dme-mir-3645- Best orthologs

dme-mir-3645	chrX:5516313-5516449 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 5516358-5516379
   star strand at position 5516429-5516449
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:5516298-5516464 -		1	A--AACAAATCGATATGGTGAGTGCAG---------GCT-GTTTATTGCGGCG-------------CT-----------------GTTTA-------CTGTTTACGATC-------------------------------GCACTGGAAGTGCG--CTTTCCGGCGCC---TTTGGAAGCCA-------------------------------------------------------GCACTCAAGTTTCCTTCATTGTTTTCCTTTC----T----TTCCCCTCTCT---------CTCTCCCCGCAGGCAGCTTATACCGAG
droSim1	chrX:4275639-4275796 -	LASTZ	1	A--AACAAATAGAAATGGTGAGTGCAG---------GCT-GTTTATTGCGGCG-------------CT-----------------GTTTA-------TTGTTTACGATC-------------------------------GT---------GCG--CTATTCGGCGCC---TTTGGAAGCCA-------------------------------------------------------GCACTCAAGTTTCCCTCATTGTTTTCCTTTC----T----TCCCCCCCTCT---------CTCTCCCCGCAGGCAGCTTACACCGAG
droSec1	super_4:1240682-1240837 +	LASTZ	1	A--AACAAATAGAAATGGTGAGTGCAG---------GCT-GTTTATTGCGGCG-------------CT-----------------GTTTA-------CTGTTTACGATC-------------------------------GT---------GCG--CTATTCGGCGCC---TTTGGAAGCCA-------------------------------------------------------GCACTCAAGTTTCCCTCATTGTTTTCCTTTC----T----TTCC-CCCTCT----------CTCACCCGCAGGCAGCATACACCGAG
droYak2	chrX:2953226-2953406 +	LASTZ	1	A--AACAAATCGATATGGTGAGTGCAG---------GCT-GTTTATTGCGATG-------------CT-----------------GTTTA-------CTGTTTACAACCGCTT----------TC---------------GCACTGGAAGT-CG--GTTTTCGGCGCC---TTGGAAAACCA-------------------------------------------------------ACACTCAAGTTTCCTTCTTTGTTTTCCTTTT----C----TCTCCCTCTCTCTCTTTCTCTCTCTGTCGCAGGCCGCTTACACCGAG
droEre2	scaffold_4690:2867616-2867787 -	LASTZ	1	A--AACAAATCGATATGGTGAGTGCAG---------GCT-GTTTATTGCGGCG-------------CT-----------------GTTTA-------CTGTTTACGGTC-------------------------------GCACCGCAAGT-CG--CTTTTCGGCGCC---TTGGAAAACCA-------------------------------------------------------ACACTCAAGTTTCCCTCTTTGTTTTCCTTTC----T----TCTCCCTCTCTCTCTCA---CTCTCTTCGCAGGCAGCTTACACCGAG
droEug1	scf7180000409095:554359-554525 -	LASTZ	0	A--AACAAATCGATATGGTGAGTGGT---GGTGCAGCCT-GTTTACTGTTAGA-------------CT---------------CAGTTAA-------CTGTTTATTTTG-------------------------------AT-TTGGAACG-CC--CTTTTCGGCGTC---TT-GCCAACCG-------------------------------------------------------ATACTCAAGTTTCCTTCTTTGTTTTCCTCTT----T---------CTCTCC---------GTTTCGTTGTAGGCAGCTTACACCGAG
droBia1	scf7180000302069:308686-308867 +	LASTZ	0	A--AACGAATAGAGATGGTGAGTACGAGCCGG----ACT-GCTTATTGCGGCGCTGCTGCGGCTCGCT-----------------GTTTA-------CCGTTCACTATTGGCCGTTTGCCATCGTCTCG-------------AATGGAAGG-CC--GCCCTGGAAGC----CT-GGGAATCG-------------------------------------------------------GTACTCAAGTGTCCCT--T-----------CTT--TTCTT--------------------TTCTCGTTGCAGGCGGCGTACACCGAG
droTak1	scf7180000415289:630465-630594 +	LASTZ	0	A--AACAAATCGATATGGTGAGTG--------------------------------------------------------------TTTA-------CTGTTTATTATCGTGT----------GTGTTT-------------ATTGGAAGG-CC--GCTTTAACA-----------GTAAGG-------------------------------------------------------GTACTAAT-------CCTTTGTTGTCTTTTC----T----TGTC----------------TTCTCGTTGCAGGCAGCTTACACCGAG
droEle1	scf7180000491001:943150-943316 +	LASTZ	0	A--AACAAATCGATATGGTGAGCGCAA---------AGT-GTTTAATGCAGCA-------------CTGTTTGTTGTT-------GTTTA-------TTGTTTATTGTT-------------------------------GT-TCGGAGCG-CCTTATTTTGGGCGTG---TTGTGAACGGA-------------------------------------------------------GCACTCAAGTTCTCTTCTTTGTTTTTCTTTT----T----T-------------------TTTCCGATGCAGGCAGCTTACACCGAG
droRho1	scf7180000779976:765851-766001 +	LASTZ	0	A--AACAAATCGATATGGTGAGTGCAA---------AGT-GTTTATTGCAGCA-------------CT-----------------GTTTA-------TTGTTTATTGTT-------------------------------GT-TCGGAACG-CCT-TGTTCTGGCGAC---TT-GAGAACGG-------------------------------------------------------CTACTCAAGTTTATTTCTTTGTTTTTCTTT-------------------------------TTTCGATGCAGGCAGCTTACACCGAG
droFic1	scf7180000454072:2595294-2595436 +	LASTZ	0	A--AACAAATCGATATGGTGAGTGGTC---------TGT-GTTTACTGCAGCA-------------CT-----------------GTTTA-------C-GTTTGCTGTC-------------------------------G-ACCGCAAGA-CC--GTTGGCGGCGTC---TT-GAAAACGG-------------------------------------------------------ACACTCAGTTTCTGC--CTTCTGT---------------T--------------------TTCTCGTTGCAGGCAGCTTACACCGAG
droKik1	scf7180000302469:622797-622953 +	LASTZ	0	A--AACCAATCGATATGGTGAGTGGG--TCGG----CCT--------------------------------------------CCGTTTACTATTTATTGTTTATTGAG-----------------GCCAACGGCAGT--GT---------GTG--ACTTTCGCCGCC----T-GAAAACGG-------------------------------------------------------ACACTCATGTTTT-TTCTTTGTTTTTCTTGT----TTTTT--------------------TTTTCGTTGCAGGCAGCTTACACCGAG
droAna3	scaffold_13117:2022234-2022400 +	LASTZ	0	A--AACAAATCGATATGGTAAGTGCGT--GAA-----GT-AGGCAACATGACA-------------CTTTGTATATTTGACAACAATTGA-------ATGTTTACG---------------------------------------GGACCT--C--CTATTTCCCGCT---TC-GGCAG-----------CAACGATGACGACGA--------------------------------CGACTCATGTTTTCC--TTTGTTTTGTTGT-----------------------------------TTTTCAGGCAGCTTACACCGAG
droBip1	scf7180000396425:45801-45969 -	LASTZ	0	AAAAACAAATCGATATGGTAAGTGCGT--GAA-----GT-AGGCAACATGACA-------------CTTTGTATATTTAATAACAATTGA-------ATGTTTACG---------------------------------------GGAGCT-CC---TATTTCCCGCT---TC-GCCAG-----------CAACGATGACGACGT--------------------------------CGACTCATGTTTTCC--TTTGTTTTGTTGT-----------------------------------TTTTCAGGCAGCTTACACCGAG
dp4	chrXL_group1a:8129365-8129509 -	LASTZ	0	C--AACAAATCGATATGGTAAGTGGG--CTGA----AC------AGTA------------------ATTGATATC----------GTGG--------------------------------------CC------AATAT---------------------ATAGCCGCTA-----CG---------------------------TATCGTATGGCTTTTCCACTGAGTTTTGCTGGGAGCTAATGTGTTCT--TTTGT--------------------------------------TTGGTTTTACAGGCAGCTTACACCGAG
droPer1	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12928:4987995-4988105 +	LASTZ	0	T-----CAATCAATATGGTAAGTTGG--CCAA----AATTG-TTGTTGCT--------------------------TTT--------------------------------------------------------ACGAC---------------------ACGTACATTG-----TT---------------------------TATAGT----------------------------------GTGTT------TAT-------TCTTGCTACTT--------------------TTGCATTTACAGGCAGCTTACACCGAG
droMoj3	scaffold_6359:3485302-3485418 +	LASTZ	0	---------TCAATATGGTAAGTTGG--CACA----GCT-G----------------------------------------------TTG-------CTATTT----------------------------------------------------------------T---TTAGAGAGCAAATAATATG---------------TTTCGTTTGTTTTTA----------------------CAA----------TTGTTGTCTTT----------------TTCTCT---------TGTTATTTACAGGCAGCATACACCGAG
droGri2	scaffold_14853:9687493-9687620 +	LASTZ	0	C--ATTAAATCAACATGGTAAGTTGTA--TAA----ATCTA-TTTTTGCAGCTAT-CTGCAGCA--TT-----------------GTGT--------------------------------------GC------ACTAT---------------------ATACACATTA-----ATGAGT-------------------------------------------------------GTAATAAT------TTTGTTGTT----------------T--------------------TTGTTTTTACAGGCAGCTTACACCGAG

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	AAACAAATCGATATGGTGAGTGCAGGCTGTTTATTGCGGCGCTGTTTACTGTTTACGATCG------CACTGGAAGTGCGCTTTCCGGCGCCTTTGGAAGCCAGCACTCAAGTTTCCTTCATTGTTTTCCTTTCTTTCCCCTCTCTCTCTCC---------CCGCAGGCAGCTTATACCGAG
droSim1	AAACAAATAGAAATGGTGAGTGCAGGCTGTTTATTGCGGCGCTGTTTATTGTTTACGATCGT---------------GCGCTATTCGGCGCCTTTGGAAGCCAGCACTCAAGTTTCCCTCATTGTTTTCCTTTCTTCCCCCCCTCTCTCTCC---------CCGCAGGCAGCTTACACCGAG
droSec1	AAACAAATAGAAATGGTGAGTGCAGGCTGTTTATTGCGGCGCTGTTTACTGTTTACGATCGT---------------GCGCTATTCGGCGCCTTTGGAAGCCAGCACTCAAGTTTCCCTCATTGTTTTCCTTTCTTTCCC-CCTCTCTCAC----------CCGCAGGCAGCATACACCGAG
droYak2	AAACAAATCGATATGGTGAGTGCAGGCTGTTTATTGCGATGCTGTTTACTGTTTACAACCGCTTTCGCACTGGAAGT-CGGTTTTCGGCGCCTTGGAAAACCAACACTCAAGTTTCCTTCTTTGTTTTCCTTTTCTCTCCCTCTCTCTCTTTCTCTCTCTGTCGCAGGCCGCTTACACCGAG
droEre2	AAACAAATCGATATGGTGAGTGCAGGCTGTTTATTGCGGCGCTGTTTACTGTTTACGGTCG------CACCGCAAGT-CGCTTTTCGGCGCCTTGGAAAACCAACACTCAAGTTTCCCTCTTTGTTTTCCTTTCTTCTCCCTCTCTCTCTCACTCTCT---TCGCAGGCAGCTTACACCGAG

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

A--AACAAATAGAAATGGTGAGTGCAG---------GCT-GTTTATTGCGGCG-------------CT-----------------GTTTA-------TTGTTTACGATC-------------------------------GT---------GCG--CTATTCGGCGCC---TTTGGAAGCCA-------------------------------------------------------GCACTCAAGTTTCCCTCATTGTTTTCCTTTC----T----TCCCCCCCTCT---------CTCTCCCCGCAGGCAGCTTACACCGAG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................................TA-------TTGTTTACGATC-------------------------------GT---------GCG--CT......................................................................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
........................................................................................................CGATC-------------------------------GT---------GCG--CTATTCGGC...............................................................................................................................................................	19	1	2.00	0.00	0.00	2.00	0.00
.................GTGAGTGCAG---------GCT-GTTTATTGC...................................................................................................................................................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
........................................................................................TA-------TTGTTTACGATC-------------------------------GT---------GCG--CTT.....................................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
.............................................TTGCGGCG-------------CT-----------------GTTTA-------TTGTTTACGA.........................................................................................................................................................................................................................	25	1	2.00	0.00	0.00	0.00	2.00
......................................................................................................TGCGATC-------------------------------GT---------GCG--CTGTTCGGCG..............................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..................................................GCG-------------CT-----------------GTTTA-------TTGTTTACGATC-------------------------------G.......................................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.................GTGAGTGCAG---------GCT-GTTTAT......................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................TTGTTTACGATC-------------------------------GT---------GCG--CTATTCGGC...............................................................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
..................TGAGTGCAG---------GCT-GTTTATTGC...................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................TTACGATC-------------------------------GT---------GCG--CTATTCGGT...............................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........TAGAAATGGTGAGTGCAG---------GCT-............................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................TTCGGCGCC---TTTGGAAGAC...............................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................TTACGATC-------------------------------GT---------GCG--CTATTCGG................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................ATTCGGCGCC---TTTGGAAGCC...............................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................TTACGATC-------------------------------GT---------GCG--CTATTCGGCGC.............................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
.................GTGAGTGCAG---------GCT-GTTTATTGCGGCA-------------..................................................................................................................................................................................................................................................................	26	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................GTTTACGATC-------------------------------GT---------GCG--CTATTCGGCGCC---TT.......................................................................................................................................................	29	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................C---TTTGGAAGCCA-------------------------------------------------------GCACTCAAGT.............................................................................	22	1	1.00	0.00	0.00	1.00	0.00

droSec1

A--AACAAATAGAAATGGTGAGTGCAG---------GCT-GTTTATTGCGGCG-------------CT-----------------GTTTA-------CTGTTTACGATC-------------------------------GT---------GCG--CTATTCGGCGCC---TTTGGAAGCCA-------------------------------------------------------GCACTCAAGTTTCCCTCATTGTTTTCCTTTC----T----TTCC-CCCTCT----------CTCACCCGCAGGCAGCATACACCGAG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................................................A-------CTGTTTACGATC-------------------------------GT---------GCG--CTA.....................................................................................................................................................................	21	1	2.00	2.00	0.00	0.00
...........................................................................................................................................................................TTTGGAAGCCA-------------------------------------------------------GCACTCAAGA.............................................................................	21	1	2.00	1.00	0.00	1.00
.................GTGAGTGCAG---------GCT-GTTTATTGCGG.................................................................................................................................................................................................................................................................................	24	1	2.00	2.00	0.00	0.00
.......................................................................................................................................................................C---TTTGGAAGCCA-------------------------------------------------------GCACTCAAG..............................................................................	21	1	2.00	2.00	0.00	0.00
...........................................................................................................................................................................TTTGGAAGCCA-------------------------------------------------------GCACTCAAGT.............................................................................	21	1	2.00	2.00	0.00	0.00
.......................................................................................................................................................................C---TTTGGAAGCCA-------------------------------------------------------GCACTCAAGT.............................................................................	22	1	2.00	1.00	1.00	0.00
.....................................................................................................................................................................GCC---TTTGGAAGCCA-------------------------------------------------------GCACTCAAG..............................................................................	23	1	1.00	0.00	0.00	1.00
.......................................................................................................ACGATC-------------------------------GT---------GCG--CTGTTCGGCG..............................................................................................................................................................	21	1	1.00	1.00	0.00	0.00
..................................................................................................TGTTTACGATC-------------------------------GT---------GCG--CTATT...................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00
...................................................................................................................................................................GCGCC---TTTGGAAGCCA-------------------------------------------------------GCACTCAAG..............................................................................	25	1	1.00	0.00	1.00	0.00
.......................................................................................TTA-------CTGTTTACGATC-------------------------------GT---------GCG--CTATT...................................................................................................................................................................	25	1	1.00	1.00	0.00	0.00
......................................................................................................TACGATC-------------------------------GT---------GCG--CTATTCGGCT..............................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
.................GTGAGTGCAG---------GCT-GTTTATTGCGA.................................................................................................................................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00
....ACAAGTAGAAGTGGTGAGTGCA..........................................................................................................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
...........................................................................................................................................................................TTTGGAAGCCA-------------------------------------------------------GCACTCAAG..............................................................................	20	1	1.00	1.00	0.00	0.00
............................................................................................................................................................................TTGGAAGCCA-------------------------------------------------------GCACTCAAGT.............................................................................	20	1	1.00	0.00	0.00	1.00
........................................................................................TG-------CTGTTTACGATC-------------------------------GT---------GCG--CTA.....................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
.......AATAGAAATGGTGAGTGCA..........................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
.........................................................................................A-------CCTTTTACGATC-------------------------------GT---------GCG--CTAT....................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
....ACAAATAGAAATGGTGAG..............................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.......................................................................................................................................................................C---TTTGGAAGCCA-------------------------------------------------------GCACTCAAGC.............................................................................	22	1	1.00	1.00	0.00	0.00
.......................................................................................................................................................................C---TTTGGAAGCCA-------------------------------------------------------GCACTCTAG..............................................................................	21	1	1.00	1.00	0.00	0.00
...................................................CG-------------CT-----------------GTTTA-------CTGTTTACGATC-------------------------------........................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
................................................CGTCG-------------CT-----------------GTTTA-------CTGTTTT............................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

A--AACAAATCGATATGGTGAGTGCAG---------GCT-GTTTATTGCGATG-------------CT-----------------GTTTA-------CTGTTTACAACCGCTT----------TC---------------GCACTGGAAGT-CG--GTTTTCGGCGCC---TTGGAAAACCA-------------------------------------------------------ACACTCAAGTTTCCTTCTTTGTTTTCCTTTT----C----TCTCCCTCTCTCTCTTTCTCTCTCTGTCGCAGGCCGCTTACACCGAG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.................GTGAGTGCAG---------GCT-GTTTATTGC...................................................................................................................................................................................................................................................................................	22	2	3.00	0.00	0.00	0.00	0.00	3.00
.................GTGAGTGCAG---------GCT-GTTTATT.....................................................................................................................................................................................................................................................................................	20	2	1.50	0.00	0.00	0.00	0.00	1.50
........ATCGATATGGTGxGAGCAG---------GC..............................................................................................................................................................................................................................................................................................	20	2	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................C---TTGGAAAACCC-------------------------------------------------------ACACTCAAGC.............................................................................	22	2	0.50	0.00	0.00	0.00	0.50	0.00
.................GTGAGTGCAG---------GCT-GTTTTTTG....................................................................................................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50	0.00
.................GTGAGTGCAG---------GCT-GTTTATTG....................................................................................................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
..........CGATATGGTGxGAGCAG---------GC..............................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
...........................................................................................................................................................................TTGGAAAACCA-------------------------------------------------------ACACTCAAGT.............................................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
.................GTGAGTGCAG---------GCT-GTTTATTTC...................................................................................................................................................................................................................................................................................	22	2	0.50	0.50	0.00	0.00	0.00	0.00

droEre2

A--AACAAATCGATATGGTGAGTGCAG---------GCT-GTTTATTGCGGCG-------------CT-----------------GTTTA-------CTGTTTACGGTC-------------------------------GCACCGCAAGT-CG--CTTTTCGGCGCC---TTGGAAAACCA-------------------------------------------------------ACACTCAAGTTTCCCTCTTTGTTTTCCTTTC----T----TCTCCCTCTCTCTCTCA---CTCTCTTCGCAGGCAGCTTACACCGAG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........ATCGATATGGTGxGAGCAG---------GC..............................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................A----T----TCTCCCTCTCTCGCTCA---CT.........................	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................................TTGTCGGCGCC---TTGGAAAACCA-------------------------------------------------------ACACT..................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................GTC-------------------------------GCACCGCAAGT-CG--CTTTTCGG................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00

droEug1

A--AACAAATCGATATGGTGAGTGGT---GGTGCAGCCT-GTTTACTGTTAGA-------------CT---------------CAGTTAA-------CTGTTTATTTTG-------------------------------AT-TTGGAACG-CC--CTTTTCGGCGTC---TT-GCCAACCG-------------------------------------------------------ATACTCAAGTTTCCTTCTTTGTTTTCCTCTT----T---------CTCTCC---------GTTTCGTTGTAGGCAGCTTACACCGAG

Size

Hit Count

Total Norm

droBia1

A--AACGAATAGAGATGGTGAGTACGAGCCGG----ACT-GCTTATTGCGGCGCTGCTGCGGCTCGCT-----------------GTTTA-------CCGTTCACTATTGGCCGTTTGCCATCGTCTCG-------------AATGGAAGG-CC--GCCCTGGAAGC----CT-GGGAATCG-------------------------------------------------------GTACTCAAGTGTCCCT--T-----------CTT--TTCTT--------------------TTCTCGTTGCAGGCGGCGTACACCGAG

Size

Hit Count

Total Norm

droTak1

A--AACAAATCGATATGGTGAGTG--------------------------------------------------------------TTTA-------CTGTTTATTATCGTGT----------GTGTTT-------------ATTGGAAGG-CC--GCTTTAACA-----------GTAAGG-------------------------------------------------------GTACTAAT-------CCTTTGTTGTCTTTTC----T----TGTC----------------TTCTCGTTGCAGGCAGCTTACACCGAG

Size

Hit Count

Total Norm

droEle1

A--AACAAATCGATATGGTGAGCGCAA---------AGT-GTTTAATGCAGCA-------------CTGTTTGTTGTT-------GTTTA-------TTGTTTATTGTT-------------------------------GT-TCGGAGCG-CCTTATTTTGGGCGTG---TTGTGAACGGA-------------------------------------------------------GCACTCAAGTTCTCTTCTTTGTTTTTCTTTT----T----T-------------------TTTCCGATGCAGGCAGCTTACACCGAG

Size

Hit Count

Total Norm

droRho1

A--AACAAATCGATATGGTGAGTGCAA---------AGT-GTTTATTGCAGCA-------------CT-----------------GTTTA-------TTGTTTATTGTT-------------------------------GT-TCGGAACG-CCT-TGTTCTGGCGAC---TT-GAGAACGG-------------------------------------------------------CTACTCAAGTTTATTTCTTTGTTTTTCTTT-------------------------------TTTCGATGCAGGCAGCTTACACCGAG

Size

Hit Count

Total Norm

droFic1

A--AACAAATCGATATGGTGAGTGGTC---------TGT-GTTTACTGCAGCA-------------CT-----------------GTTTA-------C-GTTTGCTGTC-------------------------------G-ACCGCAAGA-CC--GTTGGCGGCGTC---TT-GAAAACGG-------------------------------------------------------ACACTCAGTTTCTGC--CTTCTGT---------------T--------------------TTCTCGTTGCAGGCAGCTTACACCGAG

Size

Hit Count

Total Norm

droKik1

A--AACCAATCGATATGGTGAGTGGG--TCGG----CCT--------------------------------------------CCGTTTACTATTTATTGTTTATTGAG-----------------GCCAACGGCAGT--GT---------GTG--ACTTTCGCCGCC----T-GAAAACGG-------------------------------------------------------ACACTCATGTTTT-TTCTTTGTTTTTCTTGT----TTTTT--------------------TTTTCGTTGCAGGCAGCTTACACCGAG

Size

Hit Count

Total Norm

droAna3

A--AACAAATCGATATGGTAAGTGCGT--GAA-----GT-AGGCAACATGACA-------------CTTTGTATATTTGACAACAATTGA-------ATGTTTACG---------------------------------------GGACCT--C--CTATTTCCCGCT---TC-GGCAG-----------CAACGATGACGACGA--------------------------------CGACTCATGTTTTCC--TTTGTTTTGTTGT-----------------------------------TTTTCAGGCAGCTTACACCGAG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................................................................................................................................................................GATGACGACGA--------------------------------GGACGCAT...............................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................................................GACGATGATGACGA--------------------------------CGAC...................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...............................................................................................................................................................................................GACGATGACGACGA--------------------------------CGAG...................................................................................	18	44	0.02	0.00	0.00	0.00	0.02

droBip1

AAAAACAAATCGATATGGTAAGTGCGT--GAA-----GT-AGGCAACATGACA-------------CTTTGTATATTTAATAACAATTGA-------ATGTTTACG---------------------------------------GGAGCT-CC---TATTTCCCGCT---TC-GCCAG-----------CAACGATGACGACGT--------------------------------CGACTCATGTTTTCC--TTTGTTTTGTTGT-----------------------------------TTTTCAGGCAGCTTACACCGAG

Size

Hit Count

Total Norm

dp4

C--AACAAATCGATATGGTAAGTGGG--CTGA----AC------AGTA------------------ATTGATATC----------GTGG--------------------------------------CC------AATAT---------------------ATAGCCGCTA-----CG---------------------------TATCGTATGGCTTTTCCACTGAGTTTTGCTGGGAGCTAATGTGTTCT--TTTGT--------------------------------------TTGGTTTTACAGGCAGCTTACACCGAG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........GATATGGTAGCTGGG--CTG.....................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...........GATATGGTAGATGGG--CTG.....................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......AATCGATAAGGTAAATGGG--........................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........GATATGGTAGGTGGG--CTA.....................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

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

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

T-----CAATCAATATGGTAAGTTGG--CCAA----AATTG-TTGTTGCT--------------------------TTT--------------------------------------------------------ACGAC---------------------ACGTACATTG-----TT---------------------------TATAGT----------------------------------GTGTT------TAT-------TCTTGCTACTT--------------------TTGCATTTACAGGCAGCTTACACCGAG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

---------TCAATATGGTAAGTTGG--CACA----GCT-G----------------------------------------------TTG-------CTATTT----------------------------------------------------------------T---TTAGAGAGCAAATAATATG---------------TTTCGTTTGTTTTTA----------------------CAA----------TTGTTGTCTTT----------------TTCTCT---------TGTTATTTACAGGCAGCATACACCGAG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.............................................................................................................................................................................AGAGAGTAAATAATATT---------------TT.....................................................................................................................	19	2	44.00	34.00	0.50	1.50	8.00
.............................................................................................................................................................................AGAGAGTAAATAATATT---------------TTT....................................................................................................................	20	1	9.00	9.00	0.00	0.00	0.00
.............................................................................................................................................................................AGAGAGTAAATAATATT---------------T......................................................................................................................	18	2	3.00	0.00	0.00	0.00	3.00
..............................................................................................................................................................................GAGAGTAAATAATATT---------------TTT....................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00
...............................................................................................................................................................................AGAGTAAATAATATT---------------TTT....................................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00

droGri2

C--ATTAAATCAACATGGTAAGTTGTA--TAA----ATCTA-TTTTTGCAGCTAT-CTGCAGCA--TT-----------------GTGT--------------------------------------GC------ACTAT---------------------ATACACATTA-----ATGAGT-------------------------------------------------------GTAATAAT------TTTGTTGTT----------------T--------------------TTGTTTTTACAGGCAGCTTACACCGAG	Size	Hit Count	Total Norm	V109 Male body
...................................................................................................................................................................................................................................................................................................................................G	20	41	0.02	0.02

Generated: 04/20/2012 at 05:15:07 EDT

dme-mir-3645

chrX:5516313-5516449 -

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