block665662- Best orthologs

block665662	chr2R:1365763-1365863 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 1365784-1365805
   star strand at position 1365844-1365861
   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	chr2R:1365748-1365878 -		1	GCCTAGTTCTCTCT-CGCTGGCTT--GAGTTAAGTAAAAATAAACTC-------------------------------------------AGAAACT---AA---------------------------------------------------------------------------------------AAATAATTTCT----------------------------G-AGTT------------------------------------------------------TCTTTT------TAGTTTCTGA-------------------------------------------------------------------------------GT-----------------------------TTCTTTT-------TA-------------CTTAA-CTTAAGT--------------------------------AAAAGT-A-AAAAAAACA----AGTAACT
droSim1	chr3R:3312089-3312223 +	LASTZ	0	GTGAAATAAAC----------------------------ATGGAAAA---------------------------AT-----------------AAAC---TA--------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATTATTTTCCGAAATATTTT-------T---------ATTAAATTAAACTTTCGGTTTG--------------------------------ATAA-----G-----------------------------------------------------------------------ATTTTTCTTTTTTAAGCT-AGTTAACTTG------------AAGACACAATAAT---TAA--A------ACAATAAA-GTTGC
droSec1	super_0:5232275-5232400 -	LASTZ	0	TCTGTTTAGATA--------ATAT--AAA---------------------------------------------AT-----------------ACTT---AA---------------------------------------------------------------------------------------AAACT-ACCTAAATACCTTTA--------------------AAACTATTTTAAAAC-------------------------------------------TCATTA------AATTTTCTGA-------------------------------------------------------------------------------GCATCCTTTAATTTTGTTGTAA------------------------------ATTTCCGGTTTAA-AATAA--------------------------------------------------AT----A-TAACT
droYak2	chrU:7699741-7699868 -	LASTZ	0	GCCGAGAATCCTTC-CACTGGATT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTGTTTAGTTCTGAAAAGATACAACAGTTTATTTATTTTTTGTGGGTTTCAGTT---------------TTTTAAGTACA-----------------------------TTTA-------GA-------------TTTAT-GTAGAGT--------------------------------TAAAGTTT-AAGA--AAA----A-CAATT
droEre2	scaffold_4690:10662768-10662889 +	LASTZ	0	TTCCCCGATTTCTTCCAATAGAG------TT----------------TTGCAAAGAAAGATTGTAATTTGAAA---------------------AAT----------------------------------------------------------------------------------------------CCA-ATTTA------------------------------TATA------------------------------------------------------TA---------------------------------------------------------------------------------------------C-----ATACA-----------------------------ATAAG--------CTTAAATTTACTATTTAA-----AGT--------------------------------AAAAGT-A-AAAAATATA----A-GTAGC
droEug1	scf7180000409589:17030-17151 -	LASTZ	0	TAAAAATA----------------------------------AGGTC-------------------------------------------GAAATTT---AA---------------------------------------------------------------------------------------AAATA-ATTTA----------------------------A-GCTT-----------TTTGCTTCGAAAAATAAGATTATTTTGTTTTC-----------------------------------------------------------------------------TCTAGATTTT--TT---------------G-----TTTGA-----------------------------GCAAG-ATCCAT------------------A----------------------------------GGT---AATGGT-A-AAAAATAAA----G---TTA
droBia1	scf7180000302412:53148-53274 -	LASTZ	0	GCCTAATATTATAT-TGATGACTT--CAAACAT-TCATAGAGGC---TCGTTA------------------ATAAAATTAAGG----TTTGTAAAAT---AA--------TAAATATTT------------------------------------------------------------------------------TTT----------------------------A-TTTC------------------------------------------------------TA-------------------A-------------------------------------------------------------------------------AT-----------------------------TAATTTT-------A---------TCCTTTTTAA-AGTAA-A-----------------------------------AAA--A------ATAA-------AAA
droTak1	scf7180000414114:18056-18179 -	LASTZ	0	TTACTCGTTGTG----ATCGGGTT-----------------------GC----------------------AATTAATGTAGG----TA-----------------------------------------------------------------------------------CAACC-------------------------------------------------------------------------CGTGAAAATTAAAAAAAGTTTAATTTC-----------------------------------------------------------------------------TGGCGTTTTT--TT---------------G-----TTATA-----------------------------GCTAG--------TTTTCATTT---ACTTAA-AAA-AAT-----------------------------------ACA--A------GTAA-------AAA
droEle1	scf7180000490214:566191-566317 -	LASTZ	0	TATTTTTCACCC----AATAATTT--TATTTAAAAAAA---------------------------------AAAATATATAAG----TTCGGAGACT---AA--------AAACTATTTTTAATTTAAATTTTAAGTTTTTTCTTCCGATTATC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------TTTGA-TTTATA------------------------------GAT---CAC----------AA----A-TCACT
droRho1	scf7180000779438:6612-6740 -	LASTZ	0	CCCATCCCTTTTTC--AATAACAT--AAGTTAACGTAACATAG---------------------------------ATTAAGA----TT------------------------------------------------------------------------------------------------------------TG-----------------------------AAAACTTATTTTTAGTC---------------------------------------T---CTTAAG------TAATA-GAGA-------------------------------------------------------------------------------AGA----------------------------TTCAATA-------AATAAGAATAA--------A--GTTAAA--------------------------------AAAAA----AAAA--AAA----A-AAGTA
droFic1	scf7180000454069:4434-4563 -	LASTZ	0	TATTTTGCTGAC----------CA--TAGCTACTGT-----------------------------------AAAATATGCAAGCTTTTTCGCAAACTGTTAAAAATAAATAGACGATTTTG--------CTTTAGGGTTTTTATTCG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GA-----------------------------TTTA-------TA-------------TTTAA-TGTAAAC--------------------------------AAAAAC-A-AA----AAA----A-AAAGG
droKik1	scf7180000302385:653912-654032 -	LASTZ	0	TTTTAAGTCTTTGT-AGATGAGCT-----------------------TCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTAAAAAACTAACTCGTTT-------G---------AATAA-------------------------------------------------------------------------------ATATAACCCTGTTTCATTATATATTCCTAATTTTTCTTA------AC-------------CCTAA-CTTACC---------------------------AATAAT---TAT--C------CAAA-------AAA
droAna3	scaffold_13340:15609788-15609911 -	LASTZ	0	CTCTTCCTCCGGCT-TCATGATTT--TTTGAAACTAAAATGAAA-TG------------------------------------------CAGAAATG---TA---------------------------------------------------------------------------------------ACAGGGTTTTT---------GAAATAATATTATGTTTTTGATATTTGCCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAA-------G------AT-----TCTTAA-GTTAAGA-----------------------------------ATA--A------ACAA-------AAA
droBip1	scf7180000395052:42630-42754 +	LASTZ	0	TAGATCAGTCTT----ACTGTTTTTTTTGTT----AAA-ATAATATA-------------------------------------------TAAAACA---AT---------------------------------------------------------------------------------------AAATAATATAT----------------------------A-AATT------------------------------------------------------TACTTTTA---------------------------------------------------------------CTTA-----G-----------------------------------------------------------------------ACTTTTCTAATTCA-----A-A----------ATAGTATTGGTCAATTAATTAT---TGT--A------AAAA-------AAA
dp4	Unknown_group_314:10340-10462 -	LASTZ	0	GACCAGGTTTCCCA-TGCAAGAACTAGATTTATAA--AGTTCATTTT------------------------AAAACTTGCATATAACTCCGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTCC----------------------------------------------------------------------------GTTGTATTTTG----------------------------------------ACTAG-G----AACAAAATTATTCTTATTAA-ATTAAAT-------------------------------------T----------AA----A-TTAAA
droPer1	super_56:319063-319192 -	LASTZ	0	CCCGAATACTTTGT-AGCTAAAGC------------------------------------TTATGGTCTAGAAAATATTCAGC----TT------------------------------------------------------------------------------------------------------------------------------------------------------------T-CAATTTGAAAATTAAAAATAT-----TTTTGGTGGTATTTTTA-------------------A-------------------------------------------------------------------------A-----CTAAA-----------------------------GTTTGACTTTAA------AA-----CCTCTA-GAA--AA-----------------------------------GCT--T------GAAA-------TAA
droWil1	scaffold_180764:2005052-2005182 -	LASTZ	0	TTTGGTTGGTTGTT-TTTAAGTAT-----------AAAATAAAT-TA-------------------------------------------AGAAATT---AT---------------------------------------------------------------------------------------AAAATATGTTA----------------------------G-AGTG------------------------------------------------------TTTGTT---------------------------------------------------------------TGGTTTCGGTG---------------TTGAAATGA-T-----------------------------ATATGATA---ATGTAAGAT--------ATA----------------------------------GGT---AAATGT-G-ATATATAGA----A-AGATT
droVir3	scaffold_13049:25084925-25085038 +	LASTZ	0	AAGTAAAAAT-----------------------------ATGATATC--------------------------------------------TCAATA---AA---------------------------------------------------------------------------------------AAATTACTTTC----------------------------A-AGTT------------------------------------------------------TCTTTTTC---------------------------------------------------------------ATCT-----TTTTTTTTTATTTTA----------------------------------------ATTAA------A---------------------T--------------------ATTTACCAAATAACT--GAAGAT-A-ACAACAATA---TT-TTACT
droMoj3	scaffold_6500:769823-769955 -	LASTZ	0	GTAAAGTGATAA----------------------------------A-------------------------------------------GAAAATA---AA---------------------------------------------------------------------------------------ATGAA-A-------------------------------------------------T-AAATGTACAAATAAAATA-TAATTTTTTT------------TTATTTTTATTTTATTTTATTA-------------------------------------------------------------------------------TTATT-----------------------------ATTAT--------TTTTT-------TTTTAA-CTTAAGTTAAATTGAAAAAAG-------------------------------CAATA---GC-TGACT
droGri2	scaffold_15110:11942882-11943003 +	LASTZ	0	GCTGAGAATTCTCT-ACTGGGAGT-------------------------------------------------------------------------------------------------------------------------------ATCTCTTGGTTTAATTTAGTATAAGCGGCTGGAACTATAAGACAATCTG----------------------------C-AACT------------------------------------------------------ATTTTT---------------------------------------------------------------TTT-----------------------------------------------------------------TT-------TG-------------TATAA-CTAAAAA--------------------------------AAAGAT-A-AAAGATACA----A---GTA

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	GCCTAGTTCTCTCTCGCTGGCTTGAGTTAAGTAAAAATAAACTCAGAAACTAAAAATAATTTCTGAGTTTCTTTTTAGTTTCTGAGTTTCTTTTTACTTAACTTAAGTAAAAGTAAAAAAAACAAGTAACT

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

GTGAAATAAAC----------------------------ATGGAAAA---------------------------AT-----------------AAAC---TA--------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATTATTTTCCGAAATATTTT-------T---------ATTAAATTAAACTTTCGGTTTG--------------------------------ATAA-----G-----------------------------------------------------------------------ATTTTTCTTTTTTAAGCT-AGTTAACTTG------------AAGACACAATAAT---TAA--A------ACAATAAA-GTTGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................................................................................................................................................................................................................................................................................................ATTAAATTTTCxGTTTG--------------------------------AT..................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT---TAA--T------ACAATAAA-GCTG.	18	1	1.00	0.00	1.00	0.00	0.00
.............................................AA---------------------------TT-----------------AAAC---TA--------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTTATT.........................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.00	0.25	0.00

droSec1

TCTGTTTAGATA--------ATAT--AAA---------------------------------------------AT-----------------ACTT---AA---------------------------------------------------------------------------------------AAACT-ACCTAAATACCTTTA--------------------AAACTATTTTAAAAC-------------------------------------------TCATTA------AATTTTCTGA-------------------------------------------------------------------------------GCATCCTTTAATTTTGTTGTAA------------------------------ATTTCCGGTTTAA-AATAA--------------------------------------------------AT----A-TAACT

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

GCCGAGAATCCTTC-CACTGGATT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTGTTTAGTTCTGAAAAGATACAACAGTTTATTTATTTTTTGTGGGTTTCAGTT---------------TTTTAAGTACA-----------------------------TTTA-------GA-------------TTTAT-GTAGAGT--------------------------------TAAAGTTT-AAGA--AAA----A-CAATT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGAGA--------------------------------TAAAGTTT-AAAA--AA............	19	2	0.50	0.50	0.00	0.00	0.00	0.00

droEre2

TTCCCCGATTTCTTCCAATAGAG------TT----------------TTGCAAAGAAAGATTGTAATTTGAAA---------------------AAT----------------------------------------------------------------------------------------------CCA-ATTTA------------------------------TATA------------------------------------------------------TA---------------------------------------------------------------------------------------------C-----ATACA-----------------------------ATAAG--------CTTAAATTTACTATTTAA-----AGT--------------------------------AAAAGT-A-AAAAATATA----A-GTAGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
............................................................................................................................................................................................................................................................................................................................................................................................................................................................TACTATTTAA-----AGT--------------------------------AAAATA-......................	19	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAGT-A-AATAAxATA----A-GTA..	19	1	1.00	0.00	0.00	0.00	1.00

droEug1

TAAAAATA----------------------------------AGGTC-------------------------------------------GAAATTT---AA---------------------------------------------------------------------------------------AAATA-ATTTA----------------------------A-GCTT-----------TTTGCTTCGAAAAATAAGATTATTTTGTTTTC-----------------------------------------------------------------------------TCTAGATTTT--TT---------------G-----TTTGA-----------------------------GCAAG-ATCCAT------------------A----------------------------------GGT---AATGGT-A-AAAAATAAA----G---TTA

Size

Hit Count

Total Norm

droBia1

GCCTAATATTATAT-TGATGACTT--CAAACAT-TCATAGAGGC---TCGTTA------------------ATAAAATTAAGG----TTTGTAAAAT---AA--------TAAATATTT------------------------------------------------------------------------------TTT----------------------------A-TTTC------------------------------------------------------TA-------------------A-------------------------------------------------------------------------------AT-----------------------------TAATTTT-------A---------TCCTTTTTAA-AGTAA-A-----------------------------------AAA--A------ATAA-------AAA

Size

Hit Count

Total Norm

droTak1

TTACTCGTTGTG----ATCGGGTT-----------------------GC----------------------AATTAATGTAGG----TA-----------------------------------------------------------------------------------CAACC-------------------------------------------------------------------------CGTGAAAATTAAAAAAAGTTTAATTTC-----------------------------------------------------------------------------TGGCGTTTTT--TT---------------G-----TTATA-----------------------------GCTAG--------TTTTCATTT---ACTTAA-AAA-AAT-----------------------------------ACA--A------GTAA-------AAA

Size

Hit Count

Total Norm

droEle1

TATTTTTCACCC----AATAATTT--TATTTAAAAAAA---------------------------------AAAATATATAAG----TTCGGAGACT---AA--------AAACTATTTTTAATTTAAATTTTAAGTTTTTTCTTCCGATTATC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------TTTGA-TTTATA------------------------------GAT---CAC----------AA----A-TCACT

Size

Hit Count

Total Norm

droRho1

CCCATCCCTTTTTC--AATAACAT--AAGTTAACGTAACATAG---------------------------------ATTAAGA----TT------------------------------------------------------------------------------------------------------------TG-----------------------------AAAACTTATTTTTAGTC---------------------------------------T---CTTAAG------TAATA-GAGA-------------------------------------------------------------------------------AGA----------------------------TTCAATA-------AATAAGAATAA--------A--GTTAAA--------------------------------AAAAA----AAAA--AAA----A-AAGTA

Size

Hit Count

Total Norm

droFic1

TATTTTGCTGAC----------CA--TAGCTACTGT-----------------------------------AAAATATGCAAGCTTTTTCGCAAACTGTTAAAAATAAATAGACGATTTTG--------CTTTAGGGTTTTTATTCG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GA-----------------------------TTTA-------TA-------------TTTAA-TGTAAAC--------------------------------AAAAAC-A-AA----AAA----A-AAAGG

Size

Hit Count

Total Norm

droKik1

TTTTAAGTCTTTGT-AGATGAGCT-----------------------TCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTAAAAAACTAACTCGTTT-------G---------AATAA-------------------------------------------------------------------------------ATATAACCCTGTTTCATTATATATTCCTAATTTTTCTTA------AC-------------CCTAA-CTTACC---------------------------AATAAT---TAT--C------CAAA-------AAA

Size

Hit Count

Total Norm

droAna3

CTCTTCCTCCGGCT-TCATGATTT--TTTGAAACTAAAATGAAA-TG------------------------------------------CAGAAATG---TA---------------------------------------------------------------------------------------ACAGGGTTTTT---------GAAATAATATTATGTTTTTGATATTTGCCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAA-------G------AT-----TCTTAA-GTTAAGA-----------------------------------ATA--A------ACAA-------AAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
CTCTTCCTCCGGCG-TCATG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................................................................................ATAATATTTTTTTTTTGATA...................................................................................................................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33

droBip1

TAGATCAGTCTT----ACTGTTTTTTTTGTT----AAA-ATAATATA-------------------------------------------TAAAACA---AT---------------------------------------------------------------------------------------AAATAATATAT----------------------------A-AATT------------------------------------------------------TACTTTTA---------------------------------------------------------------CTTA-----G-----------------------------------------------------------------------ACTTTTCTAATTCA-----A-A----------ATAGTATTGGTCAATTAATTAT---TGT--A------AAAA-------AAA

Size

Hit Count

Total Norm

dp4

GACCAGGTTTCCCA-TGCAAGAACTAGATTTATAA--AGTTCATTTT------------------------AAAACTTGCATATAACTCCGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTCC----------------------------------------------------------------------------GTTGTATTTTG----------------------------------------ACTAG-G----AACAAAATTATTCTTATTAA-ATTAAAT-------------------------------------T----------AA----A-TTAAA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CCCGAATACTTTGT-AGCTAAAGC------------------------------------TTATGGTCTAGAAAATATTCAGC----TT------------------------------------------------------------------------------------------------------------------------------------------------------------T-CAATTTGAAAATTAAAAATAT-----TTTTGGTGGTATTTTTA-------------------A-------------------------------------------------------------------------A-----CTAAA-----------------------------GTTTGACTTTAA------AA-----CCTCTA-GAA--AA-----------------------------------GCT--T------GAAA-------TAA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..........................................................................................................................................................................................................................................................................AT-----TTTTGGTGGxATTATTA-------------------......................................................................................................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................TA-------------------A-------------------------------------------------------------------------A-----CAAAA-----------------------------CTTTGACTTT..........................................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
.......................................................................................TT------------------------------------------------------------------------------------------------------------------------------------------------------------T-CAATTTGAAAATTTG.....................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

TTTGGTTGGTTGTT-TTTAAGTAT-----------AAAATAAAT-TA-------------------------------------------AGAAATT---AT---------------------------------------------------------------------------------------AAAATATGTTA----------------------------G-AGTG------------------------------------------------------TTTGTT---------------------------------------------------------------TGGTTTCGGTG---------------TTGAAATGA-T-----------------------------ATATGATA---ATGTAAGAT--------ATA----------------------------------GGT---AAATGT-G-ATATATAGA----A-AGATT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......GGTTGTT-GTTAATTAT-----------AA......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	4.00	0.00	4.00	0.00	0.00
.....................................AATAAAT-TT-------------------------------------------AGAATTT---AT---------------------------------------------------------------------------------------..............................................................................................................................................................................................................................................................................................................................................	18	6	0.33	0.00	0.00	0.00	0.33
................ATAAGCAT-----------AAAATAAAT-T.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATATAGA----A-AGATT	19	2	0.50	0.00	0.50	0.00	0.00
.............T-TTTAAGTCT-----------AAAAAAAA................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.........TAGTT-GTTAAGTAT-----------AAAATA..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GA-G-ATATATAGA----A-AAATT	18	3	0.33	0.00	0.33	0.00	0.00
....................................................................................................................................................................................................GATA----------------------------G-AGTG------------------------------------------------------TTTGCT---------------------------------------------------------------TGG...................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

AAGTAAAAAT-----------------------------ATGATATC--------------------------------------------TCAATA---AA---------------------------------------------------------------------------------------AAATTACTTTC----------------------------A-AGTT------------------------------------------------------TCTTTTTC---------------------------------------------------------------ATCT-----TTTTTTTTTATTTTA----------------------------------------ATTAA------A---------------------T--------------------ATTTACCAAATAACT--GAAGAT-A-ACAACAATA---TT-TTACT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..................................................................................................................................................................................................................................................................................................CTTTTC---------------------------------------------------------------ATCT-----TTTATTTT...................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

GTAAAGTGATAA----------------------------------A-------------------------------------------GAAAATA---AA---------------------------------------------------------------------------------------ATGAA-A-------------------------------------------------T-AAATGTACAAATAAAATA-TAATTTTTTT------------TTATTTTTATTTTATTTTATTA-------------------------------------------------------------------------------TTATT-----------------------------ATTAT--------TTTTT-------TTTTAA-CTTAAGTTAAATTGAAAAAAG-------------------------------CAATA---GC-TGACT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................................................................ATA---AC---------------------------------------------------------------------------------------ATGAT-A-------------------------------------------------T-AAATGT..............................................................................................................................................................................................................................................................................	18	2	1.00	1.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................TTTTTA-------------------------------------------------------------------------------TTATT-----------------------------ATTAT--------TTTTG-------T..........................................................................	22	14	0.07	0.07	0.00	0.00	0.00

droGri2

GCTGAGAATTCTCT-ACTGGGAGT-------------------------------------------------------------------------------------------------------------------------------ATCTCTTGGTTTAATTTAGTATAAGCGGCTGGAACTATAAGACAATCTG----------------------------C-AACT------------------------------------------------------ATTTTT---------------------------------------------------------------TTT-----------------------------------------------------------------TT-------TG-------------TATAA-CTAAAAA--------------------------------AAAGAT-A-AAAGATACA----A---GTA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:16:17 EDT

block665662

chr2R:1365763-1365863 -

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