dme-mir-4939- Best orthologs

dme-mir-4939	chr2R:18872733-18872842 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 18872760-18872780
   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:18872718-18872857 -		1	ATGCACATTTA--TTTGGCATCATGCTTCTGC-----------GA------------------TCTCTA------------------CCAATTTTCCT------------------TGCACTCTTTG------TCCTTTCCAAAAGTGAC--------------------ACGGGTGCAGGTGAAGA---TTCGGAA------GAG----GACGACGA-AAAC-GACTGCA-A---CCGGACGACTCTTGGT
droSim1	chr2R:17459524-17459663 -	LASTZ	4	ATCCACATTTA--TTTGGCATCATGCTTCTGC-----------GA------------------GCTCTA------------------CCACTTCTCCT------------------TGCACTCTTTG------TCCTTTCCAAAAGCGAC--------------------ACTGATGCTGGTGAAGA---TTCGGAG------GAG----GACGACAG-CGAA-GACTGCA-A---CAGGACGACTCTTGGT
droSec1	super_9:2164747-2164886 -	LASTZ	4	ATCCACATTTA--TTTGGCATCATGCTTCTGC-----------GA------------------GCTCTA------------------CCACTTCTCCT------------------TGCACTCTTTG------TCCTTTCCAAAAGCGAC--------------------ACTGATGCAGGTGAAGA---TTCAGAG------GAG----GACGACAG-CGAA-GACTGCA-A---CAGGACGACTCTTGGT
droYak2	chr2R:18832811-18832950 -	LASTZ	4	AACCGCGTTTA--TTTGCCAAAATGCTGCTCC-----------GA------------------GCTCTA------------------CCACTTCTGCT------------------CACACTCTGTGTGTTGGTCCTCTCCAACGACGAC--------------------ACGGATGCAGATGAAGA---AGAGGAA------GAG----G---A----CGAC-GACTGCA-A---CAAGGCGACTCTTGGT
droEre2	scaffold_4845:20234099-20234238 -	LASTZ	4	AACCACGTTTA--TTTGCCATAATGCTGCTCC-----------GA------------------ACTCTG------------------CTCCT------------------------TACGCTCTTCGTGTTTGTCCTTGCCAAAAACGAT--------------------ACGATTGCAGAAGTAGA---GGAAGAGTCGGACGAG----G---A----CGAA-GGATGCA-A---CAAGGCGACTCTTGGT
droEug1	scf7180000409672:6848444-6848567 -	LASTZ	0	ACCA-ATATCG--TTTGCCACAATGATACTAC-----------CA------------------GTTCTG------------------CCACTCCTTCT------------------AGGACTTTTTGTATCTGTCCAGT------GTGGC--------------------AAGTTCCCACCATCG-------------------------GAATA----CGAA-GAGTGCA-G---CAATGCAACTATTGGC
droBia1	scf7180000301754:4157293-4157441 -	LASTZ	0	AACCAATGTCA--TTCGCAATAATGATGCCAA-----------AA------------------GCTGTG------------------CCCCTCCTTCT------------------GGGGCTCCTCGTGCTCGTTCTCTCCGATCCCTAT--------------CCCGGTCGTGCGGATTACACGGA---TCCAGAG------GAG----GAGGA----GGCT-AAGTGCA-A---CAATAAGACTATTGGT
droTak1	scf7180000415411:112699-112853 +	LASTZ	0	AACCAGTTTTA--ATCGAGACCGTGATGCTAA-----------GA------------------GCTCTA------------------CCACTCTTTCT------------------AGGGCTATTCCTGATCGTTCATTCCGATCCCTTC--------CCAGATCCCTTTCCCGCTACCTATACGGA---TCCGGAG------GAG----GAGGA----AGCT-AAGTGCA-A---TTCTAAAACAATCGGT
droEle1	scf7180000491283:40306-40430 +	LASTZ	0	AGCCAATTTCA--TTTGCGATAATGATTCTAC-----------CA------------------GCTCTA------------------CAACTCTTCCT------------------AGGATTGTTGGTGCTCGTATATTCCGAGGACGAC--------------------GAGGAAAT---------------------------A----GAAGC----GGAC-AAGTGCA-G---AAACGCCACTATGGGA
droRho1	scf7180000767166:1286-1419 -	LASTZ	0	AATCAATTCTA--TTTGCGATAATGATTCTAC-----------CAGTG---------------GCGCTA------------------CCACTCTTTCT------------------AGGGCTGTGTGTGCTCGTCCTTTCCGAGGACT--------------------------------CGGAGGA---CTCGGAA------ATG----GAAGT----CGAC-AAGTGCG-A---CAACACCACTATTGGC
droFic1	scf7180000454066:2882629-2882771 -	LASTZ	0	AGCCAATTCCA--TTTGCGATCATGATTCTGT-----------CG------------------ACTCTG------------------CTACTCATCCT------------------GGGGATGACTGTATTTGTTCTTTCCGATGAAACT--------------------ACAACCACAACCAAGAAACCTTCGGAG------GAT----A---A----CGAT-AGCTGCA-A---CAAGACGACCATTGGC
droKik1	scf7180000302408:508066-508140 -	LASTZ	0	TTGAAAGTTTAAACTCAATTCCATGATTCTGC------GGC--CAAAA---------------AGCTTA------------------TTACTTCCTCT------------------AGCATTCTCTA------TTCCTCC----------------------------------------------------------------------------------------------------------------
droAna3	scaffold_13266:15204126-15204261 -	LASTZ	0	ATTTAAGAGCT--TTTCCCTTCAAAGCCTAAACAGTTGACACAAAATGTGGC---------------TA------------------CC----------------------------------------------CTTCTTGCTAGTGGC--------------------ACTGCCTTGGGGGACTG---TG-G----------TGGGGGGAGGTCCTCTGAC-ATTGGCCAATCTTAGCCGAATCATTGGA
droBip1	scf7180000396385:367904-368012 -	LASTZ	0	AAGCAGTT-GA--CTCAGAATG--------------------------TGGC---------------TA------------------CCTATCTTTCT------------------A----------------------------GTGGC--------------------ACTGCCAT-GGTGGACA---GTTGCGG------AGG----GACGTCCC-CAGTCGTTGTCCAATCTTACCCGAATTGTTGGA
dp4	chr3:14089101-14089284 -	LASTZ	0	AAGCAATT-AG--TTTGCCATT--------------------------TGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATT----CGAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTTAGTAAC----------------TCCCAGAACAACA---AA-A----------TGAACAAAGCTCGATCCGC-GTTCGCC-G---CCGCCCTTCTTTTGCT
droPer1	super_4:1228949-1229132 +	LASTZ	0	AAGCAATT-AG--TTTGCCATT--------------------------TGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATT----CAAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTTAGTAGC----------------TCCCAGAACAACA---AA-A----------TGAACAAAGCTCGATCCGC-GTTCGCC-G---CCGCCCTTCTTTTGCT
droWil1	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:24343095-24343103 -	LASTZ	0	AT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTGGC
droGri2	scaffold_15112:3934700-3934745 -	LASTZ	0	ATATTCAATA-----TGC------------------------------------------------TGA------------------GCACATCTTCT------------------GAAAGCATTTCAGACTTTC---------------------------------------------------------------------------------------------------------------------

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	ATGCACATTTATTTGGCATCATGCTTCTGCGATCTCTACCAATTTTCCTTGCACTCT------TTGTCCTTTCCAAAAGTGACACGGGTGCAGGTGAAGATTCGGAAGAGGACGACGAAAACGACTGCAACCGGACGACTCTTGGT
droSim1	ATCCACATTTATTTGGCATCATGCTTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGATGCTGGTGAAGATTCGGAGGAGGACGACAGCGAAGACTGCAACAGGACGACTCTTGGT
droSec1	ATCCACATTTATTTGGCATCATGCTTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGATGCAGGTGAAGATTCAGAGGAGGACGACAGCGAAGACTGCAACAGGACGACTCTTGGT
droYak2	AACCGCGTTTATTTGCCAAAATGCTGCTCCGAGCTCTACCACTTCTGCTCACACTCTGTGTGTTGGTCCTCTCCAACGACGACACGGATGCAGATGAAGAAGAGGAAGAGGACGAC------GACTGCAACAAGGCGACTCTTGGT
droEre2	AACCACGTTTATTTGCCATAATGCTGCTCCGAACTCTGCTCCTT------ACGCTCTTCGTGTTTGTCCTTGCCAAAAACGATACGATTGCAGAAGTAGAGGAAGAGTCGGACGAGGACGAAGGATGCAACAAGGCGACTCTTGGT

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	None
UNAFold Image																	None	None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

ATCCACATTTA--TTTGGCATCATGCTTCTGC-----------GA------------------GCTCTA------------------CCACTTCTCCT------------------TGCACTCTTTG------TCCTTTCCAAAAGCGAC--------------------ACTGATGCTGGTGAAGA---TTCGGAG------GAG----GACGACAG-CGAA-GACTGCA-A---CAGGACGACTCTTGGT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
............................CTAC-----------GA------------------GCTCTA------------------CCACTC...............................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................GA---TTTGGAC------GAG----GACGAC....................................	18	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................................................................................GGTGAAGA---TTCGGAG------GAG----GAC.......................................	21	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................GAGGA---TTCGGAG------GAG----GTC.......................................	18	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................AG----AACGACAG-CGxA-GACTG.......................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................................................AG-CGAA-GACTGCA-A---CAGGACGACT......	24	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................GAGGA---TTCGGAT------GAG----GAC.......................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

ATCCACATTTA--TTTGGCATCATGCTTCTGC-----------GA------------------GCTCTA------------------CCACTTCTCCT------------------TGCACTCTTTG------TCCTTTCCAAAAGCGAC--------------------ACTGATGCAGGTGAAGA---TTCAGAG------GAG----GACGACAG-CGAA-GACTGCA-A---CAGGACGACTCTTGGT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...................................................................................................................................................................................GCTGAAGA---TTCCGAG------GAG----..........................................	18	1	1.00	0.00	1.00	0.00
....................................................................................................................................................................................................G------GAG----AACGACAG-CGAA-GAG.........................	19	1	1.00	0.00	1.00	0.00
.........................................................................................................................................................................................GA---ATCAGAG------GAG----GAGGAC....................................	18	1	1.00	0.00	1.00	0.00
.............TTTGGCATCCTGGTTCTG.............................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.........................................................................................................................................................................................GA---TTCAGAG------GCG----GAGGACA...................................	19	1	1.00	0.00	1.00	0.00

droYak2

AACCGCGTTTA--TTTGCCAAAATGCTGCTCC-----------GA------------------GCTCTA------------------CCACTTCTGCT------------------CACACTCTGTGTGTTGGTCCTCTCCAACGACGAC--------------------ACGGATGCAGATGAAGA---AGAGGAA------GAG----G---A----CGAC-GACTGCA-A---CAAGGCGACTCTTGGT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..............................................................................................................................................................................................AGAAGAA------GAG----G---A----CGAC-GACT........................	20	1	2.00	0.00	0.00	2.00	0.00	0.00
.................................................................................................................................................................................................GGAA------GAG----G---A----CGAC-GAGCG.......................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................................GGAAGA---AGAGGAA------GAG----G---A----GGA..............................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................AGA---AGACGAA------GAG----G---A----GGA..............................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................................................GAGGAC------GAG----G---A----CGAC-GATT........................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................AAGAAGATGAAGA---AGAGGA........................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................CGATGAAGA---TGAGGAA------GAG----G---A----.................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................GATGAAGA---AGAGGAG------GAG----G---A----TG...............................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................GAGGA---CGAGGAA------GAG----G---A----C................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................GA---GGAGGAC------GAG----G---A----CGAC-............................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................AGAGGAA------GAG----G---A----GGAG-GA..........................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................ATGAAGA---TGAGGCA------GAG----..........................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................A---AGAGGAA------GAG----G---A----GGAG-G...........................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
......................................................................................................................................................................................GATGA---AGAGGAG------GAG----G---A----CG...............................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................TGAAGA---AAAGGAG------GAG----G---A----.................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................GATGAAGA---GGAGGAG------GAG----G---......................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................GATGAGGA---CGAGGAA------GAG----G---......................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................GAAGA---AGAGGAA------GAG----G---A----GGAG-GA..........................	23	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AACCACGTTTA--TTTGCCATAATGCTGCTCC-----------GA------------------ACTCTG------------------CTCCT------------------------TACGCTCTTCGTGTTTGTCCTTGCCAAAAACGAT--------------------ACGATTGCAGAAGTAGA---GGAAGAGTCGGACGAG----G---A----CGAA-GGATGCA-A---CAAGGCGACTCTTGGT

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

ACCA-ATATCG--TTTGCCACAATGATACTAC-----------CA------------------GTTCTG------------------CCACTCCTTCT------------------AGGACTTTTTGTATCTGTCCAGT------GTGGC--------------------AAGTTCCCACCATCG-------------------------GAATA----CGAA-GAGTGCA-G---CAATGCAACTATTGGC

Size

Hit Count

Total Norm

droBia1

AACCAATGTCA--TTCGCAATAATGATGCCAA-----------AA------------------GCTGTG------------------CCCCTCCTTCT------------------GGGGCTCCTCGTGCTCGTTCTCTCCGATCCCTAT--------------CCCGGTCGTGCGGATTACACGGA---TCCAGAG------GAG----GAGGA----GGCT-AAGTGCA-A---CAATAAGACTATTGGT

Size

Hit Count

Total Norm

droTak1

AACCAGTTTTA--ATCGAGACCGTGATGCTAA-----------GA------------------GCTCTA------------------CCACTCTTTCT------------------AGGGCTATTCCTGATCGTTCATTCCGATCCCTTC--------CCAGATCCCTTTCCCGCTACCTATACGGA---TCCGGAG------GAG----GAGGA----AGCT-AAGTGCA-A---TTCTAAAACAATCGGT

Size

Hit Count

Total Norm

droEle1

AGCCAATTTCA--TTTGCGATAATGATTCTAC-----------CA------------------GCTCTA------------------CAACTCTTCCT------------------AGGATTGTTGGTGCTCGTATATTCCGAGGACGAC--------------------GAGGAAAT---------------------------A----GAAGC----GGAC-AAGTGCA-G---AAACGCCACTATGGGA

Size

Hit Count

Total Norm

droRho1

AATCAATTCTA--TTTGCGATAATGATTCTAC-----------CAGTG---------------GCGCTA------------------CCACTCTTTCT------------------AGGGCTGTGTGTGCTCGTCCTTTCCGAGGACT--------------------------------CGGAGGA---CTCGGAA------ATG----GAAGT----CGAC-AAGTGCG-A---CAACACCACTATTGGC

Size

Hit Count

Total Norm

droFic1

AGCCAATTCCA--TTTGCGATCATGATTCTGT-----------CG------------------ACTCTG------------------CTACTCATCCT------------------GGGGATGACTGTATTTGTTCTTTCCGATGAAACT--------------------ACAACCACAACCAAGAAACCTTCGGAG------GAT----A---A----CGAT-AGCTGCA-A---CAAGACGACCATTGGC

Size

Hit Count

Total Norm

droKik1

TTGAAAGTTTAAACTCAATTCCATGATTCTGC------GGC--CAAAA---------------AGCTTA------------------TTACTTCCTCT------------------AGCATTCTCTA------TTCCTCC----------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droAna3

ATTTAAGAGCT--TTTCCCTTCAAAGCCTAAACAGTTGACACAAAATGTGGC---------------TA------------------CC----------------------------------------------CTTCTTGCTAGTGGC--------------------ACTGCCTTGGGGGACTG---TG-G----------TGGGGGGAGGTCCTCTGAC-ATTGGCCAATCTTAGCCGAATCATTGGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................................................................................................................TGGC--------------------ACGGACTTGGGGG.....................................................................	17	1	8.00	0.00	0.00	8.00	0.00
...................................................................................................................................................GGC--------------------ACGGCCTTGGGGAA....................................................................	17	1	4.00	0.00	0.00	4.00	0.00
..................................................................................................................................................................................GTGGGACTG---xG-G----------TGGGGGGA........................................	19	1	2.00	0.00	2.00	0.00	0.00
..................................................................................................................................................TGGC--------------------ACGGCCTTGGGGA.....................................................................	17	1	2.00	0.00	0.00	2.00	0.00
..................................................................................................................................................TGGC--------------------ACGGACTTGGGG......................................................................	16	1	2.00	0.00	0.00	2.00	0.00
......................................................................................................................................................................................GAGGG---TG-G----------TGGGGGGAGG......................................	18	1	2.00	0.00	2.00	0.00	0.00
...................................................................................................................................................................................TGGGAxTG---TG-G----------TGGGGGG.........................................	17	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................TA---TG-G----------CGGGGGGAGGTC....................................	17	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................................................................TGGC--------------------ACGGCCTTGGGGAA....................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................................................................TGGC--------------------ACGGCCTTxGGGGAC...................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................CTGGC--------------------ACGGCCTTGGGGGA....................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................CTTGGGGGACTG---AC-G----------TGGG............................................	19	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................CTGGC--------------------ACGGCCTTGGGG......................................................................	17	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................ACTGGC--------------------ACGGCCTTGGGG......................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................................................................TGGC--------------------ACGGCCTTxGGGGACT..................................................................	19	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................................TTGGGGTCCTG---TG-G----------TGG.............................................	17	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................CTTGGGGTACTG---TG-G----------TGGAG...........................................	20	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................CCTTGGGGGACTG---AG-G----------TGGGGA..........................................	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................................TTGGGGGACTG---AG-G----------TGGA............................................	18	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................CCCTGGGGGACTG---AG-G----------TGGG............................................	20	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................CTGGC--------------------ACTGCCTTGGGGA.....................................................................	18	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................GC--------------------ACGGCCTTGGGGAAC...................................................................	17	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................CTTGGGGGACTG---TA-G----------CGGG............................................	19	1	1.00	0.00	0.00	1.00	0.00

droBip1

AAGCAGTT-GA--CTCAGAATG--------------------------TGGC---------------TA------------------CCTATCTTTCT------------------A----------------------------GTGGC--------------------ACTGCCAT-GGTGGACA---GTTGCGG------AGG----GACGTCCC-CAGTCGTTGTCCAATCTTACCCGAATTGTTGGA

Size

Hit Count

Total Norm

dp4

AAGCAATT-AG--TTTGCCATT--------------------------TGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATT----CGAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTTAGTAAC----------------TCCCAGAACAACA---AA-A----------TGAACAAAGCTCGATCCGC-GTTCGCC-G---CCGCCCTTCTTTTGCT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
............................................................................................................................................................................................................TGAACAAAGCTCGATCCGC-GTT.........................	22	1	1.00	1.00	0.00	0.00	0.00

droPer1

AAGCAATT-AG--TTTGCCATT--------------------------TGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATT----CAAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTTAGTAGC----------------TCCCAGAACAACA---AA-A----------TGAACAAAGCTCGATCCGC-GTTCGCC-G---CCGCCCTTCTTTTGCT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.....................................................................................................ATAGTCCCAAAGCTTTTCGCTGATTG.............................................................................................................................	26	1	4.00	0.00	0.00	0.00	0.00	4.00
.............................................................................................................................................................................................................GAACAAAGCTCGATCCGC-GTT.........................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
............................................................................................................................................................................................................TGAACAAAGCTCGATCCG..............................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................GCTCGATCCGC-GTTCTGC-G---CC..............	21	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................ATCGGGGxAATACGCAATC................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

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

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

AT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTGGC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

ATATTCAATA-----TGC------------------------------------------------TGA------------------GCACATCTTCT------------------GAAAGCATTTCAGACTTTC---------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:20:03 EDT

dme-mir-4939

chr2R:18872733-18872842 -

Known_mirbase

intergenic

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