dme-mir-4982- Best orthologs

dme-mir-4982	chr2R:14607673-14607792 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 14607740-14607761
   star strand at position 14607703-14607723
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:14607658-14607807 +		1	TTTT-GAGTC--------------GAAAGGA-CCAAC-TTTGCTGGCATT--------CGGTGGCCAATAATGCAATTGCATGTCC--------------------------TTGTT--------------------------G------CTGTTGCA-----ATG---------------------------TTGCAGCTGGAATTGCAATTGC---ATTTCTAGT------T---GCC------------GCTG--CTGCTGCTCGAGTGGCAATTA--GCTGGGTGTCTC
droSim1	chr2R:13317686-13317836 +	LASTZ	5	TTTTCGAGTC--------------GAAAGGA-CCAAC-TTTGCTGGCATT--------CGCTGGCCAATAATGCAATTGCGTGTCC--------------------------TTGTT--------------------------G------CTGTTGCA-----ATG---------------------------TTGCAGCTGGAATTGCAATTGC---ATTTCTAGT------T---GCC------------GCTG--CTGCTGCTCGAGTGGCAATTA--GCTGGGTGTCTC
droSec1	super_1:12115359-12115508 +	LASTZ	5	TTTC-GAATC--------------GAAAGGA-CCAAC-TTTGCTGGCATT--------CGCTGGCCAATAATGCAATTGCATGTCC--------------------------TTGTT--------------------------G------CAGTTGCA-----ATG---------------------------TTGCAGCTGGAATTGCAATTGC---ATTTCTAGT------T---GCC------------GCTG--CTGCTGCTCGAGTGGCAATTA--GCTGGGTGTCTC
droYak2	chr2R:14591968-14592144 -	LASTZ	5	TTTTCGGGTC--------------GAAAGGA-CCAACTTTTGTTGGCATT--------CGCTGGCCAATAATGCAATTGCGTGTCC--------------------------TTGTT--------------------------G------CTGTTGCA-----ATGTTGCAACTTGCA--------------------ACTGGAATTGCAATTGC---ATTTCTAGTTGCTTCTCCTCTTTTT---CCTGCTGCTC--CTACTCCTCGAGTGGCAATTA--GCTGGGTGTCTC
droEre2	scaffold_4845:8798992-8799150 +	LASTZ	5	TTTC-GCGTC--------------GAAAGGA-CCAAC-TTTGCTGGCACT--------CGCTGGCCAATAATGCAATTGCGTGTCA--------------------------TTGTT--------------------------G------CTGTTGCA-----ATG---------------------------TTGCAACTGGAATTGCAATTGC---ATTTCTAGTTGCTCCTCATGCT------------GCTG--CTGCTCCTCGAGTGGCAATTA--GCTGGGTGTCTC
droEug1	scf7180000409663:750613-750768 -	LASTZ	0	TTTTTCCTTC--------------GAAAGGA-CCAAC-TTCGATGAGATT--------TGCTGGCTAGAAATGCAATTGCGTGTCC--------------------------TTGTT--------------------------G------CAGTTGCACAGCCATG---------------------------TTGC------ACTTGTAATTGC---AATTCTAGTTGCTGTT---TGT------------GCCG--CTGCTGCTCGAGTGGCAATTA--GCAGGGTGTCTC
droBia1	scf7180000302292:1790364-1790532 -	LASTZ	0	CGCC-GCGGA--------------AGAAGGA-CCAAC-TTCGATGGCATT--------TGCTGGCCAATAATGTAATTTCGTGTCC--------------------------TTGCT--------------------------G------CACTTGCAACGACAAG-------TTGCAA-T-GCCC------------GCTGCACTTGTAATTGC---AGTTCTAGTTGCT------GCC------GCT---GCTGGCCTGCTGCTCGAGTGGCAATTA--GCAGGGTGTCTC
droTak1	scf7180000415991:23390-23548 +	LASTZ	0	TTGA---GGG--------------AAAAGGA-CCAAC-TTCGATGAGATT--------AGCTGGCGAATAATGCAATCGCGTGACC--------------------------TTGTT--------------------------G------CAGTTGCATTGGCAAG-------TTGCAAGTTGCTC------------GCTGCCCCAGCAAATGC---AATTCTAGT------T---GC---------------AG--CTGCTGCTCGAGTGGCAATTA--GCAGGGTGTCTC
droEle1	scf7180000490996:1014509-1014655 -	LASTZ	0	TCCC-GGCTC----------------AAAGC-TCACC-TTCTTCTGCACT--------GGCTTGGCCATCA-GCTGTTGC-TG--------------------------------TT--------------------------G------CTGTTG-------ATG-------CTGCTG-C-TG---------TTGCAGTTGCTGCTGCAGTTGC---TGTTGCTGT------T---GCT------------GCTG--CTGCTGCTGCAGCGGGTAGTA--GCCATGCGGCAG
droRho1	scf7180000766409:161897-162055 -	LASTZ	0	TTGC-TAGAA--------------AAAATAGGCAAAC-TTCGATGAGCTT--------TGCTGGAAAATAATGCAATTGCGTGTTC--------------------------GTGCT--------------------------G------TAGTTGAAATGGCATG-------TTGCAA-T-GCTT------------ACTGCACTTGTAAGTGC---AATTTCAGT------T---GC---------------AG--CTGCTGCTCTAGTGGCAATTA--GCAGGGTGTCTC
droFic1	scf7180000453811:359819-359967 -	LASTZ	0	TTCC-GAGGA--------------AAAAGGG-ACAAC-TTCGATGACATT--------TACTGGCCAATAATGCAATTGCGTG----------------------------------------------------------------------TTGCAATGGCAAG-------TTGCAA-C-ACTA------------GTTTCACTTGCAAGTGC---AATTTTCGT------T---GCA------------ACTG--CTGCTGCTCGAGAAGCAATTA--GCAGGGTGTCTC
droKik1	scf7180000302682:297395-297515 +	LASTZ	0	TTTT-G------------------AAAAGGA-CAAAG-TTCGATGCGATTTGCTCTTTCGCTGGCCCATAATGCAATTGCA---GC--------------------------TTGGC--------------------------T------CTGTTGCA-----ATA-----------------TTC------------GGTGCCCTT------------------------------------------------------TAACCCAAGAGGCAATTA--GCTGGGCGTCTC
droAna3	scaffold_13334:1368045-1368196 +	LASTZ	0	TTTT-GAGCT--------------G------------------------------------------------CAGTTGC------------------------AGATAAAGTTACAGTTGTTGTTGCTACTT---TCACGTTGTTGTTGTTGTTGT-------TG---------------------------CGGCAGCTGCAGTTGCAGTTGC---AGTTGCAAT------T---GTTGCTGCAGCT---GTTGGCC--TAATGAGAGTGGCCAGCAATGCGGCACGAATC
droBip1	scf7180000396006:46261-46375 +	LASTZ	0	T-----------------------------------------------------------------------GCACTTGC-TGTAC--------------------------CTGTT--------------------------G------CA------C----ATGTTG----CACCTG-T-TGCTG------CTGCTGCTGCACTTGCACTTGCTGCACTTGCACT------T---GCT------------GTTG--CTGCTGCTGAGGTGGCAGATA--GCCGGGTGC-TT
dp4	chrXL_group3a:862470-862596 -	LASTZ	0	A----------------------------------AC-TCTGCTGCCAGT--------AGTTGGCCATTGAGAAAATTGTGTGCCCTGGAATTTAATTCATTGCAAACAA-ATTGCT--------------------------G------CTGCT----------------------------------------------G---CTGCTGCTGC---TGCTGTTGT------T---GCT------------GCTG--CTGCCGTTGCAGTGGCAATT---------------
droPer1	super_15:2034074-2034206 +	LASTZ	0	A----------------------------------AC-TCTGCTGCCAGT--------AGTTGGCCATTGAGAAAATTGTGTGCCCTGGAATTTAATTCATTGCAAACAA-ATTGCT--------------------------G------CTGCT-------------------------------------------GCCGCTGCTGCTGTTGT---TGTTGTGGT------T---GCT------------GCTG--CTGCCGTTGCAGTGGCAATT---------------
droWil1	scaffold_181096:6674642-6674780 +	LASTZ	0	CTTG-GTGCCGTATCAAAGCTGGCATATAGT-TCAAC-TTCTTCA----T--------CGGTGGCAT-----------------------------------------CAC-----------------------------------------GTTGCAGTTG-TTG-------TTGTTG-T-TGTTGTTGCTGTTGCAGCTGTTGTTGTTGCTGT---TGTTGTTGC------T---GCA------------GCTG--CTGCTGCTCAAGTG---------------------
droVir3	scaffold_12822:1548557-1548661 -	LASTZ	0	TGTT---------------------------------------------------------------------------------G--------------------------CTGCT--------------------------G------CTGTTGCAATTG-TTG-------CTGCAG-C-TGTT------------GTTGCTGTTGCAGCTGC---AGCTGTAAC------TGTTGCT------------GCTG--CTGGGCATAGAGCTGCTCCTG--GT--AGTGCTTG
droMoj3	scaffold_6540:8945968-8946087 +	LASTZ	0	AGCC--------------------AGCATCG-ACAAC-TTGGCTGCAATT--------CA--------------------------------------------------GGTTGCAGCTACTGCTGTTGCCTGTTGCCTGTTG------CCGTTGCC-------G---------------------------TTGCTGCTGCAGTTGCAGTTGC---AGTTGTAGT------T---ACC------------GTTG--CAATTGC----------------------------
droGri2	scaffold_15245:16288597-16288735 +	LASTZ	0	TGTT-G--------------------------TCAGC-GTTGTCGT--TG--------TGCTTGTTGATTTTCCAGTTGCT----G--------------------------CTGTT--------------------------G------CTGTTGCAGTTGC-AG-------TTGCA--------------------GCTGTTGCTGCTGTTGC---AGTTGCAGTTGTTGCT---GC---------------TG--CTGCTGTTGTTGTTGGTGTTG--TC-GGTGGTGTC

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	TT-TTGAGTCGAAAGGACCAACT-TTGCTGGCATTCGGTGGCCAATAATGCAATTGCATGTCCTTGTTGCTGTTGCAATGTTGC-------AGCTGGAATTGCAATTGCATTTCTAGTTG------------------CCGCTGCTGCTGCTCGAGTGGCAATTAGCTGGGTGTCTC
droSim1	TTTTCGAGTCGAAAGGACCAACT-TTGCTGGCATTCGCTGGCCAATAATGCAATTGCGTGTCCTTGTTGCTGTTGCAATGTTGC-------AGCTGGAATTGCAATTGCATTTCTAGTTG------------------CCGCTGCTGCTGCTCGAGTGGCAATTAGCTGGGTGTCTC
droSec1	TT-TCGAATCGAAAGGACCAACT-TTGCTGGCATTCGCTGGCCAATAATGCAATTGCATGTCCTTGTTGCAGTTGCAATGTTGC-------AGCTGGAATTGCAATTGCATTTCTAGTTG------------------CCGCTGCTGCTGCTCGAGTGGCAATTAGCTGGGTGTCTC
droYak2	TTTTCGGGTCGAAAGGACCAACTTTTGTTGGCATTCGCTGGCCAATAATGCAATTGCGTGTCCTTGTTGCTGTTGCAATGTTGCAACTTGCAACTGGAATTGCAATTGCATTTCTAGTTGCTTCTCCTCTTTTTCCTGCTGCTCCTACTCCTCGAGTGGCAATTAGCTGGGTGTCTC
droEre2	TT-TCGCGTCGAAAGGACCAACT-TTGCTGGCACTCGCTGGCCAATAATGCAATTGCGTGTCATTGTTGCTGTTGCAATGTTGC-------AACTGGAATTGCAATTGCATTTCTAGTTGCTCCTC---------ATGCTGCTGCTGCTCCTCGAGTGGCAATTAGCTGGGTGTCTC

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

TTTTCGAGTC--------------GAAAGGA-CCAAC-TTTGCTGGCATT--------CGCTGGCCAATAATGCAATTGCGTGTCC--------------------------TTGTT--------------------------G------CTGTTGCA-----ATG---------------------------TTGCAGCTGGAATTGCAATTGC---ATTTCTAGT------T---GCC------------GCTG--CTGCTGCTCGAGTGGCAATTA--GCTGGGTGTCTC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................................................................................CAGCTxGAATTGCAATGGC---...........................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

TTTC-GAATC--------------GAAAGGA-CCAAC-TTTGCTGGCATT--------CGCTGGCCAATAATGCAATTGCATGTCC--------------------------TTGTT--------------------------G------CAGTTGCA-----ATG---------------------------TTGCAGCTGGAATTGCAATTGC---ATTTCTAGT------T---GCC------------GCTG--CTGCTGCTCGAGTGGCAATTA--GCTGGGTGTCTC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................................................................................................................................................................................TGGCAGTTA--GCTGGTTGT...	18	1	3.00	0.00	0.00	3.00
...............................................................................................................................................................................................................................................................G--CAGCTGCTCGAGxGGCAAT................	19	1	1.00	0.00	1.00	0.00
...........................................................................................................................................................GCA-----ATG---------------------------CTTCAGCTGGAA........................................................................................	18	1	1.00	0.00	1.00	0.00
................................................................................ATGTxC--------------------------TTGAT--------------------------G------CAGTTGC........................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TTTTCGGGTC--------------GAAAGGA-CCAACTTTTGTTGGCATT--------CGCTGGCCAATAATGCAATTGCGTGTCC--------------------------TTGTT--------------------------G------CTGTTGCA-----ATGTTGCAACTTGCA--------------------ACTGGAATTGCAATTGC---ATTTCTAGTTGCTTCTCCTCTTTTT---CCTGCTGCTC--CTACTCCTCGAGTGGCAATTA--GCTGGGTGTCTC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...TCGGGTA--------------GAAAGGA-CCAT.................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..TTCGGCTC--------------GxAAGGA-CCA..................................................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................................................................TGGCAGTTA--GCTGGTTGT...	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TTTC-GCGTC--------------GAAAGGA-CCAAC-TTTGCTGGCACT--------CGCTGGCCAATAATGCAATTGCGTGTCA--------------------------TTGTT--------------------------G------CTGTTGCA-----ATG---------------------------TTGCAACTGGAATTGCAATTGC---ATTTCTAGTTGCTCCTCATGCT------------GCTG--CTGCTCCTCGAGTGGCAATTA--GCTGGGTGTCTC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................................................................................................................................................................................................................................................................TGGCAGTTA--GCTGGTTGT...	18	1	4.00	0.00	0.00	0.00	4.00
...........................................................................................................................................................................................................................................AAGCT------------GCTG--CTGCTCCTCCA........................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................................................................CTCATGCT------------GCTG--CTCGTC.............................	18	8	0.13	0.00	0.00	0.00	0.13

droEug1

TTTTTCCTTC--------------GAAAGGA-CCAAC-TTCGATGAGATT--------TGCTGGCTAGAAATGCAATTGCGTGTCC--------------------------TTGTT--------------------------G------CAGTTGCACAGCCATG---------------------------TTGC------ACTTGTAATTGC---AATTCTAGTTGCTGTT---TGT------------GCCG--CTGCTGCTCGAGTGGCAATTA--GCAGGGTGTCTC

Size

Hit Count

Total Norm

droBia1

CGCC-GCGGA--------------AGAAGGA-CCAAC-TTCGATGGCATT--------TGCTGGCCAATAATGTAATTTCGTGTCC--------------------------TTGCT--------------------------G------CACTTGCAACGACAAG-------TTGCAA-T-GCCC------------GCTGCACTTGTAATTGC---AGTTCTAGTTGCT------GCC------GCT---GCTGGCCTGCTGCTCGAGTGGCAATTA--GCAGGGTGTCTC

Size

Hit Count

Total Norm

droTak1

TTGA---GGG--------------AAAAGGA-CCAAC-TTCGATGAGATT--------AGCTGGCGAATAATGCAATCGCGTGACC--------------------------TTGTT--------------------------G------CAGTTGCATTGGCAAG-------TTGCAAGTTGCTC------------GCTGCCCCAGCAAATGC---AATTCTAGT------T---GC---------------AG--CTGCTGCTCGAGTGGCAATTA--GCAGGGTGTCTC

Size

Hit Count

Total Norm

droEle1

TCCC-GGCTC----------------AAAGC-TCACC-TTCTTCTGCACT--------GGCTTGGCCATCA-GCTGTTGC-TG--------------------------------TT--------------------------G------CTGTTG-------ATG-------CTGCTG-C-TG---------TTGCAGTTGCTGCTGCAGTTGC---TGTTGCTGT------T---GCT------------GCTG--CTGCTGCTGCAGCGGGTAGTA--GCCATGCGGCAG

Size

Hit Count

Total Norm

droRho1

TTGC-TAGAA--------------AAAATAGGCAAAC-TTCGATGAGCTT--------TGCTGGAAAATAATGCAATTGCGTGTTC--------------------------GTGCT--------------------------G------TAGTTGAAATGGCATG-------TTGCAA-T-GCTT------------ACTGCACTTGTAAGTGC---AATTTCAGT------T---GC---------------AG--CTGCTGCTCTAGTGGCAATTA--GCAGGGTGTCTC

Size

Hit Count

Total Norm

droFic1

TTCC-GAGGA--------------AAAAGGG-ACAAC-TTCGATGACATT--------TACTGGCCAATAATGCAATTGCGTG----------------------------------------------------------------------TTGCAATGGCAAG-------TTGCAA-C-ACTA------------GTTTCACTTGCAAGTGC---AATTTTCGT------T---GCA------------ACTG--CTGCTGCTCGAGAAGCAATTA--GCAGGGTGTCTC

Size

Hit Count

Total Norm

droKik1

TTTT-G------------------AAAAGGA-CAAAG-TTCGATGCGATTTGCTCTTTCGCTGGCCCATAATGCAATTGCA---GC--------------------------TTGGC--------------------------T------CTGTTGCA-----ATA-----------------TTC------------GGTGCCCTT------------------------------------------------------TAACCCAAGAGGCAATTA--GCTGGGCGTCTC

Size

Hit Count

Total Norm

droAna3

TTTT-GAGCT--------------G------------------------------------------------CAGTTGC------------------------AGATAAAGTTACAGTTGTTGTTGCTACTT---TCACGTTGTTGTTGTTGTTGT-------TG---------------------------CGGCAGCTGCAGTTGCAGTTGC---AGTTGCAAT------T---GTTGCTGCAGCT---GTTGGCC--TAATGAGAGTGGCCAGCAATGCGGCACGAATC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.............................................................................TGC------------------------AGATAACGTAACAGTT.............................................................................................................................................................................	19	1	2.00	0.00	1.00	0.00	1.00
...................................................................................................................................TT---TGACGTTGTTGTTGTTG............................................................................................................................................	19	4	0.50	0.00	0.00	0.00	0.50
............................................................................................................................................GCTGTTGTTGTTGTTGT-------TG---------------------------CGGCGGC.............................................................................................	26	1	2.00	0.00	2.00	0.00	0.00
............................................................................................................................................................................................................GTTGCAGTGGC---AGTTGAAA...................................................................	19	2	0.50	0.50	0.00	0.00	0.00
...........................................................................................................................................................................................................AGCTGAAGTTGC---AGTTGCA....................................................................	19	32	0.03	0.03	0.00	0.00	0.00
........................G------------------------------------------------CAGTTGC------------------------AGATAGAGATACA................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...................................................................................................................................TT---TGACGTTGTTGTTGTTT............................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................GTTGCAGTTGC---AGTGGCC....................................................................	18	34	0.03	0.00	0.03	0.00	0.00
................................................................................................................................................TTGTTGTAGTTGT-------CG---------------------------CGGC................................................................................................	19	4	0.25	0.25	0.00	0.00	0.00
...............................................................................................................................................GTTGTTGTTGTTGT-------TG---------------------------CGGG................................................................................................	20	10	0.10	0.00	0.10	0.00	0.00
.............................................................................TGC------------------------AGATAACGTAACAGT..............................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................TTGTTGTTGTTGTTGT-------TG---------------------------G...................................................................................................	19	48	0.02	0.02	0.00	0.00	0.00
............................................................................................................................................GTTATTGTTGTTGTTGT-------TG---------------------------....................................................................................................	19	39	0.03	0.03	0.00	0.00	0.00
...............................................................................................................................................GTTGTTGTTGTTGT-------TG---------------------------CCA.................................................................................................	19	21	0.05	0.00	0.05	0.00	0.00
.............................................................................................................................................GTGTTGTTGTTGTTGT-------TG---------------------------....................................................................................................	18	45	0.02	0.00	0.02	0.00	0.00
.....................................................................................................................................................................................................AGCTGAAGTTGCAGTTGC---A..........................................................................	19	32	0.03	0.03	0.00	0.00	0.00

droBip1

T-----------------------------------------------------------------------GCACTTGC-TGTAC--------------------------CTGTT--------------------------G------CA------C----ATGTTG----CACCTG-T-TGCTG------CTGCTGCTGCACTTGCACTTGCTGCACTTGCACT------T---GCT------------GTTG--CTGCTGCTGAGGTGGCAGATA--GCCGGGTGC-TT

Size

Hit Count

Total Norm

dp4

A----------------------------------AC-TCTGCTGCCAGT--------AGTTGGCCATTGAGAAAATTGTGTGCCCTGGAATTTAATTCATTGCAAACAA-ATTGCT--------------------------G------CTGCT----------------------------------------------G---CTGCTGCTGC---TGCTGTTGT------T---GCT------------GCTG--CTGCCGTTGCAGTGGCAATT---------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.............................................................................................................................................................................................................................................................CTG--CTGCCGATGCTGTGGC...................	19	18	0.06	0.00	0.00	0.06	0.00

droPer1

A----------------------------------AC-TCTGCTGCCAGT--------AGTTGGCCATTGAGAAAATTGTGTGCCCTGGAATTTAATTCATTGCAAACAA-ATTGCT--------------------------G------CTGCT-------------------------------------------GCCGCTGCTGCTGTTGT---TGTTGTGGT------T---GCT------------GCTG--CTGCCGTTGCAGTGGCAATT---------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........................................................................................................................................................................................................TGCTGGTGTTGT---TGTTGT.....................................................................	18	269	0.01	0.00	0.00	0.00	0.00	0.01
......................................................................................................................................................CTGCT-------------------------------------------GCCGATGCTGCTGT.................................................................................	19	296	0.01	0.00	0.00	0.00	0.01	0.00
............................................................................................................................................................................................................GCTGCTGTTGT---TCTTGTTGT------T---GC......................................................	23	37	0.03	0.00	0.00	0.00	0.00	0.03
................................................................................................................................................................................................................TTGTTGx---TGTTGTGGT------T---GCT------------.........................................	19	11	0.09	0.09	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................TTGTTGx---TGTTGTGGT------T---GCT------------GCT......................................	22	9	0.11	0.11	0.00	0.00	0.00	0.00
..........................................................................................................................................................................................................TTGTTGCTGTTGT---TGTTGTGGT------T---........................................................	23	23	0.04	0.04	0.00	0.00	0.00	0.00
.................................................................CATTGAGAATATTGTGGGC.................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................................................................TGCTGCTGTTGT---TGTTTAG....................................................................	19	6	0.17	0.17	0.00	0.00	0.00	0.00
......................................................................................................................................................CTGCT-------------------------------------------GCCGATGCTGCTTT.................................................................................	19	12	0.08	0.00	0.00	0.00	0.08	0.00
.........................................................................................................................................................CT-------------------------------------------GCCGTTGCTGCTATTGT---...........................................................................	19	35	0.03	0.00	0.00	0.00	0.03	0.00
...................................................................................................................................................................................................................TTGT---TGATGTGTT------T---GCT------------G........................................	18	3	0.33	0.00	0.33	0.00	0.00	0.00
...................................................................................................................................................................................................................TTGT---TGATGTGTT------T---GCT------------GC.......................................	19	3	0.33	0.00	0.00	0.00	0.00	0.33
.............................................................................................................A-AATGTT--------------------------G------CTGCT-------------------------------------------GCCGC..........................................................................................	18	27	0.04	0.00	0.00	0.00	0.00	0.04
..........................................................................................................................................................................................................................TGTTGTTGT------T---GCT------------GCCG--CTGCCG.............................	23	34	0.03	0.03	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................TGTTGT---TGATGTGTT------T---GCT------------.........................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................GCTGTTGT---CGTTGTCGT------T---G.......................................................	19	19	0.05	0.05	0.00	0.00	0.00	0.00

droWil1

CTTG-GTGCCGTATCAAAGCTGGCATATAGT-TCAAC-TTCTTCA----T--------CGGTGGCAT-----------------------------------------CAC-----------------------------------------GTTGCAGTTG-TTG-------TTGTTG-T-TGTTGTTGCTGTTGCAGCTGTTGTTGTTGCTGT---TGTTGTTGC------T---GCA------------GCTG--CTGCTGCTCAAGTG---------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................................................................................................................................................TTG-T-TGTTGTTGCTGTTGCC...............................................................................................	20	301	0.01	0.00	0.00	0.00	0.01
.....................................................................................................................................................................G-------TTGATG-T-GGTTGTTGCTGTT..................................................................................................	21	27	0.07	0.04	0.00	0.04	0.00
..............................................................................................................................................................................TGTTG-T-TGTTGTTGCCGTTGCA...............................................................................................	22	38	0.05	0.00	0.05	0.00	0.00
..........................................................................................................................................................TGCAGTTG-TTG-------CAGTTG-T-TGT............................................................................................................	21	10	0.20	0.00	0.20	0.00	0.00
...............................................................................................................................................................................................................................................................................T---------------------	20	2	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................TTG-TTA-------TTGTTG-T-TCTTGTTGC......................................................................................................	22	43	0.05	0.00	0.05	0.00	0.00
.............................................................................................................................................................................TTGTTG-T-TGTTGTTGCCGTTGA................................................................................................	22	22	0.09	0.00	0.05	0.05	0.00
........................................................................................................................................................................................TTGGTGTTGTTGCAGCTGT..........................................................................................	19	27	0.07	0.00	0.00	0.07	0.00
................................................................................................................................................................................................GTTGCAGCTGTTCTTGGT...................................................................................	18	5	0.40	0.00	0.00	0.00	0.40
...............................................................................................................................................................TTG-TTG-------TTGTTG-T-TGTTGTTGC......................................................................................................	22	31	0.06	0.00	0.06	0.00	0.00
.................................................................................................................................................................................................................................GC------T---TCC------------GCTG--CTGCTGCTC..........................	19	35	0.06	0.00	0.06	0.00	0.00
............................................................................................................................................................................................TGGTGTTGCAGGTGTTGTTG.....................................................................................	20	5	0.40	0.20	0.20	0.00	0.00
.....................................................................................................................................................................G-------TTGATG-T-TGTTGTTGCCGT...................................................................................................	20	30	0.03	0.00	0.03	0.00	0.00
................................................................................................................................................................................TTG-T-TGTTGTTGCAGTAGC................................................................................................	19	38	0.03	0.03	0.00	0.00	0.00
...........................................................................................................................................................................................................TGTTGTTGCTGT---TGTTGTTGC------A---G.......................................................	23	30	0.03	0.00	0.03	0.00	0.00
........................................................................................................................................................................................................TGTTGTTGTCGCTCT---TGTTG......................................................................	20	35	0.03	0.00	0.00	0.03	0.00
.............................................................................................................................................................................TTGTTG-T-TGTTGTTGCTGTTGC................................................................................................	22	124	0.01	0.00	0.00	0.01	0.00
...............................................................................................................................................................................GTTG-T-TGTTGTTGCTGTC..................................................................................................	18	75	0.01	0.00	0.01	0.00	0.00
.............................................................................................................................................................................TTGTTA-T-TGTTGTTGCCGTTGC................................................................................................	22	8	0.13	0.00	0.00	0.13	0.00
.............................................................................................................................................................AGTTG-CTG-------TTGTTG-T-TGT............................................................................................................	18	44	0.02	0.00	0.02	0.00	0.00
..............................................................................................................................................................................TGTTG-T-TGTTGTTTCTGTT..................................................................................................	19	28	0.04	0.04	0.00	0.00	0.00
.................................................................................................................................................................G-TTG-------TTGTTG-T-TGTTGTTGC......................................................................................................	20	437	0.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................TTCAGTTG-TTG-------TTGTTG-T-TG.............................................................................................................	20	110	0.01	0.00	0.01	0.00	0.00
..........................................................................................................................................................................................................TTGTTGTTGCAGT---TGTTGTTG...................................................................	21	40	0.03	0.00	0.00	0.03	0.00
.....................................................................................................................................................................G-------TTGGTG-T-TGTTGTTGCTATTGC................................................................................................	23	9	0.11	0.00	0.11	0.00	0.00
................................................................................................................................................................TG-TTG-------TTGTTG-T-TGATGTTGCTGT...................................................................................................	24	13	0.08	0.00	0.00	0.08	0.00
...........................................................................................................................................................................................TGGCTGTTGCAGCTGTTG........................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
..........................................................................................................................................................................................................TTCATGTTGCTGT---TGTTGTT....................................................................	20	50	0.02	0.00	0.02	0.00	0.00
................................................................................................................................................................TG-TTG-------TTGTTG-T-TGTGGTTGCT.....................................................................................................	22	44	0.02	0.00	0.02	0.00	0.00
...............................................................................................................................................................TTG-TTG-------TTGTTG-T-TGTTGTCGC......................................................................................................	22	37	0.03	0.00	0.03	0.00	0.00
...............................................................................................................................................................................................................................................................................T---------------------	21	2	0.50	0.00	0.50	0.00	0.00
.............................................................................................................................................................................TTGTTG-T-TGTTGTTGCTGTTT.................................................................................................	21	18	0.06	0.00	0.00	0.06	0.00
....................................................................................................................................................................................................................TGT---TGTTCTTGC------T---GTA------------GCT......................................	19	43	0.02	0.00	0.00	0.02	0.00
...............................................................................................................................................................................GTTG-T-TGTTGTTGCTGTTGCCT..............................................................................................	22	29	0.03	0.00	0.00	0.03	0.00
...............................................................................................................................................................................................................................................................................T---------------------	26	2	0.50	0.00	0.00	0.00	0.50
..............................................................................................................................................................................TGTTG-T-TGTTGTTGCTGTTGC................................................................................................	21	231	0.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................................................................TTGTTGTTGCTGT---TGTTTTTGG------T---........................................................	23	30	0.03	0.00	0.03	0.00	0.00
...............................................................................................................................................................................................................................................................................T---------------------	23	2	0.50	0.00	0.50	0.00	0.00
...................................................................................................................................................................TAG-------TTGTTG-T-TGTAGTTGCTGTTG.................................................................................................	24	21	0.05	0.05	0.00	0.00	0.00
...................................................................................................................................................................TTG-------TTGTTG-T-TGTTGTTTCTG....................................................................................................	21	44	0.02	0.00	0.00	0.02	0.00
................................................................................................................................................................TG-TTG-------TTGTTG-T-TGTTGTTGCT.....................................................................................................	22	38	0.03	0.00	0.03	0.00	0.00
........................................................................................................................................................GTTGCAGTGG-TTG-------TTGGTG-T-T..............................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................TG-TTG-------TTGTTG-T-TATTGTTGCT.....................................................................................................	22	46	0.02	0.00	0.02	0.00	0.00
................................................................................................................................................................................................GTTCCAGCTGxTGTTGTTGC.................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
...............................................................................................................................................................................................................................................................................T---------------------	19	2	0.50	0.00	0.50	0.00	0.00
..................................................................................................................................................................................G-T-TGTTGTTGCTGTTGCCG..............................................................................................	19	50	0.02	0.00	0.00	0.02	0.00
.............................................................................................................................................................................ATGTTG-T-TGTTGTTGCTGT...................................................................................................	19	45	0.02	0.00	0.00	0.02	0.00
.........................................................................................................................................................................................................GTTGTTGTTGGTGT---TGTTCTTGC------............................................................	23	331	0.00	0.00	0.00	0.00	0.00
...................................................................................................................................................................TTG-------TTGTTG-T-TGTGGTTGCT.....................................................................................................	20	50	0.02	0.00	0.02	0.00	0.00
.....................................................................................................................................................................G-------TTGTTG-T-TGTTGTTTCTTTT..................................................................................................	21	21	0.05	0.05	0.00	0.00	0.00
.............................................................................................................................................................................TTGTTG-T-TGATGTTGCTGTTG.................................................................................................	21	38	0.03	0.00	0.03	0.00	0.00
................................................................................................................................................................TA-TTG-------TTGTTG-T-TGTTTTTGCT.....................................................................................................	22	51	0.02	0.00	0.02	0.00	0.00
.........................................................................................................................................................................................................GTTGTTCTTGCTGT---TGTTG......................................................................	19	44	0.02	0.00	0.02	0.00	0.00
.....................................................................................................................................................................G-------TGGTTG-T-TGTTGTTGCTCT...................................................................................................	20	25	0.04	0.00	0.04	0.00	0.00
........................................................................................................................................................GTTGCGGTTG-TTG-------TTTTTG-.................................................................................................................	19	461	0.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................GTTG-TTG-------TTGGTG-T-TGTTCTTGC......................................................................................................	23	331	0.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................................TCTTT-T-TGTTGTTGCTGTTG.................................................................................................	20	46	0.02	0.00	0.02	0.00	0.00
..............................................................................................................................................................................TCTTT-T-TGTTGTTGCTGTT..................................................................................................	19	51	0.02	0.00	0.02	0.00	0.00
.................................................................................................................................................................................TG-T-TGTTGTTGCTGTTGCCG..............................................................................................	20	44	0.02	0.00	0.00	0.02	0.00
..............................................................................................................................................................................TGTTG-T-TGTTGTTGCTGTTGCCA..............................................................................................	23	34	0.03	0.00	0.00	0.00	0.03
................................................................................................................................................................................TTG-T-TGTTGTTGCTGTTGTAG..............................................................................................	21	21	0.05	0.00	0.00	0.05	0.00
..........................................................................................................................................................TTCAGTTG-TTG-------TTGTTG-T-TGT............................................................................................................	21	67	0.01	0.00	0.01	0.00	0.00
..........................................................................................................................................................................................................TTGTTGTTGCAGT---TGTTGTT....................................................................	20	41	0.02	0.00	0.02	0.00	0.00
.........................................................................................................................................................................................................GTCGTCGTTGCTGT---TGTTGTT....................................................................	21	36	0.03	0.00	0.00	0.03	0.00
.................................................................................................................................................................T-TTG-------TTGTTG-T-TGTTGTTGC......................................................................................................	20	70	0.01	0.00	0.00	0.01	0.00
...............................................................................................................................................................................GTTG-T-TGTTGTTCCTGTAG.................................................................................................	19	41	0.02	0.00	0.00	0.00	0.02
.............................................................................................................AC-----------------------------------------GTTGCTGTTG-TTG-------TTGTTG-T-...............................................................................................................	22	37	0.03	0.00	0.03	0.00	0.00
...................................................................................................................................................................TTG-------TTGTTG-T-TGTTGTTACTG....................................................................................................	21	46	0.02	0.00	0.02	0.00	0.00
...........................................................................................................................................................................................................TGTTGTTGCTGT---TGTGGTC....................................................................	19	50	0.02	0.00	0.00	0.02	0.00
...............................................................................................................................................................................................................................................................................T---------------------	19	2	0.50	0.00	0.50	0.00	0.00
..........................................................................................................................................................................................................TTGATGTTGCTGT---TGTTGT.....................................................................	19	47	0.02	0.02	0.00	0.00	0.00
............................................................................................................................................................TAGTTG-TTG-------TTGTTG-T-TTTTGTTGC......................................................................................................	25	29	0.03	0.03	0.00	0.00	0.00
.............................................................................................................................................................................TTGTTG-T-TGTTGTTGCTGTTA.................................................................................................	21	18	0.06	0.00	0.00	0.06	0.00
..........................................................................................................................................................................................................TTGTTGTTGCTGT---TGTTG......................................................................	18	43	0.02	0.00	0.02	0.00	0.00
.............................................................................................................................................................................TTGTTG-T-TxTTGTTGCCGTTGC................................................................................................	21	8	0.13	0.00	0.00	0.13	0.00
..........................................................................................................................................................................................................TTGTTTATGCTGT---TGTTGTTGC------T---........................................................	23	51	0.02	0.00	0.00	0.02	0.00
..............................................................................................................................................................................TGTTG-T-TGTTGTTGCTGTTGCCT..............................................................................................	23	24	0.04	0.00	0.00	0.00	0.04
...............................................................................................................................................................TTG-TTG-------TTGTTG-A-TGTTGTTGCTG....................................................................................................	24	33	0.03	0.00	0.03	0.00	0.00
...........................................................................................................................................................................................................TGTTGTTGCTGT---TGTTGTT....................................................................	19	33	0.03	0.00	0.03	0.00	0.00
.....................................................................................................................................................................G-------TTGTTA-T-TGTTGTTGCTGTTA.................................................................................................	22	25	0.04	0.04	0.00	0.00	0.00
....................................................................................................................................................................TG-------TTGGTG-T-TGTTGTTGCTGTCG.................................................................................................	23	19	0.05	0.00	0.05	0.00	0.00
...............................................................................................................................................................................................................................................................................T---------------------	24	2	0.50	0.50	0.00	0.00	0.00
..............................................................................................................A-----------------------------------------GTTTCAGTTG-TTG-------TTGTT...................................................................................................................	19	6	0.17	0.17	0.00	0.00	0.00
............................................................................................................GAC-----------------------------------------GTTGCTGTTG-TTG-------TTGTTG-T-...............................................................................................................	23	17	0.06	0.00	0.06	0.00	0.00
..............................................................................................................................................................GTTG-TTG-------TTGTTG-T-TGATGTTGCT.....................................................................................................	24	42	0.02	0.02	0.00	0.00	0.00
...................................................................................................................................................................TTG-------TTGTTG-T-TGATGTTGCTGT...................................................................................................	22	19	0.05	0.00	0.05	0.00	0.00
..................................................................................................................................................................................................................................C------T---TCC------------GCTG--CTGCTGCTC..........................	18	41	0.02	0.00	0.02	0.00	0.00
............................................................................................................................................................................................................GTTGTTGCTGT---TGTTGTTGG------T---........................................................	21	40	0.03	0.03	0.00	0.00	0.00
...........................................................................................................................................................................................................................GTTGTTGC------T---GCA------------GCTG--CTGCTGC............................	23	53	0.02	0.00	0.02	0.00	0.00
.........................................................................................................................................................................................................GTTGTTGTTACTGT---TGTTGT.....................................................................	20	41	0.02	0.00	0.02	0.00	0.00

droVir3

TGTT---------------------------------------------------------------------------------G--------------------------CTGCT--------------------------G------CTGTTGCAATTG-TTG-------CTGCAG-C-TGTT------------GTTGCTGTTGCAGCTGC---AGCTGTAAC------TGTTGCT------------GCTG--CTGGGCATAGAGCTGCTCCTG--GT--AGTGCTTG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
............................................................................................................................................................................................................................GTGTAAC------TGTTGGT------------GCTG--...................................	18	6	0.33	0.00	0.00	0.00	0.33	0.00
.............................................................................................................................................................................................................................TGTAAC------TGTTGGT------------GCTG--A..................................	18	3	0.67	0.00	0.00	0.00	0.33	0.33
..............................................................................................................................................................................................................................................CT------------CCTG--CTGGGGATAGAGC......................	19	2	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................................................................................CAATTx-TTG-------CTGCAT-C-TGTT------------...............................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................................................................................GCATGGAGCCGCTCCTG--GT--........	19	2	0.50	0.00	0.00	0.50	0.00	0.00
......................................................................................................................................................................................................GTTGCTGTTGCAGCTGG---AGT........................................................................	20	19	0.05	0.05	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................................................TGTAAC------TGTTGGT------------GCTG--G..................................	18	5	0.20	0.00	0.00	0.00	0.20	0.00
...............................................................................................................................................................................................................................................T------------CCTG--CTGGGGATAGAGC......................	18	2	0.50	0.50	0.00	0.00	0.00	0.00
......................................................................................................................................................CTGTTGCCATTG-GTG-------CTG.....................................................................................................................	18	28	0.04	0.00	0.00	0.00	0.04	0.00
......................................................................................................................................................CTGTTGCCATTG-GTG-------CTGC....................................................................................................................	19	26	0.04	0.00	0.00	0.00	0.04	0.00

droMoj3

AGCC--------------------AGCATCG-ACAAC-TTGGCTGCAATT--------CA--------------------------------------------------GGTTGCAGCTACTGCTGTTGCCTGTTGCCTGTTG------CCGTTGCC-------G---------------------------TTGCTGCTGCAGTTGCAGTTGC---AGTTGTAGT------T---ACC------------GTTG--CAATTGC----------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
............................................................................................................................................................................................................GTTGCAGTCGC---AGTTGGAG...................................................................	19	14	0.07	0.07	0.00	0.00	0.00
........................................................................................................................................................................................................TGCAGTTGCAGTTGC---CGGTG......................................................................	20	17	0.06	0.00	0.00	0.00	0.06
..............................................................................................................................................TG------CCGTTGGC-------G---------------------------TTGCTGCTT...........................................................................................	20	5	0.20	0.00	0.00	0.20	0.00
............................................................................................................................................................................................................GTTGGAGTTGC---AGTTGAA....................................................................	18	13	0.08	0.08	0.00	0.00	0.00

droGri2

TGTT-G--------------------------TCAGC-GTTGTCGT--TG--------TGCTTGTTGATTTTCCAGTTGCT----G--------------------------CTGTT--------------------------G------CTGTTGCAGTTGC-AG-------TTGCA--------------------GCTGTTGCTGCTGTTGC---AGTTGCAGTTGTTGCT---GC---------------TG--CTGCTGTTGTTGTTGGTGTTG--TC-GGTGGTGTC	Size	Hit Count	Total Norm	V109 Male body
.....................................................................................................................................................................................................................................TTGCT---GC---------------TG--CTGCTGTTCTCGTT.....................	23	49	0.02	0.02
............................................................................TTGCT----G--------------------------CTGTT--------------------------G------CTGTTGCCG......................................................................................................................................	21	51	0.02	0.02

Generated: 04/20/2012 at 05:35:06 EDT

dme-mir-4982

chr2R:14607673-14607792 +

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