dme-mir-4960- Best orthologs

dme-mir-4960	chrX:463935-464036 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 463999-464019
   star strand at position 463961-463982
   mutations
   read mismatches

Notes: There has been large insertion and deletions since yakuba and earlier that cause the structure to vary.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:463920-464051 +		1	TGGAGTGACCAGC----------------------------AC--AACACAAGGCCTGCCGCCCAA-GAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCAAGCCCAGAAGTCC--------GGCAGTCGAG---------AA--------------------------------------------TCACGAGGGAC--TG------------------------------------GGACCTTGGGCTTACGGTTCTCAGTTTGGCTTGACATGCATCAGCATCAT
droSim1	chrX_random:776904-777034 +	LASTZ	4	CGGAGTGACCAGC----------------------------AC--ATCACAAGGCCTGGTGCCCAA-GAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCAAGCCCAGGAGTCC--------GGCAGTCGAG---------AA--------------------------------------------TCACGAGGGAC--TG-----------------------------------GGGCCTT--GGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droSec1	super_10:310837-310968 +	LASTZ	4	CGGAGTGACCAGC----------------------------AC--ATCACAAGGCCTGGTGCCCAA-GAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCAAGCCCAGGAGTCC--------GGCAGTCGAG---------AA--------------------------------------------TCACGAGGGAC--TG------------------------------------GGGCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droYak2	chrX:383437-383616 +	LASTZ	0	TGCAATGCCCACC----------------------------AC--AACACAAGGCCTGATGCCCGA-GAATCG-GTTTA----------------------------TTTCCTCCTCTTCCGC-------------------------------------------------------------------------------------------------------------------AGGCCCAGGAGTCC--------GGCAGTCGAGCAGTCGAGCTGTTCA--------------------CCCGGTCAG-----------TCCTT-GGTCC--TTGGTCCTT-----------------------------GGGCCTTGGGCTTTCGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droEre2	scaffold_4644:409107-409303 +	LASTZ	0	TGCAATGACCCTC----------------------------AC--CACACAAGGCCCGATGCCCGG-GAATCG-GTTTA----------------------------TTTCCTCTTCTTCCGC-------------------------------------------------------------------------------------------------------------------AGGCCCAGGAGTCC--------GGCAGTCCGACAGTCCAGCAGTCCG----GCAGTCGAGTTGTCGAGTAGTCCAG-----------TCATGAGGGGC--TGGGGCCTT-----------------------------GGGCCTTGGGCTTACGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droEug1	scf7180000409277:848596-848784 +	LASTZ	0	TGGAATGACC-------------------------------AC--AGCACAAGGTCTTATGGCCAG-GACTTG-GTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------GA--------AGTCC--------GGCAGTCGAGCAGTCGAGCAGTCCAGCCAGCAGTC-------CGGGCAGTCCGGTGGAGAA----TC--GAGGGGTTC-C-GGG-----------------------------GAGGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droBia1	scf7180000301760:1515569-1515727 +	LASTZ	0	TGGAATGACCAGGACAGCACA-GCACAGCAGAGCACATAGCACATAGCACAAGGCCTTATGCCCAA-GTCTTG-GTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------GA--------AGTCC--------GGCAGTCG----------------------------------------------------------------------------------------------------------AGGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droTak1	scf7180000415281:255352-255504 -	LASTZ	0	TGGAATGACCGGCACAGCACAAGCACA----AGCACA-AGCAC--ATCACAAGGCCTTATGCCCAA-GACTTG-GTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------AA--------AGTCC--------GGCAGTCG----------------------------------------------------------------------------------------------------------AGGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droEle1	scf7180000491023:745050-745100 +	LASTZ	0	G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCCTTTGGGGTTTCGGTTTTCAGTTTGTCTTGACATGCATCAGCATCAT
droRho1	scf7180000779514:240474-240645 +	LASTZ	0	TGGAATGACC-------------------------------AC--AGCACAAGGCCTTTCGCCCGA-GACTTG-CTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------AA--------AGTCC--------GGCAGTTCAG---TTCAGTAGG----------------------AG-GATAAAATGGGGGGGAAGGGAGGAGGGGG--TG---------------------------------GAGGTCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droFic1	scf7180000453927:944869-945084 +	LASTZ	0	TGGAATGACC-------------------------------AC--AGCACAAGGCCTTCTGCCCAAAGACTGGGGTTTA----------------------------TTTTCTGTTTGTCGGG-----------------------------------------------------------------------------------------------------------------GAAA--------GTCCGGCAGTCCGGCAGTCGGG---------AGTCCAGTCG---ATC-------CGAG-AATCCAGTGGGAGG----TT--CGGGGGTTC-G-GGGCTTCGGGTTGGCAGAGAGTGTATGAAGTAGAGGGCCTTTGGGGTTTTGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droKik1	scf7180000302469:1859429-1859538 -	LASTZ	0	TGAAATGACC-------------------------------AC--AGCA----------------G-GTCCTG-CTTTT----------------------------CTTACTAGGGGG-CGA------------------------------------------------------------------------------------------------------------------AA--------TGGAA--------TGGAGGCG----------------------------------------------------------------------------------------------------------GTATCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droAna3	scaffold_12929:357992-358198 +	LASTZ	0	TGGAATGACC-------------------------------AC--AGCAGAAGGCCTTCTGCC-AA-GACTTGGGTGTAGATATGAGTGTGTGTGGGTGTGGGTGTGTTTT------G------GCCAGAATATGGT------GGGTGATTGTGCAGGGAGGCGTGGCAGATGGGGGGGCGG--------------------------AGGATGAAGAAGAAG------------CAGTAGCAGAGGA--------------------------------------------------------------------------------------------------------------------------------GGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droBip1	scf7180000395176:32639-32844 -	LASTZ	0	TGGAATGACC-------------------------------AC--AGCAGAAGGCCTTCTGCC-AA-GACTTTGGTGTCAAT----------GTATGTGTGTGTGTGTTT------TG------GCCAGAATATGATAGAGTAGGGGGATTGTGCATGGAGGCGTGGCAG------GGGCGG--------------------------AGGAAGAAGAAGAGGCAGAAGCAGAAACAGAAGCGG-----------------------------------------------------------------------------------------------------------------------------------AGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
dp4	chrXL_group1e:196231-196421 +	LASTZ	0	TGGAATGACC-------------------------------AC--GGCACAAGGCCTT--G-CCAA-GACTTG-TTTTA----------------------------TTTTTTGCTGATTTGGGGGCAGGAACT-GT------AGGTGCC--------------TGCCGC------GCGGGGAAGTAGAAGGGAAAGGCGTGGCTGCGAG---GACGCAG-----------------GA--------GGCTT--------CGCAGGAG----------------------------------------------------------------------------------------------------------AGAACTTTTGGGGTTTCGGTTTTGAGTTTGACTTGACATGCATCAGCATCAT
droPer1	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180777:2769923-2769983 +	LASTZ	0	CAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGAT--TG-----------------------------------ACGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droVir3	scaffold_12970:10710181-10710231 +	LASTZ	0	G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droMoj3	scaffold_6473:10704148-10704209 -	LASTZ	0	GGGG---------------------------------------------------------------GGCTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droGri2	scaffold_14853:6069294-6069344 -	LASTZ	0	G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

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	TGGAGTGACCAGCACAACACAAGGCCTGCCGCCCAAGAAACGCAAGCCCAGAAGTCCGGCAGTCGAGAATCACGAGGGACTGGGACCTTGGGCTTACGGTTCTCAGTTTGGCTTGACATGCATCAGCATCAT
droSim1	CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAAACGCAAGCCCAGGAGTCCGGCAGTCGAGAATCACGAGGGACTGGGGCCTTG-GCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droSec1	CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAAACGCAAGCCCAGGAGTCCGGCAGTCGAGAATCACGAGGGACTGGGGCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

CGGAGTGACCAGC----------------------------AC--ATCACAAGGCCTGGTGCCCAA-GAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCAAGCCCAGGAGTCC--------GGCAGTCGAG---------AA--------------------------------------------TCACGAGGGAC--TG-----------------------------------GGGCCTT--GGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................................................................................................................................................................................................................................................................................................................................................................................CGGTTTTCGATTTGGCTTGAC...............	21	2	0.50	0.00	0.00	0.00	0.50
...........................................................................................................................................................................................................................................................................GAG---------AA--------------------------------------------GCACGAGGGTC--TG-----------------------------------...................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................................................................................................................................................................TCCCGTGGGAC--TG-----------------------------------GGGCC..............................................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

CGGAGTGACCAGC----------------------------AC--ATCACAAGGCCTGGTGCCCAA-GAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCAAGCCCAGGAGTCC--------GGCAGTCGAG---------AA--------------------------------------------TCACGAGGGAC--TG------------------------------------GGGCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................................................................................................................................................................................................................................................................................................................................GGTTTTCGATTTGGCTTGAC...............	20	2	0.50	0.50	0.00	0.00

droYak2

TGCAATGCCCACC----------------------------AC--AACACAAGGCCTGATGCCCGA-GAATCG-GTTTA----------------------------TTTCCTCCTCTTCCGC-------------------------------------------------------------------------------------------------------------------AGGCCCAGGAGTCC--------GGCAGTCGAGCAGTCGAGCTGTTCA--------------------CCCGGTCAG-----------TCCTT-GGTCC--TTGGTCCTT-----------------------------GGGCCTTGGGCTTTCGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................................................................................................................................................................................................................................................................................................................................................CGGTTTTCGATTTGGCTTGAC...............	21	2	0.50	0.00	0.00	0.00	0.00	0.50
.....................................................................................................................................................................................................................................................................................................................................................................................................TCGGTTTTCGGTTTGGTTTGA................	21	2	0.50	0.00	0.00	0.00	0.50	0.00

droEre2

TGCAATGACCCTC----------------------------AC--CACACAAGGCCCGATGCCCGG-GAATCG-GTTTA----------------------------TTTCCTCTTCTTCCGC-------------------------------------------------------------------------------------------------------------------AGGCCCAGGAGTCC--------GGCAGTCCGACAGTCCAGCAGTCCG----GCAGTCGAGTTGTCGAGTAGTCCAG-----------TCATGAGGGGC--TGGGGCCTT-----------------------------GGGCCTTGGGCTTACGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.............................................................................................................................................................................................................................................................................AAAGTCCAGCAGTCCG----GT.......................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

TGGAATGACC-------------------------------AC--AGCACAAGGTCTTATGGCCAG-GACTTG-GTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------GA--------AGTCC--------GGCAGTCGAGCAGTCGAGCAGTCCAGCCAGCAGTC-------CGGGCAGTCCGGTGGAGAA----TC--GAGGGGTTC-C-GGG-----------------------------GAGGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

droBia1

TGGAATGACCAGGACAGCACA-GCACAGCAGAGCACATAGCACATAGCACAAGGCCTTATGCCCAA-GTCTTG-GTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------GA--------AGTCC--------GGCAGTCG----------------------------------------------------------------------------------------------------------AGGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

droTak1

TGGAATGACCGGCACAGCACAAGCACA----AGCACA-AGCAC--ATCACAAGGCCTTATGCCCAA-GACTTG-GTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------AA--------AGTCC--------GGCAGTCG----------------------------------------------------------------------------------------------------------AGGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

droEle1

G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCCTTTGGGGTTTCGGTTTTCAGTTTGTCTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

droRho1

TGGAATGACC-------------------------------AC--AGCACAAGGCCTTTCGCCCGA-GACTTG-CTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------AA--------AGTCC--------GGCAGTTCAG---TTCAGTAGG----------------------AG-GATAAAATGGGGGGGAAGGGAGGAGGGGG--TG---------------------------------GAGGTCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

droFic1

TGGAATGACC-------------------------------AC--AGCACAAGGCCTTCTGCCCAAAGACTGGGGTTTA----------------------------TTTTCTGTTTGTCGGG-----------------------------------------------------------------------------------------------------------------GAAA--------GTCCGGCAGTCCGGCAGTCGGG---------AGTCCAGTCG---ATC-------CGAG-AATCCAGTGGGAGG----TT--CGGGGGTTC-G-GGGCTTCGGGTTGGCAGAGAGTGTATGAAGTAGAGGGCCTTTGGGGTTTTGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

droKik1

TGAAATGACC-------------------------------AC--AGCA----------------G-GTCCTG-CTTTT----------------------------CTTACTAGGGGG-CGA------------------------------------------------------------------------------------------------------------------AA--------TGGAA--------TGGAGGCG----------------------------------------------------------------------------------------------------------GTATCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

droAna3

TGGAATGACC-------------------------------AC--AGCAGAAGGCCTTCTGCC-AA-GACTTGGGTGTAGATATGAGTGTGTGTGGGTGTGGGTGTGTTTT------G------GCCAGAATATGGT------GGGTGATTGTGCAGGGAGGCGTGGCAGATGGGGGGGCGG--------------------------AGGATGAAGAAGAAG------------CAGTAGCAGAGGA--------------------------------------------------------------------------------------------------------------------------------GGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.....................................................................................AGTGTGTGTGTGTGTGTG...................................................................................................................................................................................................................................................................................................................................	18	27	0.41	0.04	0.37	0.00	0.00
....................................................................................GTGGGTGTGTGGGTGTGGGTGT................................................................................................................................................................................................................................................................................................................................	22	1	11.00	3.00	8.00	0.00	0.00
.....................................................................................AGTGTGTGTGTGTGTGTGT..................................................................................................................................................................................................................................................................................................................................	19	22	0.36	0.00	0.36	0.00	0.00
......................................................................................GTGGGTGTGGGTGTGGGT..................................................................................................................................................................................................................................................................................................................................	18	2	3.50	0.00	3.50	0.00	0.00
............................................................................................GTGGGTGTGGGTGTGGGT............................................................................................................................................................................................................................................................................................................................	18	2	3.50	0.00	3.50	0.00	0.00
......................................................................................GTGGGAGTGGGTGTGGGT..................................................................................................................................................................................................................................................................................................................................	18	1	5.00	0.00	5.00	0.00	0.00
....................................................................................GTGGGTGTGTGGGTGTGGGTGTG...............................................................................................................................................................................................................................................................................................................................	23	1	4.00	1.00	3.00	0.00	0.00
......................................................................................GTGGGTGTGGGTGTGGGTG.................................................................................................................................................................................................................................................................................................................................	19	1	4.00	0.00	4.00	0.00	0.00
................................................................................................GTGTGTGTGTGTTGT------G------GC............................................................................................................................................................................................................................................................................................................	18	1	4.00	1.00	3.00	0.00	0.00
......................................................................................GTGGGTGTGGGTGTGGGA..................................................................................................................................................................................................................................................................................................................................	18	2	2.00	0.00	2.00	0.00	0.00
.......................................................................................................................................GT------GGGTGGTTGTGCATGG...........................................................................................................................................................................................................................................................................	18	1	3.00	2.00	1.00	0.00	0.00
....................................................................................GTGGGTGTGTGGGTGTGGGT..................................................................................................................................................................................................................................................................................................................................	20	2	1.50	0.00	1.50	0.00	0.00
.................................................................................TGTGTGTGTGTGTGGGTG.......................................................................................................................................................................................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00
..........................................................................................GTGGGTGTGTGGGTGTGT..............................................................................................................................................................................................................................................................................................................................	18	7	0.43	0.14	0.29	0.00	0.00
.......................................................................................TGTGTGTGTGTGTGGGTG.................................................................................................................................................................................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00

droBip1

TGGAATGACC-------------------------------AC--AGCAGAAGGCCTTCTGCC-AA-GACTTTGGTGTCAAT----------GTATGTGTGTGTGTGTTT------TG------GCCAGAATATGATAGAGTAGGGGGATTGTGCATGGAGGCGTGGCAG------GGGCGG--------------------------AGGAAGAAGAAGAGGCAGAAGCAGAAACAGAAGCGG-----------------------------------------------------------------------------------------------------------------------------------AGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

dp4

TGGAATGACC-------------------------------AC--GGCACAAGGCCTT--G-CCAA-GACTTG-TTTTA----------------------------TTTTTTGCTGATTTGGGGGCAGGAACT-GT------AGGTGCC--------------TGCCGC------GCGGGGAAGTAGAAGGGAAAGGCGTGGCTGCGAG---GACGCAG-----------------GA--------GGCTT--------CGCAGGAG----------------------------------------------------------------------------------------------------------AGAACTTTTGGGGTTTCGGTTTTGAGTTTGACTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
............................................................................................................................................................................................................GGAGxG---GACGCAG-----------------GA--------GGCT...............................................................................................................................................................................	18	1	9.00	7.00	0.00	2.00	0.00
.............................................................................................................................................................................................................GAGxG---GACGCAG-----------------GA--------GGCTA--------......................................................................................................................................................................	18	1	3.00	3.00	0.00	0.00	0.00
..........................................................................................................................................................................................................GATGxGAG---GACGCAG-----------------GA--------GGC................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................................................GAG---GACGCAG-----------------GA--------GGCTA--------T.....................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droPer1

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

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

CAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGAT--TG-----------------------------------ACGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

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

GGGG---------------------------------------------------------------GGCTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

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 05:29:55 EDT

dme-mir-4960

chrX:463935-464036 +

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