dme-mir-4966- Best orthologs

dme-mir-4966	chrX:19452402-19452529 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 19452435-19452456
   star strand at position 19452463-19452484
   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:19452387-19452544 +		1	GTTTCCAGGACATTGAGCTGTGTGACAACAAACTTGTCGGCACTGGAGTACTAAATATATTGCACATGTTCATGCATG-----------TTCAACATATTTAGCACTCAAGTACCGAAAAAT-GA--------------------------ACAACGAAACGAAAAATAACA---------------------------------C-GAACATCA---TGCTGCCCATTATAT
droSim1	chrX:15018266-15018398 +	LASTZ	1	ACTTTGTCGGCACTGGAGTGC------------------------------TAAATATATTGCTCATGTTCT--------CATACATG-TACAACGTATTTAGCACACGAGTACTGAAAAAT-TA--------------------------ACAACGAAACGGTTGA--ACT--------------------------------CG-GAAGTGCAATATTGAGTTTTTGATTT
droSec1	super_8:1734644-1734797 +	LASTZ	1	GTTTCCAGGACATCGAGCTGTGTGACGGC------------ACTAGAGTACTAAATATATTGCACATGTTCATACATGTTCATACATG-TAAAACATATTTAGCACTCAAGTACCGAAAAAT-GA--------------------------ACATCGAAACGGGAGA--ACA---------------------------------C-GAGCATCT---TGCTACCCATTATAT
droYak2	chrX:11886103-11886223 -	LASTZ	0	GTTTCCGGGACTTCGTACTGTATGACAG-------------------ACTATATATACAATACGAAGCCTCTG--------------------AAATTTTCTGCGCTCAAGTACCAAAAACT----------------ACCA-GCAAA---CCAACGAAACTGGAGA--AC--------------------------------TAC-GGACGGCA------------------
droEre2	scaffold_4690:9688657-9688714 +	LASTZ	0	GTTTCAGGGACTTCGCACTGTATGACAA-------------------ACTAT-----------------------------------------AAATTTTGTGCACTCAAGTACCAAA-------------------------------------------------------------------------------------------------------------------
droEug1	scf7180000409230:879958-880072 -	LASTZ	0	GTTCCTGGGATTTCGCACTGTATTACGA-------------------TTTTTACATACAATACGAAAGCTCAG--------------------AAACTAACTGCAATTAACTACCGTAAACT-AC---------------G-----------GATGAGAACGAGTTTCAACC---------------------------------C-GAGTTTCA------------------
droBia1	scf7180000302069:1151347-1151445 -	LASTZ	0	GTTTCCGGGATTTTGTATTGTATGACTAG------------------ATTCTATATACAATACGAAACCTCAG--------------------AAATTTTCTGCAGTTAACTACCATAAATC----------------GCC-----------GAGAGAACCGAA---------------------------------------------------------------------
droTak1	scf7180000415169:845112-845228 -	LASTZ	0	GTTTCCGGGATTTCGTACTGTATGCTGA-------------------ATTCTATATACAATACGAAAGCTCAG--------------------AAATTTTCTGCAGTTAACTACCATTAACT----------------ACTT-ACT------------------------------------ACGAAGGATGGATTATGGAACTAG-GGA-----------------------
droEle1	scf7180000490751:1118532-1118559 +	LASTZ	0	GTTTCCGGGATTTCGTACTGTATGACAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droRho1	scf7180000761121:190368-190478 -	LASTZ	0	GTTTCCGGGATTTCGTACTGTATGACAA-------------------ATTCTATATACAATACGAAACCTTAG--------------------AAATTTTCTGCAGTTATCTACCATTAACT----------------ACCA-G------------------TTTAA--ACACTTAATTACAACAAA----------------------------------------------
droFic1	scf7180000454073:1733485-1733611 +	LASTZ	0	ATTGCGTAGCTATTGTT-----TGCCCA-------------------AACGAATATATATTCTTTATTTTTTC--------AAATCTACT---ATATTATATTCACTCGTATTCAAGAATCT----------------TAAAAAGAAA---GAAAAGAAACCAGCGA--AG--------------------------------TCCCGAAGCTGC------------------
droKik1	scf7180000302517:1183462-1183567 +	LASTZ	0	GTTTCCGAG-TTTCGTAATGTATGGTTAT------------------ATTTGAAATACAGTACGAGACATCAG--------------------AAATTTTCGGCAGTTAGCTACCGTAAACA----------------ACCA-AAA--------ATGGAGCAAGGAGCAA---------------------------------------------------------------
droAna3	scaffold_13417:2468043-2468174 -	LASTZ	0	GTTTCCGGGATCTCGTACTGTATGAAGT-------------------TTTCTATATACAATTCGAAAACTCAG--------------------AAACTTCCTGCCGTGAGCTACCATTGATCAACGGCTGAGTATGCGACCG-GAAAGGGGACGCGAATGCGAGGACTAA-------------------------------------------------------------AG
droBip1	scf7180000395874:40397-40493 -	LASTZ	0	GTTTCCGGGATCTCGTAGTGTATGAAGT-------------------TTTATAAATACAATTCGAAAACTCAG--------------------AAACTTTCTGCCTTGAAGTACATTCATCA-ACG------------GCC------------------------------------------------------------------GAGTAATA------------------
dp4	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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	GTTTCCAGGACATTGAGCTGTGTGACAACAAACTTGTCGGCACTGGAGTACTAAATATATTGCACATGTTCATGCATG----------TTCAACATATTTAGCACTCAAGTACCGAAAAATGAACAACGAAACGAAAAATAACACGA----ACATCATGCTGCCCATTATAT
droSim1	ACTT------------------------------TGTCGGCACTGGAGTGCTAAATATATTGCTCATGTTC--------TCATACATGTACAACGTATTTAGCACACGAGTACTGAAAAATTAACAACGAAACGGTTG--AACTCGGAAGTGCAATATTGAGTTTTTGATTT
droSec1	GTTTCCAGGACATCGAGCTGTGTGA------------CGGCACTAGAGTACTAAATATATTGCACATGTTCATACATGTTCATACATGTAAAACATATTTAGCACTCAAGTACCGAAAAATGAACATCGAAACGGGAG--AACACGA----GCATCTTGCTACCCATTATAT

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	None	None	None
UNAFold Image															None	None	None	None	None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

ACTTTGTCGGCACTGGAGTGC------------------------------TAAATATATTGCTCATGTTCT--------CATACATG-TACAACGTATTTAGCACACGAGTACTGAAAAAT-TA--------------------------ACAACGAAACGGTTGA--ACT--------------------------------CG-GAAGTGCAATATTGAGTTTTTGATTT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..................TAC------------------------------TAAATATATTGCACATGTT...................................................................................................................................................................	22	1	12.00	1.00	0.00	11.00	0.00
......................................................................................TG-TACAACGTATTTAGCACACG............................................................................................................................	22	1	7.00	0.00	0.00	7.00	0.00
....................................................................................CATG-TACAACGTATTTAGCACA..............................................................................................................................	22	1	6.00	0.00	0.00	6.00	0.00
.............................................................................................................AGTACTGACAAAT-TA--------------------------ACT...............................................................................	18	1	4.00	0.00	0.00	1.00	3.00
......................................................................................TG-TACAACGTATTTAGCACACGA...........................................................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
......................................................................................TG-TACAACGTATTTGGCACACG............................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
......................................................................................TG-TACAACGTATTTAGCACACGG...........................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
..................TAC------------------------------TAAATATATTGCACATGT....................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................AAAAAT-GA--------------------------ACAACGAACC........................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..................TGC------------------------------TAAATATATTGCTCATGC....................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00

droSec1

GTTTCCAGGACATCGAGCTGTGTGACGGC------------ACTAGAGTACTAAATATATTGCACATGTTCATACATGTTCATACATG-TAAAACATATTTAGCACTCAAGTACCGAAAAAT-GA--------------------------ACATCGAAACGGGAGA--ACA---------------------------------C-GAGCATCT---TGCTACCCATTATAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................TACTAAATATATTGCACATGTT...................................................................................................................................................................	22	4	17.00	12.00	1.50	3.50
......................................................................................TG-TAAAACATATTTAGCACTC.............................................................................................................................	21	4	6.50	5.75	0.25	0.50
......................................................................................TG-TAAAACATATTTAGCACTCA............................................................................................................................	22	4	4.75	3.50	0.75	0.50
......................................................................................TG-TAAAACATATTTAGAACTCA............................................................................................................................	22	4	2.75	2.75	0.00	0.00
......................................................................................TG-TAAAACATATTTAGAACTC.............................................................................................................................	21	4	1.50	1.50	0.00	0.00
................................................TACTAAATATATTGCACATGT....................................................................................................................................................................	21	4	1.00	1.00	0.00	0.00
.................................................ACTAAATATATTGCACATGTT...................................................................................................................................................................	21	4	0.75	0.50	0.00	0.25
......................................................................................TG-TAAAACATATTTAGCACTCT............................................................................................................................	22	4	0.50	0.50	0.00	0.00
..................................................CTAAATATATTGCACATGTT...................................................................................................................................................................	20	5	0.20	0.20	0.00	0.00
................................................TACTAAATATATTGCACAAGTT...................................................................................................................................................................	22	4	0.25	0.25	0.00	0.00
.....................................................................................................................AAAAT-GA--------------------------AxAACGAAACGGGA....................................................................	20	3	0.33	0.00	0.33	0.00
......................................................................................TG-TAAAACATATTTAGCGCTCA............................................................................................................................	22	4	0.25	0.00	0.00	0.25
......................................................................................................................AAAT-GA--------------------------AxAACGAAACGGGA....................................................................	19	3	0.33	0.00	0.33	0.00
....................................................................................CATG-TAAAACATATTTAGAACTC.............................................................................................................................	23	4	0.25	0.00	0.25	0.00
................................................TACTAACTATATTGCACATGTT...................................................................................................................................................................	22	4	0.25	0.25	0.00	0.00
................................................TACTAAATATATTGCACACGTT...................................................................................................................................................................	22	4	0.25	0.25	0.00	0.00
......................................................................................TG-TACAACATATTTAGCA................................................................................................................................	18	2	0.50	0.50	0.00	0.00
......................................................................................TG-AAAAACATATTTAGCACTCA............................................................................................................................	22	4	0.25	0.00	0.00	0.25
......................................................................................TG-TAAAACATATTTAGCACT..............................................................................................................................	20	4	0.25	0.25	0.00	0.00
GCTTCGAGGACATCGAGC.......................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
....ACAGGACATCGAGCAGTG...................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
......................................................................................TG-TAAAACATATTTACAACTCA............................................................................................................................	22	4	0.25	0.25	0.00	0.00
................................................TACTAAATATATTGCACATG.....................................................................................................................................................................	20	4	0.25	0.25	0.00	0.00
....................................................................................CATG-TAAAACATATTTAGAACT..............................................................................................................................	22	4	0.25	0.25	0.00	0.00
......................................................................................TG-TAAAACATATTTAGCATTC.............................................................................................................................	21	4	0.25	0.25	0.00	0.00
......................................................................................TG-TAAAACGTATTTAGCACTCA............................................................................................................................	22	4	0.25	0.25	0.00	0.00
.................................................ACTAAATATATTGCACATGT....................................................................................................................................................................	20	4	0.25	0.25	0.00	0.00
................................................CACTAAATATATTGCACATGTT...................................................................................................................................................................	22	4	0.25	0.25	0.00	0.00
..............................................CGTACTAAATATATTGCACATG.....................................................................................................................................................................	22	4	0.25	0.00	0.25	0.00

droYak2

GTTTCCGGGACTTCGTACTGTATGACAG-------------------ACTATATATACAATACGAAGCCTCTG--------------------AAATTTTCTGCGCTCAAGTACCAAAAACT----------------ACCA-GCAAA---CCAACGAAACTGGAGA--AC--------------------------------TAC-GGACGGCA------------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................AATACGAAGCCTCTG--------------------AAATTTT.....................................................................................................................................	22	1	127.00	0.00	0.00	15.00	0.00	112.00
...........................................................ATACGAAGCCTCTG--------------------AAATTTTCT...................................................................................................................................	23	1	30.00	0.00	0.00	0.00	0.00	30.00
..........................................................AATACGAAGCCTCTG--------------------AAATTT......................................................................................................................................	21	1	22.00	0.00	0.00	1.00	0.00	21.00
...........................................................ATACGAAGCCTCTG--------------------AAATTTTCTG..................................................................................................................................	24	1	5.00	0.00	0.00	0.00	0.00	5.00
..........................................................AATACGAAGCCTCTG--------------------AAATT.......................................................................................................................................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
............................................................TACGAAGCCTCTG--------------------AAATTTTCT...................................................................................................................................	22	1	3.00	0.00	0.00	0.00	0.00	3.00
............................................................TACGAAGCCTCTG--------------------AAATTTTCTG..................................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
...........................................................ATACGAAGCCTCTG--------------------AAATTTTC....................................................................................................................................	22	1	2.00	0.00	0.00	1.00	0.00	1.00
....CCGGGACTTCGTACTGTA...................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................AATACGAAGCCTTTG--------------------GAATTTT.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................................ATACGAAGCCTCTG--------------------AAATTTT.....................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................ATACGAAGCCTCTG--------------------AAATTTTCC...................................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................AATACGAAGCATCTG--------------------AAATTTT.....................................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................ATACGAAGCCTCTG--------------------AAATTTTCTGC.................................................................................................................................	25	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................AATACGGAGCCTCTG--------------------AAATTT......................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................AATACGAAGCCTCTG--------------------AGATTTT.....................................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................TACGAAGCCTCTG--------------------AAATTTTC....................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................CAATACGAAGCCTCTG--------------------AAATTTT.....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
GTTTCCGGGACTTCGTACTGTT...................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00

droEre2

GTTTCAGGGACTTCGCACTGTATGACAA-------------------ACTAT-----------------------------------------AAATTTTGTGCACTCAAGTACCAAA-------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

GTTCCTGGGATTTCGCACTGTATTACGA-------------------TTTTTACATACAATACGAAAGCTCAG--------------------AAACTAACTGCAATTAACTACCGTAAACT-AC---------------G-----------GATGAGAACGAGTTTCAACC---------------------------------C-GAGTTTCA------------------

Size

Hit Count

Total Norm

droBia1

GTTTCCGGGATTTTGTATTGTATGACTAG------------------ATTCTATATACAATACGAAACCTCAG--------------------AAATTTTCTGCAGTTAACTACCATAAATC----------------GCC-----------GAGAGAACCGAA---------------------------------------------------------------------

Size

Hit Count

Total Norm

droTak1

GTTTCCGGGATTTCGTACTGTATGCTGA-------------------ATTCTATATACAATACGAAAGCTCAG--------------------AAATTTTCTGCAGTTAACTACCATTAACT----------------ACTT-ACT------------------------------------ACGAAGGATGGATTATGGAACTAG-GGA-----------------------

Size

Hit Count

Total Norm

droEle1

GTTTCCGGGATTTCGTACTGTATGACAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droRho1

GTTTCCGGGATTTCGTACTGTATGACAA-------------------ATTCTATATACAATACGAAACCTTAG--------------------AAATTTTCTGCAGTTATCTACCATTAACT----------------ACCA-G------------------TTTAA--ACACTTAATTACAACAAA----------------------------------------------

Size

Hit Count

Total Norm

droFic1

ATTGCGTAGCTATTGTT-----TGCCCA-------------------AACGAATATATATTCTTTATTTTTTC--------AAATCTACT---ATATTATATTCACTCGTATTCAAGAATCT----------------TAAAAAGAAA---GAAAAGAAACCAGCGA--AG--------------------------------TCCCGAAGCTGC------------------

Size

Hit Count

Total Norm

droKik1

GTTTCCGAG-TTTCGTAATGTATGGTTAT------------------ATTTGAAATACAGTACGAGACATCAG--------------------AAATTTTCGGCAGTTAGCTACCGTAAACA----------------ACCA-AAA--------ATGGAGCAAGGAGCAA---------------------------------------------------------------

Size

Hit Count

Total Norm

droAna3

GTTTCCGGGATCTCGTACTGTATGAAGT-------------------TTTCTATATACAATTCGAAAACTCAG--------------------AAACTTCCTGCCGTGAGCTACCATTGATCAACGGCTGAGTATGCGACCG-GAAAGGGGACGCGAATGCGAGGACTAA-------------------------------------------------------------AG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................ATTCGAAAACTCAG--------------------AAACTTCCT...................................................................................................................................	23	1	42.00	8.00	29.00	5.00	0.00
..........................................................AATTCGAAAACTCAG--------------------AAACTTC.....................................................................................................................................	22	1	15.00	4.00	7.00	4.00	0.00
.........................................................CAATTCGAAAACTCAG--------------------AAACTTC.....................................................................................................................................	23	1	9.00	2.00	3.00	4.00	0.00
............................................................TTCGAAAACTCAG--------------------AAACTTCCT...................................................................................................................................	22	1	6.00	1.00	4.00	1.00	0.00
.........................................................CAATTCGAAAACTCAG--------------------AAACTT......................................................................................................................................	22	1	4.00	2.00	2.00	0.00	0.00
..........................................................AATTCGAAAACTCAG--------------------AAACTTCC....................................................................................................................................	23	1	2.00	1.00	1.00	0.00	0.00
...........................................................ATTCGAAAACTCAG--------------------AAGCTTCCT...................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
....................................................ATATACAATTCGAAAACTCAG--------------------A...........................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..........................................................AATGCGAAAACTCAG--------------------AAACTTC.....................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...........................................................ATTCGAAAACTCAG--------------------AAACTTCCTT..................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................CGGCCG-GTAAGGGGACG...............................................................................	17	1	1.00	0.00	0.00	1.00	0.00
GTTTCCGGGATCTCGTACTG.....................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
...........................................................ATTCGAAGACTCGG--------------------AAACTTCCT...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
..........................................................AATTCGAAAACTCTG--------------------AAACTTC.....................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...........................................................ATTCGAAAACTCAG--------------------AAACTCCCT...................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...........................................................ATTCGAAAACTCAG--------------------AAACTTC.....................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...........................................................ATTCGAAAACTCGG--------------------AAACTTCCT...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...........................................................ATTAGAAAACTCAG--------------------AAACTTCCT...................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...........................................................ATTCGAAAGCTCAG--------------------AAACTTCCT...................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
............................................................TTCGAGAGCTCAG--------------------AAACTTCCT...................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
............................................................TTAGAAAACTCAG--------------------AAACTGCCT...................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................................CAATTCGAAAACTCAG--------------------AACCTTC.....................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.TTTCCGGGATCTCGTACTGTAT..................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................TGCGACCC-GAAAGGGGG.................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
...........................................................ATGCGAAAACTCGG--------------------AAACTTCCT...................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...........................................................ATTCGAGAGCTCAG--------------------AAACTTCCT...................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.....CGGGATCTCGTACTGTATGAAG..............................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..........................................................AATTCAAAAACTCAG--------------------AAACTTC.....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................CG-GAAAGGGGACCCGAC...........................................................................	17	1	1.00	0.00	0.00	1.00	0.00
...........................................................ATTCGAAAACTCAG--------------------AAACTTCC....................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...........................................................GTTCGAAAACTCAG--------------------AAACTTCCT...................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...........................................................ATTCGAAAGCTGAG--------------------AAACTTCCT...................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...........................................................ATTCGAGAACTCAG--------------------AAGCTTCCT...................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.........................................................CAATTCGAAAACTCGG--------------------AAACTT......................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...........................................................ATTCGAAAACTCAG--------------------AAACTTCCC...................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00

droBip1

GTTTCCGGGATCTCGTAGTGTATGAAGT-------------------TTTATAAATACAATTCGAAAACTCAG--------------------AAACTTTCTGCCTTGAAGTACATTCATCA-ACG------------GCC------------------------------------------------------------------GAGTAATA------------------

Size

Hit Count

Total Norm

dp4

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

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

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

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:13:49 EDT

dme-mir-4966

chrX:19452402-19452529 +

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