dme-mir-2279- Best orthologs

dme-mir-2279	chr2RHet:1322833-1322945 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 1322894-1322915
   star strand at position 1322858-1322879
   mutations
   read mismatches

Notes: "Many of the reported orhtologs have reads, but they are outside the miRNA size range and look like repeatable elements. "

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2RHet:1322818-1322960 -		1	TCCGATGACCCATGGCGGGAGAGGATTATGAAAGAC-AA---TTTGAAA---------------TTAAATATCTGTGTGT----------------------------GAA-------------------------------------------------ATTATTTAAAAG----------------------------------------------ATTAATTTC---------------------------------------ACGCGA-----------------------------------------------------------AGATATTTATTT---TTACATTTGTCC---------------------------------------------------------------------CTATAATAACCGGGG---------------------T----------GCCA---ACATACAT
droSim1	chr2R:265657-265782 +	LASTZ	0	AGGCAATTTTC-------------------AA--------------------------------TTAAATATCTGTGTGT----------------------------GGA-------------------------------------------------ATTATTAAAAACAATGAG------------------------TTCAAAGG--------TTTAGTTTC---------------------------------------ACGTAA-----------------------------------------------------------AGATATTTATTTTGTTTAAATT-TTCC---------------------------------------------------------------------CTAGAATAACCAGTA---------------------T----------GCCG---ACATAA-A
droSec1	super_55:122657-122779 +	LASTZ	0	AAGTAAACTTA-------------------AAA-------------------------------TTATAAATATGTGTGT----------------------------GAAATTAAT---------------------------------------------------AAACGGTAAG------------------------TTCGAAAG--------TTTAGTTTC---------------------------------------ACGCGA-----------------------------------------------------------AAGTATTTATTT---TTACATTTGTCC---------------------------------------------------------------------ATAGAATAACCGGGG---------------------G----------GCCA---ACATAA-A
droYak2	chr2h_random:1837227-1837349 -	LASTZ	0	AAGACAACTTA-------------------AAT-------------------------------TTTTATATCTGTGTGG----------------------------GAAATTAAG---------------------------------------------------AAACAGTGAG------------------------TTCGAAAA--------TTTAGTTTC---------------------------------------GTGTAA-----------------------------------------------------------AGTTATTTATTT---CTGCATTTGTCC---------------------------------------------------------------------CTAGAATAACCGAGG---------------------T----------CCCA---ACATAA-A
droEre2	scaffold_4845:21278391-21278511 +	LASTZ	0	CTCCATAACTC-------------------AACTTA---------TCTT---------------AATCGGATTTTGAAGT----------------------------G---------GCATACCTCTAAATGTTTGTGG----------------TGCAATTATCTAAAAAACTGCA------------------------TTCAAA-------------------------------------------------------------TTT-----------------------------------------------------------AAAAATTTATTTTTTTTACATTTTTTT---------------------------------------------------------------------GT-----------------------------------------------------------A
droEug1	scf7180000409463:813252-813375 -	LASTZ	0	TGACACAAATC-------------------GAGAGT--G---CACTGAGAAAAAGGCAGGGTAGCTACTTATCTGTAAGA----------------------------GGA-------------------------------------------------AAAACTTAAGAA-ATAAGTTCTTTTATGAAGTAATGAAATTT--------AT-TCATC---------------------------------------------------------------------------------------------------------------------------TT---TCACCTTTATTT---------------------------------------------------------------------CT-----------------------------------------------------------A
droBia1	scf7180000302069:1281651-1281776 -	LASTZ	0	GGGAAGAAATT-------------------GAAGTGCAA---ATATGCA---------------AAACATATCTATGTAC----------------------------GAT-------------------------------------------------ATTATTTAAGTT--------------------------------------TT-TTTTT---------------------------------------------------------------------------------------------------------------------------TC---AAACTTCTATGC---------------------------------------------------------------------AG--TAGTTTCTGGGGTGCATCTTATAGTGCCCAGTT----------TCAT---AAAGACAT
droTak1	scf7180000414441:15526-15661 -	LASTZ	0	TTTTATAATAC-------------------AAATTG-AA-------AAA-----------------TAAGACTTATTTGTCAATTTTTTTAAAAAAGTAACTCTTACTT--------GCGATCCCTGTAAATATTTCTATAAGTGTAATTTAAGGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACC---------------------------------------------------------------------CTATAACGAGTACAA---------------------T----------TCTT---ACATGCTT
droEle1	scf7180000486807:9902-10004 +	LASTZ	0	TGATCCATATC-------------------GGTAA--AT---TTATAAG---------------AAACTGACTTGAAAGC----------------------------GGA-------------------------------------------------AAATTTTATG------------------------------------------------------------------------------------------------------------------------------GAAATCCAATCAATATTATT---AAATTCATCAAAAGATATTTCTTC---T------------------------------------------------------------------------------------------------------------------------------------------GACA
droRho1	scf7180000767875:903-1047 +	LASTZ	0	TCGGAGCACCC-------------------GACTAT-AG---C---GTT-------------------C-TCTCTTGTTT----------------------------TGTATTAAG---------------------------------------------------AAAGGGTACA------------------------CTTTTAAA--------TTAAGTGTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------TGGAGAGTTCTGAATTTCTTAAGAGATATCATAAGTTCTTTGTAATAAGAGGTA---------------------TTTTAGCAG--TCAT---GTCTCTCA
droFic1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000298698:14727-14830 -	LASTZ	0	GAAAAACGAAG-------------------CAA----AA---CTAAAAA-----------------AA--ACATGTGTGT----------------------------GAC-------------------------------------------------ATCATTTTAAACATTAAA------------------------TTCAAA-------------------------------------------------------------ACA-----------------------------------------------------------AAACTTTGATTTGGCC------------------------------------------------------------------------------------AACACGTTTGG---------------------G----------CGCT---A-TAATAA
droAna3	scaffold_13334:5190-5293 +	LASTZ	0	AAAAAATTAGT-------------------AAAAAA-AA---TAATAAA---------------TAAAAAAAAATATGGT----------------------------GGG-------------------------------------------------ATTTTTTAAAAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATATTTTTT-------------------------------------------------------------------------------------ATATGGCAATTGGTA---------------------GTTAAATATTAGTCT---TTTTAAGA
droBip1	scf7180000395238:27783-27922 +	LASTZ	0	CGTCATGGCCA-------------------TATA----A---CGGCAGA---------------CGATGGTATGTA-------------------------------------------------------------TAA----------------TACAACTTTTCGATAAAA---------------------------------------------AAAATATATAAAATTTTTTACATTCAATTATTACAGTTTTAGACTTCACGCAA-----------------------------------------------------------ATCGTGGAGCTT---TTACATGTGCCC---------------------------------------------------------------------CTACA-------------------------------------------------------AT
dp4	Unknown_group_37:8363-8450 +	LASTZ	0	GGCAATGAGGT-------------------AGGAGG-GACAATTTTGTA---------------TTCTATAATTATCGTT----------------------------AGA-------------------------------------------------CCTACGCAAAGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATACATTTT---------------------------------------------------------------------------------------------ACTGCGG---------------------G----------TTGT---ATATT-TT
droPer1	super_5473:1216-1318 +	LASTZ	0	TATACGTGTGT-----------------------------------------------------------------AAGT----------------------------GGA-------------------------------------------------ACTATGCAGGGG----------------------------------------------AATGATTTC---------------------------------------ACATGAAGAAAGTCGATTCGCCTGTAC------------------CTA---------------------------TT---GC------ATTC---------------------------------------------------------------------CT--AA--GCTGAGG---------------------T-------TT-AAGC---TTTAACAT
droWil1	scaffold_180772:5217896-5218034 +	LASTZ	0	GCCGTTGACCA-------------------GTGGCG--G---CGCCAAA---------------GTGCACATATTCTTGT----------------------------CAG-------------------------------------------------A----------------------------------------------------------------------------------------------------------------GTTAGCTGGATAGTATGTTCCTGAAAATTCAATTAAAATTGAAAGAGGACTTGTTGCAATGAATTTTTT----TTTA----------------------------------------------------------------------------------------------------------------------ATATTTGTCTAGATTTCGACC
droVir3	scaffold_291:1622-1745 -	LASTZ	0	AAAGAATCATT-------------------AGATAA-AT---CTTTAAA---------------ATATAGATTTTTTTTT----------------------------A---------CCATATTTGTAATGATTT--------------------------------------------------------------------------------------TTGGA---------------------------------------TTGCGA-----------------------------------------------------------AATTTTTTATTT---AAATTGTTAATT---------------------------------------------------------------------ATATAATATATTAAA---------------------T----------ATTT---ATATATAT
droMoj3	scaffold_6473:7010400-7010528 +	LASTZ	0	AAAGACAAAAA-------------------AAAATA-AA-------ATA----------------AAAAA-------------------------------------------------------------------------AATAAACAAACAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGTGTAAAGAGTGCAATGCCAACAAATCATACGTAGATTTCTATATTTACATATGTAC------------ATAAATATATATATG---------------------T----------ATGC---ACATACAT
droGri2	scaffold_14906:12727535-12727642 +	LASTZ	0	TGCCGAGAAGG-------------------GAAAAC-GA---------------------------GAATACAATTTTGT----------------------------TAT-------------------------------------------------ATTATTTAATTT--------------------------------------ATCTTATC---------------------------------------------------------------------------------------------------------------------------TT---GTCCTTTTATTT---------------------------------------------------------------------GAAAGATAATTTGAA---------------------TTTGAATAAATTTAT---ATTTGTAT

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	TCCGATGACCCATGGCGGGAGAGGATTATGAAAGACAATTTGAAATTAAATATCTGTGTGTGAAATTATTTAAAAGATTAATTTCACGCGAAGATATTTATTTTTACATTTGTCCCTATAATAACCGGGGTGCCAACATACAT

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

AGGCAATTTTC-------------------AA--------------------------------TTAAATATCTGTGTGT----------------------------GGA-------------------------------------------------ATTATTAAAAACAATGAG------------------------TTCAAAGG--------TTTAGTTTC---------------------------------------ACGTAA-----------------------------------------------------------AGATATTTATTTTGTTTAAATT-TTCC---------------------------------------------------------------------CTAGAATAACCAGTA---------------------T----------GCCG---ACATAA-A

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

AAGTAAACTTA-------------------AAA-------------------------------TTATAAATATGTGTGT----------------------------GAAATTAAT---------------------------------------------------AAACGGTAAG------------------------TTCGAAAG--------TTTAGTTTC---------------------------------------ACGCGA-----------------------------------------------------------AAGTATTTATTT---TTACATTTGTCC---------------------------------------------------------------------ATAGAATAACCGGGG---------------------G----------GCCA---ACATAA-A	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........TA-------------------AAA-------------------------------TTATAAATAGGGG............................................................................................................................................................................................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00

droYak2

AAGACAACTTA-------------------AAT-------------------------------TTTTATATCTGTGTGG----------------------------GAAATTAAG---------------------------------------------------AAACAGTGAG------------------------TTCGAAAA--------TTTAGTTTC---------------------------------------GTGTAA-----------------------------------------------------------AGTTATTTATTT---CTGCATTTGTCC---------------------------------------------------------------------CTAGAATAACCGAGG---------------------T----------CCCA---ACATAA-A	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.................................................................................................................................................................................................................A--------TTTAGTTTC---------------------------------------TTGTTA-----------------------------------------------------------AGT...........................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00

droEre2

CTCCATAACTC-------------------AACTTA---------TCTT---------------AATCGGATTTTGAAGT----------------------------G---------GCATACCTCTAAATGTTTGTGG----------------TGCAATTATCTAAAAAACTGCA------------------------TTCAAA-------------------------------------------------------------TTT-----------------------------------------------------------AAAAATTTATTTTTTTTACATTTTTTT---------------------------------------------------------------------GT-----------------------------------------------------------A	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..................................AA---------TCTT---------------AATCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	16	0.19	0.06	0.00	0.00	0.13
..................................TA---------TCTT---------------AATCGGATTTTGAAGT----------------------------G---------G..................................................................................................................................................................................................................................................................................................................................................................................	24	21	0.14	0.05	0.00	0.00	0.10
...............................................TT---------------AATCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	21	28	0.07	0.00	0.00	0.00	0.07
..................................TA---------TCTT---------------AATCGGATTTTGAAGT----------------------------G---------GCA................................................................................................................................................................................................................................................................................................................................................................................	26	21	0.05	0.00	0.00	0.00	0.05
......................................................................ATTTTGAAGT----------------------------G---------GCATACCT...........................................................................................................................................................................................................................................................................................................................................................................	19	32	0.03	0.00	0.00	0.00	0.03
..................................TA---------TCTT---------------ACTCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	21	0.05	0.00	0.00	0.00	0.05
...........................................................................................................................................................................ATCTGCA------------------------TTCAAA-------------------------------------------------------------TTT-----------------------------------------------------------AAAA..........................................................................................................................................................	20	24	0.04	0.00	0.00	0.00	0.04
..........C-------------------AACTTA---------TCTT---------------AGTCGGAT.................................................................................................................................................................................................................................................................................................................................................................................................................................	19	25	0.04	0.04	0.00	0.00	0.00
..................................TA---------TCTT---------------AATCGTATTTTGGAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	9	0.11	0.00	0.00	0.00	0.11
......AACTC-------------------AACTTA---------TCTT---------------AATCGGATTTTG.............................................................................................................................................................................................................................................................................................................................................................................................................................	27	20	0.05	0.00	0.00	0.00	0.05
...........................................................................GAAGT----------------------------G---------GCATACCTCTAAATGT...................................................................................................................................................................................................................................................................................................................................................................	22	37	0.03	0.00	0.00	0.00	0.03
...........................................................................................................................................................................................................TTTAA-------------------------------------------------------------TTT-----------------------------------------------------------AAAAATTTATT...................................................................................................................................................	19	11	0.09	0.09	0.00	0.00	0.00
......AACTC-------------------AACTTA---------TCTT---------------AATCGG...................................................................................................................................................................................................................................................................................................................................................................................................................................	21	24	0.04	0.00	0.00	0.00	0.04
..................................AA---------TCTT---------------AATCGGATTTTGACGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	18	0.06	0.00	0.00	0.00	0.06
..................................TA---------TCTT---------------AATCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	21	0.05	0.00	0.00	0.00	0.05
.................................TTA---------TCTT---------------AGTTGGATTTTGA............................................................................................................................................................................................................................................................................................................................................................................................................................	20	11	0.09	0.00	0.09	0.00	0.00
..............................................ATT---------------AATCGGATTTTGAAGT----------------------------.............................................................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	0.05	0.00	0.00	0.00
..............................................................................GT----------------------------G---------GCATATCTCTAAATGT...................................................................................................................................................................................................................................................................................................................................................................	19	41	0.02	0.02	0.00	0.00	0.00
......................................................................................................................................................................TAAAAATCTGCA------------------------TTCAAA-------------------------------------------------------------TTT-----------------------------------------------------------ATAAAT........................................................................................................................................................	27	45	0.02	0.00	0.00	0.00	0.02
......................................................................ATTTTAAAGT----------------------------G---------GAATACCT...........................................................................................................................................................................................................................................................................................................................................................................	19	26	0.04	0.00	0.00	0.00	0.04
..................................TA---------TCTT---------------GATCGGATTTTGATGT----------------------------G---------...................................................................................................................................................................................................................................................................................................................................................................................	23	15	0.07	0.00	0.00	0.00	0.07
..........C-------------------AACTTA---------TCTT---------------AATCGGAT.................................................................................................................................................................................................................................................................................................................................................................................................................................	19	25	0.04	0.04	0.00	0.00	0.00
.....................................................................GATTTTGAAGC----------------------------G---------GAATACCTCTAAAT.....................................................................................................................................................................................................................................................................................................................................................................	26	19	0.05	0.00	0.00	0.00	0.05
......AACTC-------------------AACTTA---------TCTT---------------ATTCGGA..................................................................................................................................................................................................................................................................................................................................................................................................................................	22	24	0.04	0.00	0.00	0.00	0.04
..............................AACTTA---------TCTT---------------AATCGGAT.................................................................................................................................................................................................................................................................................................................................................................................................................................	18	25	0.04	0.00	0.00	0.00	0.04
.....TAACTC-------------------AGCTTA---------TCTT---------------AATCGGAATT...............................................................................................................................................................................................................................................................................................................................................................................................................................	26	11	0.09	0.09	0.00	0.00	0.00
..........................................................................................................................................................................................................TTCAAA-------------------------------------------------------------TTT-----------------------------------------------------------GCAAATTTATTTTTTT..............................................................................................................................................	25	10	0.10	0.00	0.00	0.00	0.10
......................................................................ATTTTGAAGT----------------------------G---------GCGTACCT...........................................................................................................................................................................................................................................................................................................................................................................	19	34	0.03	0.00	0.00	0.00	0.03
..............................AACTGA---------TCGT---------------AATCGGAT.................................................................................................................................................................................................................................................................................................................................................................................................................................	18	13	0.08	0.00	0.00	0.00	0.08
..............................................CTT---------------AATCGGATTTTGAAGT----------------------------.............................................................................................................................................................................................................................................................................................................................................................................................	19	26	0.04	0.04	0.00	0.00	0.00
..................................TA---------TCTT---------------GATCGGATTTTAAAGT----------------------------.............................................................................................................................................................................................................................................................................................................................................................................................	22	15	0.07	0.00	0.00	0.00	0.07
..........C-------------------AACTTA---------TCTT---------------AATCGTAT.................................................................................................................................................................................................................................................................................................................................................................................................................................	19	25	0.04	0.00	0.04	0.00	0.00
...........................................................................AAAGT----------------------------G---------GCATACCTCTAAAT.....................................................................................................................................................................................................................................................................................................................................................................	20	28	0.04	0.00	0.00	0.00	0.04
..................................TA---------TCTG---------------AATCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	23	0.04	0.00	0.04	0.00	0.00
..................................................................TCGGATTTTGAAGT----------------------------G---------GCATACCTCT.........................................................................................................................................................................................................................................................................................................................................................................	25	28	0.04	0.04	0.00	0.00	0.00
...CATAACTC-------------------AACTTA---------TCTT---------------A........................................................................................................................................................................................................................................................................................................................................................................................................................................	19	27	0.04	0.00	0.00	0.00	0.04
.............................................................................AGT----------------------------G---------GCGTACCTATAAATGTT..................................................................................................................................................................................................................................................................................................................................................................	21	29	0.03	0.03	0.00	0.00	0.00
..........C-------------------AACTTA---------TCTT---------------AATCTGAT.................................................................................................................................................................................................................................................................................................................................................................................................................................	19	26	0.04	0.00	0.04	0.00	0.00
................................................T---------------AATCGGATTTTGAAGT----------------------------G---------GCATACCT...........................................................................................................................................................................................................................................................................................................................................................................	26	25	0.04	0.04	0.00	0.00	0.00
............................................................................AAGT----------------------------G---------GCATACCTCTAAATG....................................................................................................................................................................................................................................................................................................................................................................	20	38	0.03	0.00	0.00	0.00	0.03
..............................................CTT---------------AATCGGATTTTGAATT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	22	26	0.04	0.04	0.00	0.00	0.00
..........................................................................TGAAGT----------------------------G---------GAATACCTCTAAATGT...................................................................................................................................................................................................................................................................................................................................................................	23	34	0.03	0.00	0.00	0.00	0.03
...............................................TT---------------AATCGGATTTTGAAGT----------------------------x---------GCATA..............................................................................................................................................................................................................................................................................................................................................................................	23	17	0.06	0.00	0.00	0.00	0.06
..................................................................TCGGAATTTGATGT----------------------------G---------GCATACCTCTA........................................................................................................................................................................................................................................................................................................................................................................	26	25	0.04	0.00	0.00	0.00	0.04
...................................A---------TATT---------------ATTCGGATTTTGAAGT----------------------------.............................................................................................................................................................................................................................................................................................................................................................................................	21	19	0.05	0.00	0.00	0.00	0.05
GTCCATAACTC-------------------AACTTA---------TCTT---------------C........................................................................................................................................................................................................................................................................................................................................................................................................................................	22	15	0.07	0.07	0.00	0.00	0.00
..................................TA---------TCTT---------------GATCGGATTTTGATGT----------------------------G---------G..................................................................................................................................................................................................................................................................................................................................................................................	24	15	0.07	0.00	0.00	0.00	0.07
.....TAACTC-------------------AACTTA---------TCTG---------------TATCGGAT.................................................................................................................................................................................................................................................................................................................................................................................................................................	24	12	0.08	0.00	0.00	0.00	0.08
..............................................CTG---------------AATCGGATTTTGAAGT----------------------------G---------...................................................................................................................................................................................................................................................................................................................................................................................	20	28	0.04	0.00	0.00	0.00	0.04
..................................TA---------TCTT---------------AGTCGGATTTTGAAGT----------------------------T---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	9	0.11	0.00	0.00	0.00	0.11
..................................TA---------TCTT---------------AATCGGATTGTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	21	0.05	0.00	0.05	0.00	0.00
..................................................................TCGGATTTTGATGT----------------------------G---------GCATACCTCT.........................................................................................................................................................................................................................................................................................................................................................................	25	20	0.05	0.00	0.00	0.00	0.05
..................................TA---------TCTT---------------AATCGGATTTTGAAGT----------------------------G---------...................................................................................................................................................................................................................................................................................................................................................................................	23	21	0.05	0.05	0.00	0.00	0.00
..............................................CTT---------------AATCGGATTTTGAAGT----------------------------A---------GC.................................................................................................................................................................................................................................................................................................................................................................................	22	26	0.04	0.00	0.00	0.00	0.04
.............................................TCTG---------------GATCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	23	17	0.06	0.06	0.00	0.00	0.00
..................................TA---------TCTT---------------AATCGGATTTTCAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	21	0.05	0.00	0.00	0.00	0.05
...........................................................................GAAGT----------------------------G---------GCATACCTCTAAATG....................................................................................................................................................................................................................................................................................................................................................................	21	37	0.03	0.00	0.00	0.00	0.03
.........................................................................TTGAAGT----------------------------G---------GCATACCTCTAAATGTT..................................................................................................................................................................................................................................................................................................................................................................	25	34	0.03	0.00	0.00	0.00	0.03
..............................................CTT---------------AATCGGATTTTGAAGT----------------------------G---------G..................................................................................................................................................................................................................................................................................................................................................................................	21	26	0.04	0.00	0.00	0.00	0.04
........................................................................................................................ATACCTCTAAATGTTTCTGG----------------.............................................................................................................................................................................................................................................................................................................................................	20	34	0.03	0.03	0.00	0.00	0.00
.............................................TCTT---------------AATCGGATTTTGAAGT----------------------------G---------TC.................................................................................................................................................................................................................................................................................................................................................................................	23	26	0.04	0.04	0.00	0.00	0.00
..............................................CTT---------------AATCGGAATTTTAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	22	14	0.07	0.00	0.00	0.00	0.07
.......ACTC-------------------AACTAA---------TCTT---------------AATCGG...................................................................................................................................................................................................................................................................................................................................................................................................................................	20	33	0.03	0.00	0.00	0.00	0.03
..............................AACTAA---------TCTT---------------AATCGGAAT................................................................................................................................................................................................................................................................................................................................................................................................................................	19	23	0.04	0.00	0.00	0.00	0.04
.................................TTA---------TCTG---------------AATCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	26	21	0.05	0.05	0.00	0.00	0.00
..................................TA---------TCTT---------------AGTCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	21	0.05	0.00	0.00	0.00	0.05
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................A	20	21	0.05	0.05	0.00	0.00	0.00
...................................A---------TTTT---------------AATCGGACTTTGAAGT----------------------------G---------G..................................................................................................................................................................................................................................................................................................................................................................................	23	20	0.05	0.00	0.00	0.00	0.05
..............................................CTG---------------AATCGGATTTTGAAGT----------------------------.............................................................................................................................................................................................................................................................................................................................................................................................	19	28	0.04	0.04	0.00	0.00	0.00
..................................................................TCGGATTTTGAAGT----------------------------G---------GAATAC.............................................................................................................................................................................................................................................................................................................................................................................	21	33	0.03	0.00	0.00	0.00	0.03
...................................A---------TCTT---------------AGTCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	24	26	0.04	0.00	0.00	0.00	0.04
...........................................................................CAAGT----------------------------G---------GCATACCTCTAAAT.....................................................................................................................................................................................................................................................................................................................................................................	20	40	0.03	0.00	0.00	0.00	0.03
..................................TA---------TCTG---------------AATCGGATTTTGAAGT----------------------------T---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	10	0.10	0.00	0.00	0.00	0.10
...................................A---------TCTT---------------AATCGGATTTTGAAGT----------------------------G---------GC.................................................................................................................................................................................................................................................................................................................................................................................	24	26	0.04	0.00	0.00	0.00	0.04
..................................TA---------TCTT---------------AATCGGATTTTGAAGT----------------------------T---------GC.................................................................................................................................................................................................................................................................................................................................................................................	25	21	0.05	0.00	0.00	0.00	0.05

droEug1

TGACACAAATC-------------------GAGAGT--G---CACTGAGAAAAAGGCAGGGTAGCTACTTATCTGTAAGA----------------------------GGA-------------------------------------------------AAAACTTAAGAA-ATAAGTTCTTTTATGAAGTAATGAAATTT--------AT-TCATC---------------------------------------------------------------------------------------------------------------------------TT---TCACCTTTATTT---------------------------------------------------------------------CT-----------------------------------------------------------A

Size

Hit Count

Total Norm

droBia1

GGGAAGAAATT-------------------GAAGTGCAA---ATATGCA---------------AAACATATCTATGTAC----------------------------GAT-------------------------------------------------ATTATTTAAGTT--------------------------------------TT-TTTTT---------------------------------------------------------------------------------------------------------------------------TC---AAACTTCTATGC---------------------------------------------------------------------AG--TAGTTTCTGGGGTGCATCTTATAGTGCCCAGTT----------TCAT---AAAGACAT

Size

Hit Count

Total Norm

droTak1

TTTTATAATAC-------------------AAATTG-AA-------AAA-----------------TAAGACTTATTTGTCAATTTTTTTAAAAAAGTAACTCTTACTT--------GCGATCCCTGTAAATATTTCTATAAGTGTAATTTAAGGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACC---------------------------------------------------------------------CTATAACGAGTACAA---------------------T----------TCTT---ACATGCTT

Size

Hit Count

Total Norm

droEle1

TGATCCATATC-------------------GGTAA--AT---TTATAAG---------------AAACTGACTTGAAAGC----------------------------GGA-------------------------------------------------AAATTTTATG------------------------------------------------------------------------------------------------------------------------------GAAATCCAATCAATATTATT---AAATTCATCAAAAGATATTTCTTC---T------------------------------------------------------------------------------------------------------------------------------------------GACA

Size

Hit Count

Total Norm

droRho1

TCGGAGCACCC-------------------GACTAT-AG---C---GTT-------------------C-TCTCTTGTTT----------------------------TGTATTAAG---------------------------------------------------AAAGGGTACA------------------------CTTTTAAA--------TTAAGTGTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------TGGAGAGTTCTGAATTTCTTAAGAGATATCATAAGTTCTTTGTAATAAGAGGTA---------------------TTTTAGCAG--TCAT---GTCTCTCA

Size

Hit Count

Total Norm

droFic1

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

Size

Hit Count

Total Norm

droKik1

GAAAAACGAAG-------------------CAA----AA---CTAAAAA-----------------AA--ACATGTGTGT----------------------------GAC-------------------------------------------------ATCATTTTAAACATTAAA------------------------TTCAAA-------------------------------------------------------------ACA-----------------------------------------------------------AAACTTTGATTTGGCC------------------------------------------------------------------------------------AACACGTTTGG---------------------G----------CGCT---A-TAATAA

Size

Hit Count

Total Norm

droAna3

AAAAAATTAGT-------------------AAAAAA-AA---TAATAAA---------------TAAAAAAAAATATGGT----------------------------GGG-------------------------------------------------ATTTTTTAAAAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATATTTTTT-------------------------------------------------------------------------------------ATATGGCAATTGGTA---------------------GTTAAATATTAGTCT---TTTTAAGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................T---TTTTAGGA	18	3	0.33	0.00	0.00	0.00	0.33
.....................................GA---TAATAAG---------------TAAAAAAAA................................................................................................................................................................................................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.00	0.33	0.00
...............................AAAAA-AA---TAAGAAA---------------TAGAAAA..................................................................................................................................................................................................................................................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50
.............................................TAAA---------------TAAAAAAAAAAATGGA----------------------------GG...........................................................................................................................................................................................................................................................................................................................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
................................AAAA-AA---CAATAAA---------------AAAAAAA..................................................................................................................................................................................................................................................................................................................................................................................................................................	20	25	0.04	0.00	0.00	0.00	0.04
.....................................AA---TAATAAA---------------AGAAAAAAA................................................................................................................................................................................................................................................................................................................................................................................................................................	18	13	0.08	0.00	0.00	0.00	0.08
...........................................AATGGA---------------TAAAAAAAAA...............................................................................................................................................................................................................................................................................................................................................................................................................................	16	17	0.06	0.00	0.00	0.06	0.00
................................AAAA-AA---TAAGAAA---------------TAAAGAA..................................................................................................................................................................................................................................................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
...............................AAAAA-AA---GAAAAAA---------------TAAAAAAAA................................................................................................................................................................................................................................................................................................................................................................................................................................	23	9	0.11	0.00	0.00	0.00	0.11
.................................AAA-AA---TAATAAA---------------GGAAAAA..................................................................................................................................................................................................................................................................................................................................................................................................................................	19	6	0.17	0.00	0.00	0.00	0.17
................................AAAA-AA---AAATAAA---------------CAAAAA...................................................................................................................................................................................................................................................................................................................................................................................................................................	19	43	0.02	0.00	0.02	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................................................................................ACAGTTGGTA---------------------GTTAAATA..................	18	2	0.50	0.00	0.00	0.00	0.50
..................................AA-AA---GAAGAAA---------------TAAAAAA..................................................................................................................................................................................................................................................................................................................................................................................................................................	18	10	0.10	0.00	0.00	0.00	0.10

droBip1

CGTCATGGCCA-------------------TATA----A---CGGCAGA---------------CGATGGTATGTA-------------------------------------------------------------TAA----------------TACAACTTTTCGATAAAA---------------------------------------------AAAATATATAAAATTTTTTACATTCAATTATTACAGTTTTAGACTTCACGCAA-----------------------------------------------------------ATCGTGGAGCTT---TTACATGTGCCC---------------------------------------------------------------------CTACA-------------------------------------------------------AT

Size

Hit Count

Total Norm

dp4

GGCAATGAGGT-------------------AGGAGG-GACAATTTTGTA---------------TTCTATAATTATCGTT----------------------------AGA-------------------------------------------------CCTACGCAAAGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATACATTTT---------------------------------------------------------------------------------------------ACTGCGG---------------------G----------TTGT---ATATT-TT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........................................................................................................................................................................G-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATACATTTT---------------------------------------------------------------------------------------------ACTGCGG---------------------G----------TGT............	21	2	0.50	0.50	0.00	0.00	0.00
......................................................................AATTATCGTT----------------------------AGA-------------------------------------------------CCTATGCAAAGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------A...........................................................................................................................................................	26	2	0.50	0.00	0.00	0.50	0.00
..............................................................................................................................................................................................................................................................................................................................................TACATTTG---------------------------------------------------------------------------------------------GCTGCGG---------------------G----------TTGT---A.......	21	2	0.50	0.00	0.50	0.00	0.00
.....TGAGGT-------------------AGGAGA-TACAATTTTGTA---------------TT.......................................................................................................................................................................................................................................................................................................................................................................................................................................	26	2	0.50	0.50	0.00	0.00	0.00
.............................................TGTA---------------TTCTATAATTATCGTT----------------------------AGA-------------------------------------------------CC.......................................................................................................................................................................................................................................................................................................................................	25	2	0.50	0.00	0.50	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................ATTTT---------------------------------------------------------------------------------------------ACTGAGG---------------------G----------TTGT---CT......	19	2	0.50	0.00	0.50	0.00	0.00
.....TGAGGT-------------------AGGAGG-TACAATTTGGTA---------------.........................................................................................................................................................................................................................................................................................................................................................................................................................................	24	2	0.50	0.50	0.00	0.00	0.00
............................................................................................................AGA-------------------------------------------------CCTACGCAGAGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATACA.......................................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00

droPer1

TATACGTGTGT-----------------------------------------------------------------AAGT----------------------------GGA-------------------------------------------------ACTATGCAGGGG----------------------------------------------AATGATTTC---------------------------------------ACATGAAGAAAGTCGATTCGCCTGTAC------------------CTA---------------------------TT---GC------ATTC---------------------------------------------------------------------CT--AA--GCTGAGG---------------------T-------TT-AAGC---TTTAACAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................................................................................................................................................................................................................................................................................................................T---GC------ATTC---------------------------------------------------------------------CT--AA--GCTGAGC---------------------T-------TT-AAGC---........	25	2	0.50	0.00	0.50	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................CATGAAGAAGGTCGCTTC............................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
..................................................................................................................................................................TATGCAGGGG----------------------------------------------AATGATTTC---------------------------------------A..............................................................................................................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00	0.00

droWil1

GCCGTTGACCA-------------------GTGGCG--G---CGCCAAA---------------GTGCACATATTCTTGT----------------------------CAG-------------------------------------------------A----------------------------------------------------------------------------------------------------------------GTTAGCTGGATAGTATGTTCCTGAAAATTCAATTAAAATTGAAAGAGGACTTGTTGCAATGAATTTTTT----TTTA----------------------------------------------------------------------------------------------------------------------ATATTTGTCTAGATTTCGACC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TATTTGTCTAGATTTCGACC	21	4	2.25	0.00	0.00	0.00	2.25
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................G	18	47	0.09	0.06	0.02	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TATTTGTCTGGATTTCGACC	21	4	1.00	0.00	0.00	0.00	1.00
........CTA-------------------GTGGCG--G---CGCTAAA---------------GTGC.....................................................................................................................................................................................................................................................................................................................................................................................................................................	21	9	0.22	0.00	0.22	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................................CAATGAATTTTTT----TATG----------------------------------------------------------------------------------------------------------------------ATA..................	20	3	0.33	0.00	0.33	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................................TTTG----------------------------------------------------------------------------------------------------------------------GTATTTGTCTAGATTTCGA..	23	3	0.33	0.00	0.33	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................AAGAGGACTTGTTGCAATGA..........................................................................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................C	19	48	0.02	0.00	0.00	0.02	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTATTTGTCTAGATTTCGAC.	20	4	0.25	0.00	0.25	0.00	0.00
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................G	19	44	0.02	0.02	0.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................G----------------------------------------------------------------------------------------------------------------------GTATTTGTCTAGATTTCGAC.	21	4	0.25	0.00	0.00	0.00	0.25
........CTA-------------------GTGGCG--G---CGCCAGA---------------GTGC.....................................................................................................................................................................................................................................................................................................................................................................................................................................	21	9	0.11	0.00	0.11	0.00	0.00

droVir3

AAAGAATCATT-------------------AGATAA-AT---CTTTAAA---------------ATATAGATTTTTTTTT----------------------------A---------CCATATTTGTAATGATTT--------------------------------------------------------------------------------------TTGGA---------------------------------------TTGCGA-----------------------------------------------------------AATTTTTTATTT---AAATTGTTAATT---------------------------------------------------------------------ATATAATATATTAAA---------------------T----------ATTT---ATATATAT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..............................................................................................................................GTTATGATTT--------------------------------------------------------------------------------------TTGGT---------------------------------------TTGC...........................................................................................................................................................................................................................	19	2	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................................TTTGTTATGATTT--------------------------------------------------------------------------------------TTGGT---------------------------------------TTGC...........................................................................................................................................................................................................................	22	2	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................................................................................................................................................................................................................................................................................ACTGTTAATG---------------------------------------------------------------------ATATAAT.......................................................	17	5	0.20	0.00	0.20	0.00	0.00	0.00
.............................................................................................................................TGTTATGATTT--------------------------------------------------------------------------------------TTGGT---------------------------------------TTG............................................................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
............................................................................................................................TTGTTATGATTT--------------------------------------------------------------------------------------TTGGT---------------------------------------TTGC...........................................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50	0.00
.............................................................................................................................TGTTATGATTT--------------------------------------------------------------------------------------TTGGT---------------------------------------TTGC...........................................................................................................................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................TTTGTTATGATTT--------------------------------------------------------------------------------------TTGGT---------------------------------------TTG............................................................................................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00	0.00
.................................................................................................................................ATGATTT--------------------------------------------------------------------------------------TTGGA---------------------------------------TTGTAA-----------------------------------------------------------AA............................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00	0.00

droMoj3

AAAGACAAAAA-------------------AAAATA-AA-------ATA----------------AAAAA-------------------------------------------------------------------------AATAAACAAACAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGTGTAAAGAGTGCAATGCCAACAAATCATACGTAGATTTCTATATTTACATATGTAC------------ATAAATATATATATG---------------------T----------ATGC---ACATACAT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........AA-------------------AAAATA-AA-------ATA----------------AAAAA-------------------------------------------------------------------------A.........................................................................................................................................................................................................................................................................................................................................................	19	21	0.05	0.00	0.00	0.00	0.05

droGri2

TGCCGAGAAGG-------------------GAAAAC-GA---------------------------GAATACAATTTTGT----------------------------TAT-------------------------------------------------ATTATTTAATTT--------------------------------------ATCTTATC---------------------------------------------------------------------------------------------------------------------------TT---GTCCTTTTATTT---------------------------------------------------------------------GAAAGATAATTTGAA---------------------TTTGAATAAATTTAT---ATTTGTAT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:17:00 EDT

dme-mir-2279

chr2RHet:1322833-1322945 -

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