dme-mir-4972- Best orthologs

dme-mir-4972	chr2L:3636966-3637073 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 3636992-3637013
   star strand at position 3637030-3637049
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:3636951-3637088 -		1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCTCG---------------------------GCTTTACAGATATATATA----------------TATAT-ATCGTGTATAT-----------------------ATCTGTG-------------------------------CGATCGGGATTGA-------GACTGAGG-TTGGTCC---------GAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droSim1	chr2L:3596396-3596533 -	LASTZ	4	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCG---------------------------GCTTTATATATATGTATA----------------TATAT-CGTGTATATAT-----------------------ATCTGAG-------------------------------AGATCGGGATTGA-------GACTGAGG-TTGGTCC---------GAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droSec1	super_5:1737908-1738045 -	LASTZ	4	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCTCG---------------------------GCTTTATATATATGTATA----------------TATAT-CGTGTATATAT-----------------------ATCTGAG-------------------------------AGATCGGGATTGA-------GACTGAGG-TTGGTCC---------GAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droYak2	chr2L:3630931-3631061 -	LASTZ	5	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCG---------------------------ACTATATATGTATATA----------------TATATAT--------ATAT-----------------------ATCTGTG-------------------------------AGATCGGGATTGA-------GACTGAGG-TTGGTCT---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droEre2	scaffold_4929:3675838-3675960 -	LASTZ	5	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCTCA---------------------------GCTATATATATATGT--------------------------------GTGT-----------------------ATCTGTG-------------------------------GGATCGGGATTGA-------GACTGAGG-TTGGTCT---------TAG-----------------------------------T-ACTTTTGTGGCCA--TTTGCACC
droEug1	scf7180000409554:2446749-2446886 +	LASTZ	5	CACTTGCATGGCATAAATCAAAAGCGCCGTGGGCCT-CCA------CCTAG---------------------------GCTGTATATGTGTGTGCC----AA--------TATATATATGC-----T--------------------AG---ATCTGTA-------------------------------AGATCGGGATTGA-------GACTGAGC-TTGGTCT---------TGG-----------------------------------T-GCTTTTGTGGCCA--TTTACACC
droBia1	scf7180000302408:1936903-1937038 -	LASTZ	5	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCG---------------------------GCTCCATACATATATACA----G------------------------ATAT-----------------------ATCTATG-------------------------------GGATCGGGATTGA-------AACCGAGG-CTGGTCAGCATTACTGCAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droTak1	scf7180000415399:625592-625728 -	LASTZ	5	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCT---------------------------GCTATATATATACA------------------TATATATGCGT-----T--------------------AA---ATCTATG-------------------------------GGATCGGGATTGA-------GACTGAGG-TTGGTCAGTACT----CCG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droEle1	scf7180000490728:350554-350688 -	LASTZ	5	CACTTGCATGGCATAAATCAAAAGCGCCGCAGGCCT-CCA------CTACG---------------------------ATATACCACATATATA----------------TATATATTCATG-------------------------AA---GTCTATG-------------------------------GGATCGGGATTGA-------GACTGAGGCTTGGTCT---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droRho1	scf7180000779523:343635-343767 -	LASTZ	5	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCACG--------------------------------ATATATATGTATA----GA--------TATATGTTCGTG-------------------------AA---ATCTATG-------------------------------GGATCGGGATTGA-------GTCTGGGG-TTGGTCA---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droFic1	scf7180000453924:1625288-1625423 -	LASTZ	5	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------GCTCG----------------------------CTATATAC--------A----GA--------TATATATGCGTG-------------------------AA---GTCTATG-------------------------------GGATCGGGACTGAGAACTGGGACCGAGG-TTGGTCG---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTGCACC
droKik1	scf7180000302270:976219-976364 +	LASTZ	5	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCGCCGACA--CCGCCAGATATTAT----------GTATATATATATATATATATA--------TAT------------ATATACTTGACAG---------AA---ATCTATG-------------------------------GGATCGGGATCGA-------AACTGAGG-TTGG------------------------------------------------------------GTCCA-TTTTACAC-
droAna3	scaffold_12916:5691742-5691836 -	LASTZ	0	CACTTGCAAGGCATAAATCAAAAGCGCCGTAGGCCT-CCG------CCACT---------------------------------------------------------------------------------------------------------------------------------------------ATGAGTCTGGA-------GTCTGGTG-ATGGTGG---------AGT-----------------------------------G-CCTTTTGTGGCCA--TTGGCACC
droBip1	scf7180000396568:1147600-1147682 +	LASTZ	0	CACTTGCATGGCATAAATCAAAAGCGCCATAGGCCT-CCA------C----------------------------------------------------------------------------------------------------------------------------------------------------AGACTACA-------GGCCAGTG-TTGGTGT--------------------------------------------------CATTTGTGGCCA--TTTGCACC
dp4	chr4_group3:5095808-5095886 +	LASTZ	0	CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTTTG------GAGTT--------------TTTTGTGGCACAGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG
droPer1	super_1:6587322-6587402 +	LASTZ	0	CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTTTG------GAGTT--------------TTTTGTGGCACAGTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG
droWil1	scaffold_180708:9512363-9512488 +	LASTZ	0	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTTCCA------CCTCT------------------------------ATATA-----GTATA------ATGTGTTC--------------CACATACTCGAC---------------------------------------------------------TTGGGA------GTTGAATTCGAAG-TTG-TCC---------ATG-----------------------------------T--CTTTTGTGGCCAATTTTACACC
droVir3	scaffold_12963:15108661-15108745 +	LASTZ	0	CACTCGCGTGGCATAAATCAAATGCGTTGCAGGCCG-CCG------GCGCT--------------------CCACG-------TTG------------------------------------------CACTCGAC----------------------------------------------------------------------------------------TC---------CTC-----------------------------------T-A--CTTGCGGCTA--GCAGCTCC
droMoj3	scaffold_6500:18077427-18077576 +	LASTZ	0	CACTTGTGTGGCATAAATCAAATGCGCAGCAGGCCG-CCA------GCTGA--CG--C-----------------------------------TGA------CCGTGTTG------------------CACTCGAGTCGAG------------------------T-----------------------------------------------TGAGT-GGAGTCAACTCG----CCGCAGCTTTTCATTCGCATATACCCAGCCAAGCCAAGTGGTCTTTGGGGCCA--TTTACACG
droGri2	scaffold_15126:4287105-4287265 -	LASTZ	0	CACTTGCATGGCATAAATCAAATGCGCCGCGGGCCT-TTG------CTACG---------------------------------TGC---------------------CA--------------CATGCACTCGACTCTCGCCTCTCAACACGACTGACCGAACATTGGCTGGACAAGCCAAGCTGCAGCAGATCGGGGC-----ATTCC-----------ACTCC---------AAG-----------------------------------TGGTCTTTGAGGCCA--TTTGCACG

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	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCACCTCGGC---------------TT-TACAGATATATA--------TATATATATCGTG--T----ATA-TATCTGTGCGATCGGGATTGAG-------ACTGAGGTT-GGTCC---------GAGTACTTTTGTGGCCATT-TACACC
droSim1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCAACTCGGC---------------TT-TATATATATGTA--------TATA--TATCGTGTAT----ATA-TATCTGAGAGATCGGGATTGAG-------ACTGAGGTT-GGTCC---------GAGTACTTTTGTGGCCATT-TACACC
droSec1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCACCTCGGC---------------TT-TATATATATGTA--------TATA--TATCGTGTAT----ATA-TATCTGAGAGATCGGGATTGAG-------ACTGAGGTT-GGTCC---------GAGTACTTTTGTGGCCATT-TACACC
droYak2	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCAACTCGAC---------------TA-TATATGTATATA--------TATATAT-------------ATA-TATCTGTGAGATCGGGATTGAG-------ACTGAGGTT-GGTCT---------CAGTACTTTTGTGGCCATT-TACACC
droEre2	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCACCTCAGC---------------TA-TATATATATGTG-----------------------------TG-TATCTGTGGGATCGGGATTGAG-------ACTGAGGTT-GGTCT---------TAGTACTTTTGTGGCCATT-TGCACC
droEug1	CACTTGCATGGCATAAATCAAAAGCGCCGTGGGCCTCCACCTAGGC---------------TG-TATATGTGTGTG----CCAATATATAT-ATGC---------T-AGATCTGTAAGATCGGGATTGAG-------ACTGAGCTT-GGTCT---------TGGTGCTTTTGTGGCCATT-TACACC
droBia1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCAACTCGGC---------------TC-CATACATATATA----CAGA---------------------TA-TATCTATGGGATCGGGATTGAA-------ACCGAGGCT-GGTCAGCATTACTGCAGTACTTTTGTGGCCATT-TACACC
droTak1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCAACTCTGC---------------TA-TATATATACA----------TATATAT-GCGT---------T-AAATCTATGGGATCGGGATTGAG-------ACTGAGGTT-GGTCAGTACT----CCGTACTTTTGTGGCCATT-TACACC
droEle1	CACTTGCATGGCATAAATCAAAAGCGCCGCAGGCCTCCACTACGA----------------TATACCACATATATA--------TATATAT-TCATG----------AAGTCTATGGGATCGGGATTGAG-------ACTGAGGCTTGGTCT---------CAGTACTTTTGTGGCCATT-TACACC
droRho1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCACCACGA----------------TA-----TATATGTA----TAGATATATGT-TCGTG----------AAATCTATGGGATCGGGATTGAG-------TCTGGGGTT-GGTCA---------CAGTACTTTTGTGGCCATT-TACACC
droFic1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCAGCTCG-C---------------TA-TATA------------CAGATATATAT-GCGTG----------AAGTCTATGGGATCGGGACTGAGAACTGGGACCGAGGTT-GGTCG---------CAGTACTTTTGTGGCCATT-TGCACC
droKik1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCACCGCCGACACCGCCAGATATTATG-TATATATATATATATATATATATATAT-ACTTG---ACAG---AAATCTATGGGATCGGGATCGAA-------ACTGAGGTT-GG------------------------GTCCATTTTACAC-

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

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCG---------------------------GCTTTATATATATGTATA----------------TATAT-CGTGTATATAT-----------------------ATCTGAG-------------------------------AGATCGGGATTGA-------GACTGAGG-TTGGTCC---------GAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...................................................................................................................................................................................................GGGACTGA-------GGCTGAGG-TTG............................................................................	19	1	2.00	1.00	0.00	0.00	1.00

droSec1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCTCG---------------------------GCTTTATATATATGTATA----------------TATAT-CGTGTATATAT-----------------------ATCTGAG-------------------------------AGATCGGGATTGA-------GACTGAGG-TTGGTCC---------GAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.............................................................................................ATA----------------TAGAT-CGTGTGTATA..........................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
............................................................................................................................................................GAG-------------------------------AGATCGGGAGCGA-------GA......................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCG---------------------------ACTATATATGTATATA----------------TATATAT--------ATAT-----------------------ATCTGTG-------------------------------AGATCGGGATTGA-------GACTGAGG-TTGGTCT---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....................................................................................TATGGAAATA----------------TATATAT--------ATAT-----------------------..................................................................................................................................................	21	13	0.08	0.00	0.00	0.08	0.00	0.00
........................................................................................................................................................ATCTGTG-------------------------------AGATCGGGATTGA-------GACT....................................................................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................................................................................................................................................................................................................T	18	3	0.33	0.00	0.00	0.00	0.33	0.00
.............................................................................................A----------------TATxCAT--------ATAT-----------------------ATCTGTG-------------------------------GGA.........................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCTCA---------------------------GCTATATATATATGT--------------------------------GTGT-----------------------ATCTGTG-------------------------------GGATCGGGATTGA-------GACTGAGG-TTGGTCT---------TAG-----------------------------------T-ACTTTTGTGGCCA--TTTGCACC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
................................................................................TATATATATATGT--------------------------------GAGT-----------------------GT................................................................................................................................................	19	3	0.67	0.00	0.00	0.00	0.67
.......................................................................................ATATGT--------------------------------GTGT-----------------------ATATGTG-------------------------------T...........................................................................................................	18	8	0.13	0.00	0.00	0.00	0.13
.............................................................................................................................GTxT-----------------------TGCTGTG-------------------------------GGATCGGGA...................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
........................................................................................TATGT--------------------------------GxGG-----------------------ATCTGTG-------------------------------GGA.........................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
................................................................................TATATATATATGT--------------------------------GGGT-----------------------GT................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50

droEug1

CACTTGCATGGCATAAATCAAAAGCGCCGTGGGCCT-CCA------CCTAG---------------------------GCTGTATATGTGTGTGCC----AA--------TATATATATGC-----T--------------------AG---ATCTGTA-------------------------------AGATCGGGATTGA-------GACTGAGC-TTGGTCT---------TGG-----------------------------------T-GCTTTTGTGGCCA--TTTACACC

Size

Hit Count

Total Norm

droBia1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCG---------------------------GCTCCATACATATATACA----G------------------------ATAT-----------------------ATCTATG-------------------------------GGATCGGGATTGA-------AACCGAGG-CTGGTCAGCATTACTGCAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC

Size

Hit Count

Total Norm

droTak1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCT---------------------------GCTATATATATACA------------------TATATATGCGT-----T--------------------AA---ATCTATG-------------------------------GGATCGGGATTGA-------GACTGAGG-TTGGTCAGTACT----CCG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC

Size

Hit Count

Total Norm

droEle1

CACTTGCATGGCATAAATCAAAAGCGCCGCAGGCCT-CCA------CTACG---------------------------ATATACCACATATATA----------------TATATATTCATG-------------------------AA---GTCTATG-------------------------------GGATCGGGATTGA-------GACTGAGGCTTGGTCT---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC

Size

Hit Count

Total Norm

droRho1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCACG--------------------------------ATATATATGTATA----GA--------TATATGTTCGTG-------------------------AA---ATCTATG-------------------------------GGATCGGGATTGA-------GTCTGGGG-TTGGTCA---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC

Size

Hit Count

Total Norm

droFic1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------GCTCG----------------------------CTATATAC--------A----GA--------TATATATGCGTG-------------------------AA---GTCTATG-------------------------------GGATCGGGACTGAGAACTGGGACCGAGG-TTGGTCG---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTGCACC

Size

Hit Count

Total Norm

droKik1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCGCCGACA--CCGCCAGATATTAT----------GTATATATATATATATATATA--------TAT------------ATATACTTGACAG---------AA---ATCTATG-------------------------------GGATCGGGATCGA-------AACTGAGG-TTGG------------------------------------------------------------GTCCA-TTTTACAC-

Size

Hit Count

Total Norm

droAna3

CACTTGCAAGGCATAAATCAAAAGCGCCGTAGGCCT-CCG------CCACT---------------------------------------------------------------------------------------------------------------------------------------------ATGAGTCTGGA-------GTCTGGTG-ATGGTGG---------AGT-----------------------------------G-CCTTTTGTGGCCA--TTGGCACC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.....................................................................................................................................................................................................GCTGGA-------CTCTGGTG-ATGGT..........................................................................	19	1	3.00	1.00	2.00	0.00	0.00
.............................................................................................................................................................................................................................GGTGG---------AGA-----------------------------------G-CCTTTTTTG..............	18	1	2.00	0.00	2.00	0.00	0.00
.........................................................................................................................................................................................................GA-------GTCTGGTG-ATGGGGC---------...............................................................	17	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................................................................GAG-CTGGTGG---------AGT-----------------------------------G-CCT....................	17	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................................CTGGTx-ATGGTGG---------ACT-----------------------------------G-C......................	17	1	1.00	0.00	0.00	1.00	0.00

droBip1

CACTTGCATGGCATAAATCAAAAGCGCCATAGGCCT-CCA------C----------------------------------------------------------------------------------------------------------------------------------------------------AGACTACA-------GGCCAGTG-TTGGTGT--------------------------------------------------CATTTGTGGCCA--TTTGCACC

Size

Hit Count

Total Norm

dp4

CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTTTG------GAGTT--------------TTTTGTGGCACAGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...............................................................................CACAGTGTGCGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTG..	19	1	133.00	123.00	0.00	10.00	0.00
................................................................................ACAGTGTGCGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTG..	18	1	25.00	17.00	0.00	7.00	1.00
................................................................................ACAGTGTGCGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGT.	19	1	3.00	3.00	0.00	0.00	0.00
.................................................................................TAATGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	19	11	0.18	0.18	0.00	0.00	0.00
..............................................................................GCACAGTGTGCGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTG..	20	1	2.00	1.00	0.00	1.00	0.00
...............................................................................CACAGTGTGCGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGT...	18	1	1.00	1.00	0.00	0.00	0.00
..................................................................................AGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCT	18	10	0.10	0.00	0.00	0.10	0.00
.................................................................................CTGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTTG	19	50	0.02	0.00	0.00	0.02	0.00
................................................................................ACAGTGTGCGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCG	20	1	1.00	1.00	0.00	0.00	0.00
....................................................................................TGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	19	38	0.03	0.00	0.00	0.03	0.00
..............................................................................TCACAGTGTGCGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTG..	20	1	1.00	1.00	0.00	0.00	0.00
..................................................................................AGTGTGTGxGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGGG	18	2	0.50	0.50	0.00	0.00	0.00
............................................................................TGTCAxAGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG....	19	5	0.20	0.00	0.20	0.00	0.00
..................................................................................TGTGTGTGGGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	19	46	0.02	0.02	0.00	0.00	0.00
.....................................................................................GTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	18	50	0.02	0.00	0.00	0.02	0.00
...............................................................................CTAAGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGT...	18	12	0.08	0.00	0.00	0.08	0.00
...................................................................................GTGGGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTGTG	18	4	0.25	0.25	0.00	0.00	0.00
.................................................................................TAGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGT.	18	5	0.20	0.00	0.00	0.20	0.00
...............................................................................TACCGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTG..	19	4	0.25	0.25	0.00	0.00	0.00
..................................................................................AGTGTGTGTGTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	19	44	0.02	0.02	0.00	0.00	0.00
.................................................................................TAATGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGT.	18	12	0.08	0.08	0.00	0.00	0.00
....................................................................................TGAGTGTTTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	18	2	0.50	0.00	0.00	0.50	0.00
...................................................................................GTGTGTGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	19	46	0.02	0.02	0.00	0.00	0.00
.................................................................................CAGTGTGCGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	19	1	1.00	1.00	0.00	0.00	0.00
...............................................................................CACAGTGTGCGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGT.	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................ATCAGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTG..	19	11	0.09	0.00	0.09	0.00	0.00
....................................................................................TGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	19	14	0.07	0.00	0.07	0.00	0.00
..................................................................................AGTGTGCGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGGG	18	7	0.14	0.00	0.00	0.14	0.00
................................................................................ACAGTGTGTGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCG	20	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................ATGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	18	8	0.13	0.13	0.00	0.00	0.00
.....................................................................................GTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTCTG	19	4	0.25	0.25	0.00	0.00	0.00
....................................................................................TGTGTATGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	20	58	0.02	0.02	0.00	0.00	0.00
..............................................................................TCACAGTGTGTGTGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTG..	20	1	1.00	1.00	0.00	0.00	0.00
....................................................................................TGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG	20	34	0.03	0.03	0.00	0.00	0.00

droPer1

CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTTTG------GAGTT--------------TTTTGTGGCACAGTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...................................................................................GTATGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGT.	18	62	0.05	0.02	0.00	0.00	0.00	0.03
...................................................................................GTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTTTT	20	3	1.00	1.00	0.00	0.00	0.00	0.00
...................................................................................GTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTTTT	19	6	0.50	0.33	0.00	0.00	0.17	0.00
...................................................................................GTGTGTAGATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGT.	18	4	0.50	0.50	0.00	0.00	0.00	0.00
........................................................................GTTGTGGCACAGTGTATGT...............................................................................................................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00	0.00
............................................................................CGGCGCAGTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G......	20	1	2.00	2.00	0.00	0.00	0.00	0.00
...............................................................................CGCAGTGTGTGTGTG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GT.....	18	6	0.17	0.17	0.00	0.00	0.00	0.00
..............................AGGACT-GAxACTTTG------GAGT..................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................AGTGTGTGTTTG----------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	20	4	0.25	0.25	0.00	0.00	0.00	0.00
...................................................................................GTACGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGT.	18	8	0.13	0.00	0.13	0.00	0.00	0.00
...................................................................................GTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------xTGTGAG	18	4	0.25	0.25	0.00	0.00	0.00	0.00
................................................................................ACAGTGTGTGTTTG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGT...	19	2	0.50	0.50	0.00	0.00	0.00	0.00
...................................................................................GTGTGTGTTTG----------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGT.	18	47	0.02	0.02	0.00	0.00	0.00	0.00
...................................................................................GTGCGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	19	46	0.02	0.02	0.00	0.00	0.00	0.00
...................................................................................GTATGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTTT.	18	4	0.25	0.00	0.00	0.00	0.25	0.00
...................................................................................GTATGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTATGTG	19	8	0.13	0.13	0.00	0.00	0.00	0.00
..................................................................................CGCGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGT.	19	9	0.11	0.00	0.00	0.11	0.00	0.00
....................................................................................TGTGTGTTTG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	21	6	0.17	0.17	0.00	0.00	0.00	0.00
......................................................................................TGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	19	3	0.33	0.33	0.00	0.00	0.00	0.00
.................................................................................CTGTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTTT.	20	5	0.20	0.20	0.00	0.00	0.00	0.00
...................................................................................GTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	20	42	0.02	0.00	0.02	0.00	0.00	0.00
.....................................................................................GTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	19	49	0.02	0.02	0.00	0.00	0.00	0.00
......................................................................................TGTGTTTG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	19	7	0.14	0.14	0.00	0.00	0.00	0.00
..................................................................................AGTGTGTGTGTG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGCGT.	19	51	0.02	0.00	0.02	0.00	0.00	0.00
................................................................................ACTGTGTGTGCATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTG..	20	1	1.00	0.00	1.00	0.00	0.00	0.00
..................................................................................TGTGTGTGTGTG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	22	47	0.02	0.00	0.00	0.02	0.00	0.00
..................................................................................TGTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTATGT.	19	45	0.02	0.00	0.02	0.00	0.00	0.00
..............................AGGACT-GAxACTTTG------GAGTT--------------...................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
..................................................................................TGTGTGTGTACG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGT.	19	40	0.03	0.00	0.00	0.03	0.00	0.00
....................................................................................GATGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	18	11	0.09	0.09	0.00	0.00	0.00	0.00
..................................................................................AGTGTGTGTGTG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTGT.	19	46	0.02	0.02	0.00	0.00	0.00	0.00
...................................................................................GTGTGTGACTG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGT.	18	46	0.02	0.02	0.00	0.00	0.00	0.00
.................................................................................TAGTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTC..	19	2	0.50	0.50	0.00	0.00	0.00	0.00
.....................................................................................GTGTGTGTG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	21	36	0.03	0.03	0.00	0.00	0.00	0.00
...................................................................................ATGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG	20	47	0.02	0.02	0.00	0.00	0.00	0.00
.....................................................................................GTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGAGTG	18	7	0.14	0.14	0.00	0.00	0.00	0.00

droWil1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTTCCA------CCTCT------------------------------ATATA-----GTATA------ATGTGTTC--------------CACATACTCGAC---------------------------------------------------------TTGGGA------GTTGAATTCGAAG-TTG-TCC---------ATG-----------------------------------T--CTTTTGTGGCCAATTTTACACC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...............AATCACAAGCGACGTAGGCCT......................................................................................................................................................................................................................................................................	21	1	196.00	8.00	1.00	0.00	187.00
..............AAATCACAAGCGACGTAGGCC.......................................................................................................................................................................................................................................................................	21	1	28.00	6.00	1.00	2.00	19.00
..............AAATCACAAGCGACGTAGGCCT......................................................................................................................................................................................................................................................................	22	1	15.00	1.00	1.00	1.00	12.00
................ATCACAAGCGACGTAGGCCT......................................................................................................................................................................................................................................................................	20	1	11.00	1.00	0.00	0.00	10.00
..............AAATCACAAGCGACGTAGGC........................................................................................................................................................................................................................................................................	20	1	4.00	4.00	0.00	0.00	0.00
..............AAATCACAAGCGACGTAGG.........................................................................................................................................................................................................................................................................	19	1	4.00	3.00	0.00	1.00	0.00
...............AATCACAAGCGACGTAGGCC.......................................................................................................................................................................................................................................................................	20	1	2.00	1.00	0.00	0.00	1.00
.................TCACAAGCGACGTAGGCCT......................................................................................................................................................................................................................................................................	19	1	2.00	0.00	0.00	0.00	2.00
.................TCACAAGCGACGTAGGCC.......................................................................................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
..............................................................................................................................................................................................................TTGAATTCGAAG-CTG-TGC---------...............................................................	18	1	2.00	0.00	0.00	0.00	2.00
................ATCACAAGCGACGTAGGCC.......................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................TGGA------GTTGAATTCCAAG-TT.............................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............AATCACAAGCGACGTAGGC........................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................GTTGAATTCGAAG-TTG-TCC---------ATG-----------------------------------T--......................	23	1	1.00	1.00	0.00	0.00	0.00

droVir3

CACTCGCGTGGCATAAATCAAATGCGTTGCAGGCCG-CCG------GCGCT--------------------CCACG-------TTG------------------------------------------CACTCGAC----------------------------------------------------------------------------------------TC---------CTC-----------------------------------T-A--CTTGCGGCTA--GCAGCTCC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CACTTGTGTGGCATAAATCAAATGCGCAGCAGGCCG-CCA------GCTGA--CG--C-----------------------------------TGA------CCGTGTTG------------------CACTCGAGTCGAG------------------------T-----------------------------------------------TGAGT-GGAGTCAACTCG----CCGCAGCTTTTCATTCGCATATACCCAGCCAAGCCAAGTGGTCTTTGGGGCCA--TTTACACG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........................................................................................................................................CGAG------------------------T-----------------------------------------------TGAGT-TGAGTCGACT.....................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droGri2

CACTTGCATGGCATAAATCAAATGCGCCGCGGGCCT-TTG------CTACG---------------------------------TGC---------------------CA--------------CATGCACTCGACTCTCGCCTCTCAACACGACTGACCGAACATTGGCTGGACAAGCCAAGCTGCAGCAGATCGGGGC-----ATTCC-----------ACTCC---------AAG-----------------------------------TGGTCTTTGAGGCCA--TTTGCACG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:17 EDT

dme-mir-4972

chr2L:3636966-3637073 -

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