size

Hit Count

Total Norm

droKik1

CTATTTAGA--------ATATTTTTAAACCCAG----CGACTAATTGAGAGAGCGAGAG------------------TGTCA----CTCATTGAGGCCCCTCA-GT-------------------CACTCATTTA-------C----TCACTCACTCCCTCTCTTTTCCCCCAG------T--------CGCACCCTCT----CTTTCTCTGCTATAGCACTCTCTCTTTCTGAT------------------TCC-A---------TAGCCGGGTCTC----------G--TTCGCCGCTTATTTACCGCTTCCTCAAATCAT

Size

Hit Count

Total Norm

droAna3

CCATTTAAA--------ATATTTATAAACACAG----CGACTAATTGAATGAGCGGGTG------------------AGTGAGAGTGT----------CGGCA-GTTGCTCGTTGTACTCACAAGTAC-------------------TCACT---------------------------TTC--------A----CACTCATTG-----------------------------------------G-----------AAGCGGTTCCCAGCTCGGTTTCGTTTGCGGCCGCCGTTGCCGTTTATTTGCCGCTTCCTCAAATCAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................GAGAGGGTG------------------AGTGAGAGT..............................................................................................................................................................................................................................................	18	1	2.00	1.00	1.00	0.00	0.00
..............................................................................GTGAGAGTGT----------CGGCA-GTTGC.......................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................................CAGCTCGGTTTCGTTTGCGGC....................................	21	1	1.00	1.00	0.00	0.00	0.00
..........................AACACAG----CGACxACTTGAA...................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................ACTCATTG-----------------------------------------G-----------AAGCGGTTCCC........................................................	20	1	1.00	0.00	1.00	0.00	0.00

droBip1

CCATTTAAA--------ATATTAATAAACACAG----CGACTAATTGAATGAGCGGGTG------------------AGTGAGAGTGT----------CGCCAAGTTGCTCGTTGTACTCGCAAGTAC-------------------TCACT---------------------------TTC--------A----CACTCATTG-----------------------------------------G-----------CAGCGGTTCCCAGCTCGGTTTCGTGTG----CT--GCCGCCGTTTATTTGCCGTTTCCTCAAATCAT

Size

Hit Count

Total Norm

dp4

CCGTTTAAT--------TTAGTCGAAGG--GAG----AGCCATATTCATTGAGAGGGAG------------------AGTGTGAGAGCAAGCGAGC--GGTCA-GC-GT---CAAC-GT------CAGCGTCAGGCTAGCCACTCACTCAATCGCTCTCCC-------------------T--------CACGCCCTCT----CATT-----------------------------------------------------------------CGGTTTC----------G--TTTGCCGTTTATTTGCCGTTTCCTCAAATCAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..........................................CATTCATTGGGAGGGAG------------------AG.....................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................C--AGTCA-GC-GT---CAAC-GG------CAGCGTCA...............................................................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................CA-GC-GT---CAGC-GT------CAGCTTCA...............................................................................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
..................................................................................................................................................................................................................................................................................GTTTC----------G--TTTGACGTTTAGT...................	19	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................GTCA-GC-GT---CAAC-GT------CAGCGT.................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00

droPer1

CCGTTTAAT--------TTAGTCGAAGG--GAG----AGCCATATTCATTGAGAGGGAG------------------AGTGTGAGAGCAAGCGAGC--GGTCA-GC-GT---CAAC-GT------CAGCGTCAGGCTAGCCACTCACTCAATCGCTCTCCC-------------------T--------CACGCCCTCT----CATT-----------------------------------------------------------------CGGTTTC----------G--TTTGCCGTTTATTTGCCGTTTCCTCAAATCAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...................................................................................................GTCA-GC-GT---CAAC-GT------CAGC...................................................................................................................................................................................................	18	1	2.00	0.00	1.00	0.00	0.00	1.00
...............................................................................................C--AGTCA-GC-GT---CAAC-GC------CAGCGTCAGGC............................................................................................................................................................................................	27	1	2.00	0.00	0.00	0.00	0.00	2.00
......................................................................................................A-GA-GT---CAAC-GT------CAGTGTCAG..............................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

AAATGAAAT--------GTATTTATTTT--TAACGCTCGACTAATTGAGTGACGAAAAG------------------GGGGG---CAGATGGCAAA--GAGCT-AC-AG---TTGA-GT------GAATGAGTGATTCTTCTCTCCCTCTCTTTTTGTCTT-------------------T--------CTCTTTCTCT----CTGTCTCTGTTAGT-CACTCAATTTAGGTGAGAGACTCAATGTTGTCCCCTCCAA---------CAAGTAGGTTTCA---------G--TTTG--CTTTATTTGCCGTTTCCTCAAATCAT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................................................................................................................................................................TTTGTCT----CTGTCTCTCTT..............................................................................................................	18	20	0.10	0.00	0.00	0.00	0.10
....................................................................................................................................................................................T--------CTCTTTCTCT----CTCTCTGTGTT..............................................................................................................	22	18	0.06	0.06	0.00	0.00	0.00
................................................................................................................................................................................................................................................................AA---------CAAGxAGGTGTCA---------G--TTT.............................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................TCTGTTAGT-CACTCAATTTAGGTGAGA........................................................................................	27	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................CTCxGTGTTTGTCTT-------------------T--------CTCTT..................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................GCT-AC-AG---TTGA-GT------GAATGAGT...............................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................TC-------------------T--------CTCTTTCTCT----CTGTCTCGG................................................................................................................	22	5	0.20	0.00	0.00	0.20	0.00

droVir3

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

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

G------------------------------------------------------------------------------------------------------------TC-----GCT------CAA-------------------TCTGT----TGCGCTCATTTCACTCAGTGATTT----------C----TGTTCGTT-----------------------------------------------------------------------------------------CATTCTGTTTATTTGCCGTTTCCTCGACGCAT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......................................................................................................................................................................................................................................................................................................TCTGTTTATTTGCCGTTTCCTCGAC....	25	1	1.00	1.00	0.00	0.00	0.00

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:15 EDT

sblock216052

chr2L:12421882-12421990 -

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