dme-mir-4964- Best orthologs

dme-mir-4964	chrX:8859833-8859945 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 8859898-8859920
   star strand at position 8859861-8859884
   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	chrX:8859818-8859960 +		1	TCGCCATGCTTCGACAATT-TTTGAATGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CGAATAAATATG-----TATTTATGTATA----TTTT--T----T--TATATGGTACGTATTTATTTGTCTGCAAATGGCTGCC--------------------------------AAGGAG--TGCTACATAATCAA-TTTGT----TTGTT
droSim1	chrX:7057967-7058102 +	LASTZ	5	TCGCCATGCTTCGACAATT-TTTGAATGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CGAATAAATATG-----TATTTATGTATA----TATA--T----T--TATAT-------ACGCATTCGTCTGCAAATGGCTGCC--------------------------------ATGGAG--TGCTACATAATCAA-TTTGT----TTGTT
droSec1	super_34:222375-222488 +	LASTZ	5	TCGCCATGCTTCGACAATT-TTTGAATGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CGAATAAATATG-----TATTTATGTTTA----TATA--T----T-------------------------------TGGCTGCC--------------------------------ATGGAG--TGCTACATAATCAA-TTTGT----TTGTT
droYak2	chrX:12451967-12452096 -	LASTZ	4	TTGCCATGCTTGGACAATT-TTTGAATGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CGAATAAATATG-----TATTTATGTGTA----GATA--------------T-------ATGTATTTGTCTGAAAATGGCTGCC--------------------------------AAGGAG--TGCTACATAATCAA-TTTGC----TTATT
droEre2	scaffold_4690:6251913-6252052 -	LASTZ	4	TTGCCATGCTTGGACAATT-TTTGAATGGTCCTTT------C-------------------------CATCCCCAAGG---------------------CGAATAAATATG-----TTTGTGTGTACGAGTATATA--T----T--TATAT-------ATGTATCGGTCTGCAAATGGCTGCC--------------------------------AATGAG--TGCTTCAAAATCAA-ATTGT----TTGTT
droEug1	scf7180000408176:293546-293674 +	LASTZ	5	TTGCCATGCTTGGACAATT-TTTGAATGGTTCTTTGAATGGT-------------------------CATGCCCAAAG---------------------------GCGTCG-----TCTTAG--TATA----TATATTT----T--GATAT----------------CCCCCAAATCGCTGTC--------------------------------GAGGAGGTGGCTACATAATCAA-TTTGT----TTGTT
droBia1	scf7180000301760:2585945-2586054 +	LASTZ	5	TTGCCATGCTTGGACTAAT-TTTGAACGGCCCTTT------G-------------------------CCAGCCGCCGG---------------------CGAATAAATGTG-----TATATATACATG---------------------------------------------AAGGGATGCC--------------------------------AAGAAG--TGCTTCATAATCAA-TTTGT----TTGTC
droTak1	scf7180000415169:1065824-1065935 -	LASTZ	5	TTTCCATGCTTGGACAATT-TTTGAATGGTCCTTT------T-------------------------CTTGCCCCAAG---------------------CGAATAAATGTA-----TATATAGGTATAAATATATA--T----T------T-------------------------G--------------------------------------GAGGAG--TGCTACATAATCAA-TTTGT----TTGTT
droEle1	scf7180000491006:2358806-2358931 +	LASTZ	5	TTTTCATGCTTGGACAATT-TTTGAGTTGTCCTTT------T-------------------------TATGCCCAAGC---------------------CGAGTATATGTA-----TATATAAGTATA----TTTA--T-----------------------ATATAACCACAAATGGAAGCC--------------------------------AAGGAG--TGCTTCATAATCAA-TTTGT----TTGTA
droRho1	scf7180000779841:367202-367332 +	LASTZ	5	TTTCCATGCTTGGACAATT-TTTGAACGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CCAATATATATA-----CATATATATATA----TATA--------------A-------GTCTATATGTCTACAAATGGATGGC--------------------------------AAGGAG--TGGTACATAATCAATTTAGC----TTGTT
droFic1	scf7180000453829:828317-828436 +	LASTZ	5	TTTCCATGCTTGGACAATT-TTTGAATGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CGAATAAATATG-----TATATATATA------TATA--T----T-----------------------TGCACAAATGGATACC--------------------------------AAAGAG--TGCTGCATAATCAA-TTTAT----TTGTT
droKik1	scf7180000302698:232066-232210 -	LASTZ	0	TTTCCACGCTTGGACAGTTCTCTGAATGGTCCTTT------TTGCGCTTGGGGGAAT--------------------G---------------------TAGCTAAATGTA-----GGTTTATGTATC----TATATTTTAATAACTGTGTCAAATATCTATATCTATCAACAAA--------------------------------------------CT--GGCTACATAATCAA-TTTGT----TTGTT
droAna3	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	chrXL_group1e:8134181-8134346 +	LASTZ	0	TTTCCATGCTTGGACAATTCTTTGAACGGTCGTCC------C---------------T----TTTTGCCAGCCCAAGGGGGGAGGGATGGGGGGGGGGGGGAATAAATATA-----TCAACAA----A----AATA--C----T-----------------CGTAAGGCGAATAATGGCAAC-GTCTGGGGTGAGCGATTGAGAGTTGTATCTGG-----A--AGCTATATAATC-----------------
droPer1	super_13:433852-434017 -	LASTZ	0	TTTCCATGCTTGGACAATTCCTTGAACGGTCGTCC------C---------------GCCCGGTTTGCCAGCCCAAGGGGC----GGCGGGGGGAGGGGGGAATAAGTATA-----TCAACAA----A----AATA--C----T-----------------CGTAAGGCGAATAATGGCAAC-GCCTGGGGTGAGCGATTGAGAGTTGTATCTGG-----A--AGCTATATAATC-----------------
droWil1	scaffold_181150:832777-832852 +	LASTZ	0	ATGTCTTCCATTCCCTATT-TGCGTATTTTCTTT---------------------------------------CAGTA---------------------TAAATGAATATG-----TATGAGTCGA------AATA--C----C-----------------T-----------------------------------------------------------------------------ATAA----ATGAT
droVir3	scaffold_12726:2732407-2732514 +	LASTZ	0	TGGA------TCAACAAAT-GCCGCACATTTCTTT--------------------------------CTTGCTTTCGT---------------------TC-ACAATTTCTCTTGTAATATAATC---AATTTTTA--T----------------------------TCAATT--------------------------------------------CATA--CGATTCACATTCAA-TTCGTT---TGACT
droMoj3	scaffold_6500:9117978-9118115 -	LASTZ	0	CA----AGCTGCGACTATG-TAATTAAAATTGTAT------G--TATCAGCGGGTCT----------ATTGCTATGTG---------------------TGTATAGGTGTG-----TGTGTGTGTGTA------TG--------------T-------GTGTGTATGTGTGCATATACAAAGC--------------------------------CATAAT--AGCATAAAACTCGA-TAAGC----CTGGC
droGri2	scaffold_15110:597989-598133 +	LASTZ	0	TCGCCATATTTCGTTGAAT-T-------CTTCGCC------ATATATC---------G---------TATGAT---------------------------TTATATATATA-----TATATAAATATA----TATA--TATATTTCGGCTCCAAATATTTTTTATATTTTGCAAAGACTTGCT--------------------------------GTG--G--TTTTTCATAAGTGAGTTTGA-ATATTGTA

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	TCGCCATGCTTCGACAATTTTTGAATGGTCCTTT------TCATGCCCAA-GGCGAATAAATATGTA------TTTATGTATATTTTTTTATATGGTACGTATTTATTTGTCTGCAAATGGCTGCCAAGGAG--TGCTACATAATCAATTT-GTTTGTT
droSim1	TCGCCATGCTTCGACAATTTTTGAATGGTCCTTT------TCATGCCCAA-GGCGAATAAATATGTA------TTTATGTATATATATTTATAT-------ACGCATTCGTCTGCAAATGGCTGCCATGGAG--TGCTACATAATCAATTT-GTTTGTT
droSec1	TCGCCATGCTTCGACAATTTTTGAATGGTCCTTT------TCATGCCCAA-GGCGAATAAATATGTA------TTTATGTTTATATAT-----------------------------TTGGCTGCCATGGAG--TGCTACATAATCAATTT-GTTTGTT
droYak2	TTGCCATGCTTGGACAATTTTTGAATGGTCCTTT------TCATGCCCAA-GGCGAATAAATATGTA------TTTATGTGTAGAT------AT-------ATGTATTTGTCTGAAAATGGCTGCCAAGGAG--TGCTACATAATCAATTT-GCTTATT
droEre2	TTGCCATGCTTGGACAATTTTTGAATGGTCCTTT------CCATCCCCAA-GGCGAATAAATATGTTTGTGTGTACGAGTATATATTTAT--AT-------ATGTATCGGTCTGCAAATGGCTGCCAATGAG--TGCTTCAAAATCAAATT-GTTTGTT
droEug1	TTGCCATGCTTGGACAATTTTTGAATGGTTCTTTGAATGGTCATGCCCAAAGGCGT-------CGTC------TTAGTATATATATTTTGATAT----------------CCCCCAAATCGCTGTCGAGGAGGTGGCTACATAATCAATTT-GTTTGTT
droBia1	TTGCCATGCTTGGACTAATTTTGAACGGCCCTTT------GCCAGCCGCC-GGCGAATAAATGTGTA------TATATACAT---------------------------------GAAGGGATGCCAAGAAG--TGCTTCATAATCAATTT-GTTTGTC
droTak1	TTTCCATGCTTGGACAATTTTTGAATGGTCCTTT------TCTTGCCCCA-AGCGAATAAATGTATA------TATAGGTATAAATATATATTT-------------------------G------GAGGAG--TGCTACATAATCAATTT-GTTTGTT
droEle1	TTTTCATGCTTGGACAATTTTTGAGTTGTCCTTT------TTATGCCCAA-GCCGAGTATATGTATA------TATAAGTATATTTATATATA-----------------ACCACAAATGGAAGCCAAGGAG--TGCTTCATAATCAATTT-GTTTGTA
droRho1	TTTCCATGCTTGGACAATTTTTGAACGGTCCTTT------TCATGCCCAA-GGCCAATATATATACA------TATATATATATAT------AA-------GTCTATATGTCTACAAATGGATGGCAAGGAG--TGGTACATAATCAATTTAGCTTGTT
droFic1	TTTCCATGCTTGGACAATTTTTGAATGGTCCTTT------TCATGCCCAA-GGCGAATAAATATGTA------TATATATATATAT------T-----------------TGCACAAATGGATACCAAAGAG--TGCTGCATAATCAATTT-ATTTGTT

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

TCGCCATGCTTCGACAATT-TTTGAATGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CGAATAAATATG-----TATTTATGTATA----TATA--T----T--TATAT-------ACGCATTCGTCTGCAAATGGCTGCC--------------------------------ATGGAG--TGCTACATAATCAA-TTTGT----TTGTT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................................................................................................TATG-----TATATATGTATA----TATG--..................................................................................................................	20	30	0.03	0.00	0.03	0.00	0.00
........................................................................................................................TATGTATA----TAGA--T----C--TATAT-------AC............................................................................................	21	1	1.00	0.00	1.00	0.00	0.00

droSec1

TCGCCATGCTTCGACAATT-TTTGAATGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CGAATAAATATG-----TATTTATGTTTA----TATA--T----T-------------------------------TGGCTGCC--------------------------------ATGGAG--TGCTACATAATCAA-TTTGT----TTGTT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...................................................................................................................................................................................................................................GCATAATCxA-TTTGT----TTGT.	18	1	1.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................CATAATCxA-TTTGT----TTGTT	18	1	1.00	0.00	1.00	0.00

droYak2

TTGCCATGCTTGGACAATT-TTTGAATGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CGAATAAATATG-----TATTTATGTGTA----GATA--------------T-------ATGTATTTGTCTGAAAATGGCTGCC--------------------------------AAGGAG--TGCTACATAATCAA-TTTGC----TTATT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................................................................................................................................TGACAAxGGCTGCC--------------------------------AAGGAG--.............................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TTGCCATGCTTGGACAATT-TTTGAATGGTCCTTT------C-------------------------CATCCCCAAGG---------------------CGAATAAATATG-----TTTGTGTGTACGAGTATATA--T----T--TATAT-------ATGTATCGGTCTGCAAATGGCTGCC--------------------------------AATGAG--TGCTTCAAAATCAA-ATTGT----TTGTT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.................................................................................................................................GTATATA--T----T--TCTAT-------GTGT..........................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................ACAAATTTG-----TTTGTGTGT...............................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......TGCTTGGACTACT-TTTGAAT.................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................AGGATATA--T----G--TATAT-------ATG...........................................................................................	18	4	0.25	0.00	0.00	0.00	0.25

droEug1

TTGCCATGCTTGGACAATT-TTTGAATGGTTCTTTGAATGGT-------------------------CATGCCCAAAG---------------------------GCGTCG-----TCTTAG--TATA----TATATTT----T--GATAT----------------CCCCCAAATCGCTGTC--------------------------------GAGGAGGTGGCTACATAATCAA-TTTGT----TTGTT

Size

Hit Count

Total Norm

droBia1

TTGCCATGCTTGGACTAAT-TTTGAACGGCCCTTT------G-------------------------CCAGCCGCCGG---------------------CGAATAAATGTG-----TATATATACATG---------------------------------------------AAGGGATGCC--------------------------------AAGAAG--TGCTTCATAATCAA-TTTGT----TTGTC

Size

Hit Count

Total Norm

droTak1

TTTCCATGCTTGGACAATT-TTTGAATGGTCCTTT------T-------------------------CTTGCCCCAAG---------------------CGAATAAATGTA-----TATATAGGTATAAATATATA--T----T------T-------------------------G--------------------------------------GAGGAG--TGCTACATAATCAA-TTTGT----TTGTT

Size

Hit Count

Total Norm

droEle1

TTTTCATGCTTGGACAATT-TTTGAGTTGTCCTTT------T-------------------------TATGCCCAAGC---------------------CGAGTATATGTA-----TATATAAGTATA----TTTA--T-----------------------ATATAACCACAAATGGAAGCC--------------------------------AAGGAG--TGCTTCATAATCAA-TTTGT----TTGTA

Size

Hit Count

Total Norm

droRho1

TTTCCATGCTTGGACAATT-TTTGAACGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CCAATATATATA-----CATATATATATA----TATA--------------A-------GTCTATATGTCTACAAATGGATGGC--------------------------------AAGGAG--TGGTACATAATCAATTTAGC----TTGTT

Size

Hit Count

Total Norm

droFic1

TTTCCATGCTTGGACAATT-TTTGAATGGTCCTTT------T-------------------------CATGCCCAAGG---------------------CGAATAAATATG-----TATATATATA------TATA--T----T-----------------------TGCACAAATGGATACC--------------------------------AAAGAG--TGCTGCATAATCAA-TTTAT----TTGTT

Size

Hit Count

Total Norm

droKik1

TTTCCACGCTTGGACAGTTCTCTGAATGGTCCTTT------TTGCGCTTGGGGGAAT--------------------G---------------------TAGCTAAATGTA-----GGTTTATGTATC----TATATTTTAATAACTGTGTCAAATATCTATATCTATCAACAAA--------------------------------------------CT--GGCTACATAATCAA-TTTGT----TTGTT

Size

Hit Count

Total Norm

droAna3

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

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

Size

Hit Count

Total Norm

dp4

TTTCCATGCTTGGACAATTCTTTGAACGGTCGTCC------C---------------T----TTTTGCCAGCCCAAGGGGGGAGGGATGGGGGGGGGGGGGAATAAATATA-----TCAACAA----A----AATA--C----T-----------------CGTAAGGCGAATAATGGCAAC-GTCTGGGGTGAGCGATTGAGAGTTGTATCTGG-----A--AGCTATATAATC-----------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................................GAxGGATGGGGGGGGGGGGTA......................................................................................................................................................	20	1	4.00	2.00	0.00	2.00	0.00
.................................................................................GAxGGATGGGGGGGGGGGGA.......................................................................................................................................................	19	1	4.00	1.00	0.00	3.00	0.00
..................................................................................AGGGGTGGGGGGAGGGGG........................................................................................................................................................	18	1	3.00	3.00	0.00	0.00	0.00
..............................................................................GAGGAxGGATGGGGGGGGG...........................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
...............................................................................GAGAGGAATGGGGGGGGGG..........................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................................................................AAGGGGGGAGGGGTGGGG................................................................................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00
..........................................................................AAGGGGGGAGGGAAGGAGGGGG............................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
............................................................................GGGGGGGGGGAGGGGGGG..............................................................................................................................................................	18	4	0.25	0.00	0.00	0.25	0.00
..............................................................................AGGGAGGGATGGAGGGGG............................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
............................................................................GGGGGGGGGGGTGGGGGGGG............................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
..................................................................................GAGGATGGGGGGGGGGGGG.......................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...........................................................................AGGGGGGAGGGAAGGGGGG..............................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...........................................................................AGGGGGGAGGGAGGGGGAGGG............................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.................................................................................GATGGxxGGGGTGGGGGGGG.......................................................................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00
...................................................................................GAGATGGGGGGGGGAGGG.......................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
...........................................................................AAGGGGGGGGGATGGGGGG..............................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.................................................................................GAxGGATGGGGGGGGGGGGT.......................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.................................................................................GAxGGATGGGGGGGGGGGGAA......................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.................................................................................GAxGGATGGGGGGGGGGGGGTA.....................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................GAGGAGGGATGGGGAGGG............................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................................................GAxGGATGGGGGGGGGGGGC.......................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
................................................................................AGAGGGATGGGGGGGTGG..........................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droPer1

TTTCCATGCTTGGACAATTCCTTGAACGGTCGTCC------C---------------GCCCGGTTTGCCAGCCCAAGGGGC----GGCGGGGGGAGGGGGGAATAAGTATA-----TCAACAA----A----AATA--C----T-----------------CGTAAGGCGAATAATGGCAAC-GCCTGGGGTGAGCGATTGAGAGTTGTATCTGG-----A--AGCTATATAATC-----------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..........................................................................AAGGGGC----GGxGGAGGGAGGG..........................................................................................................................................................	19	2	1.50	0.00	0.00	0.00	1.50	0.00
..........................................................................AAGGGGC----GGxGGGGGGAGGGGG........................................................................................................................................................	21	1	2.00	0.00	0.00	0.00	2.00	0.00
..........................................................................AAGGGGC----GGxGGGGGGAGGGCG........................................................................................................................................................	21	1	2.00	0.00	0.00	0.00	2.00	0.00
..........................................................................AAGGGGG----GGCGGGGGGAGC...........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GGCGGGGGAGG............................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGTC----GGxGGGGGGAGGG..........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................AGGGGC----GGACGGGGGAGG...........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GGxGCGGGGAGGG..........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................AGGGGC----GGxGGAGGGAGGGG.........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GGxGGGGGGAGGGC.........................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................TAGGGGA----GGCGGGGGGAG............................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................GGGGC----GGAGGGGGGTGGGG.........................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................GC----GGCxGGGGGAGGGGCGAA.....................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................AGGGGC----GGTGGGGGGAGT...........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................AGGGGC----GGTGGGGGGGGG...........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GGxGGAGGGAGG...........................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
..........................................................................AAGGGGC----GGCxTGGGGAGGGG.........................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................CTAGGGAC----GGCGGGGGGA.............................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................TAAGGGGC----GGxGGGGGGAGGGG.........................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................GGGGGGGGGAGGGGGGGA.....................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................GGC----GGxGGGGGGAGGGGGT.......................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................AGGGGC----GGCGGGTGGGGG...........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................ATGGGGC----xGCGGGGGGAGG...........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................TC----GGxGGGGGGAGGGGGGA......................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................AGGGGT----GGCGGTGGGAGGGGGG.......................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................AAGGGGC----GGCxGGGGGAGA...........................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................AGGGGC----GGxGGTGGGAGGG..........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GACxGGGGGAGG...........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................AGGGGC----GGxGTGGGGAGGG..........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................GGGC----GGAGGGGTGAGGGGG........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GCCGGGGGGAGA...........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................GCGx----GGCGGGGGGACGGGG........................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................................GTGGC----GGAGGGGGGAGGGG.........................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................AAGGGGC----GGxGGGGGGAGGG..........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GGxGGGGGGAGGGT.........................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................GGGGGAGGGAGGGGGGAAT....................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................AAGGGGC----GGxGGGGGGATG...........................................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33	0.00
..........................................................................AAGGGGC----GGxGGGGAGAGG...........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GGxGGGGGGATGGGG........................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GGxGGGGGGAGA...........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................ATGGGGC----GGTGGGGGGAGG...........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................AAGGGGC----GGxGGAGGGAGGGG.........................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................................AGGGGGGAGAGGGGAATAAG.................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

ATGTCTTCCATTCCCTATT-TGCGTATTTTCTTT---------------------------------------CAGTA---------------------TAAATGAATATG-----TATGAGTCGA------AATA--C----C-----------------T-----------------------------------------------------------------------------ATAA----ATGAT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...................................................................................................TAAATGAATxTG-----TATGTGT.................................................................................................................................	18	1	3.00	0.00	3.00	0.00	0.00
........................................................................................................................................................................................................................................................TGAT	19	3	0.67	0.00	0.67	0.00	0.00
...................................................................................................TAAATGAATxTG-----TATGTGTC................................................................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
...................................................................................................TAAATGAATATG-----TGTGTGT.................................................................................................................................	19	3	0.33	0.00	0.00	0.33	0.00
.............................................................................A---------------------TAAATGAATATC-----TAGGAG..................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

TGGA------TCAACAAAT-GCCGCACATTTCTTT--------------------------------CTTGCTTTCGT---------------------TC-ACAATTTCTCTTGTAATATAATC---AATTTTTA--T----------------------------TCAATT--------------------------------------------CATA--CGATTCACATTCAA-TTCGTT---TGACT

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CA----AGCTGCGACTATG-TAATTAAAATTGTAT------G--TATCAGCGGGTCT----------ATTGCTATGTG---------------------TGTATAGGTGTG-----TGTGTGTGTGTA------TG--------------T-------GTGTGTATGTGTGCATATACAAAGC--------------------------------CATAAT--AGCATAAAACTCGA-TAAGC----CTGGC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TCGCCATATTTCGTTGAAT-T-------CTTCGCC------ATATATC---------G---------TATGAT---------------------------TTATATATATA-----TATATAAATATA----TATA--TATATTTCGGCTCCAAATATTTTTTATATTTTGCAAAGACTTGCT--------------------------------GTG--G--TTTTTCATAAGTGAGTTTGA-ATATTGTA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:51 EDT

dme-mir-4964

chrX:8859833-8859945 +

Known_mirbase

intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup