dme-mir-282-as- Best orthologs

dme-mir-282-as	chr3L:3251022-3251118 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 3251036-3251057
   star strand at position 3251079-3251100
   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	chr3L:3251007-3251133 -		1	TCCGTTTT------------------CGCTGATTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAGAAGGAAA-CTATA--------G-TTAAAGAAC-----------GG-------------
droSim1	chr3L:2784381-2784507 -	LASTZ	4	TCCGTTTT------------------CGCTGATTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-CTTTA--------G-TTTAAGAAC-----------GG-------------
droSec1	super_2:3244745-3244871 -	LASTZ	3	TCCGTTTT------------------CGCTGATTGTTCACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-CTTTA--------T-TTTAAGAAC-----------GG-------------
droYak2	chr3L:3795918-3796050 -	LASTZ	3	TCCGTTTT------------------CGCTGATTTTTCACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGTA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-CTGAT--A-TAACGGATATAGAAC-----------GA-------------
droEre2	scaffold_4784:5933708-5933834 -	LASTZ	4	TCCGTTTT------------------CGCTGCTTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTTGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-CTGTG--------G-TGATAGAAC-----------GA-------------
droEug1	scf7180000409466:975797-975923 -	LASTZ	4	TCCGTTTT------------------TGCTGACTTTTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTAGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTC--------G-GTGTATAAC-----------GG-------------
droBia1	scf7180000302428:2604017-2604144 -	LASTZ	4	TCCGATTC------------------CGATGATTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG--TTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-TCTGC----------ACTTAGAAG-----------GGTAC----------
droTak1	scf7180000415378:123710-123845 +	LASTZ	4	TCCGTTTTC-----------------TGATGATTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGA-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGTAGATTG-CAGATTCTCG-ATTTAGAAT-----------GG-------------
droEle1	scf7180000491249:2016913-2017039 +	LASTZ	4	GCCGTTTT------------------TGATGCTTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTT--------G-AGTTAGAAC-----------AG-------------
droRho1	scf7180000757706:21549-21675 +	LASTZ	4	TCCGTTTT------------------TGCTGATTTTTCGCCTTTGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTATT--------G-GATTAGAAC-----------GG-------------
droFic1	scf7180000454105:1571232-1571357 -	LASTZ	4	GCCCTCTT------------------CGCTGCTCTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAGA-TTCTC--------G-G-CCAGAAC-----------GG-------------
droKik1	scf7180000302391:353031-353159 -	LASTZ	4	TCCGCCTTT-----------------CGCTGCACATTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-ATTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTC--------GGATTCAGAAC-----------GG-------------
droAna3	scaffold_13337:7556582-7556720 -	LASTZ	3	TCCGTTTTTG----------------TGATGTCTTGTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGA-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAA-TTTTC-GATTTTCG-AATTAGAAC-----------GGCCA----------
droBip1	scf7180000395543:216902-217046 -	LASTZ	4	TCCGTTTTAA----------------TGATGACT-TTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATC--------GAA--AACACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAA-TTTTC--------G-ATTTAGAACGTAGAGCATATTGCCACGCCCACACG
dp4	chrXR_group8:3299974-3300083 +	LASTZ	3	TCCGCTTT------------------TGATGCATTTCTTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA----------------------------------------------------
droPer1	super_65:103931-104040 +	LASTZ	3	TCCGCTTT------------------TGATGCATTTCTTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA----------------------------------------------------
droWil1	scaffold_181136:1999668-1999787 -	LASTZ	5	T--------------------------GTTGTATTTTCTCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGAA------TCCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGATA-TATTA-ATATT------ACATAAA-----GGAA--AA-------------
droVir3	scaffold_12758:910696-910814 +	LASTZ	4	--CGCCCT------------------CGCTGCTT-GTCCCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGACCGT-ATATCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTT--------------GTCGGAC-----------GC-------------
droMoj3	scaffold_6680:1963284-1963406 +	LASTZ	3	TCT----C------------------TGCTGTT-TGACCCCTTGCTACACCTAACCTCTCATAGGCTATGTCTGATCTT-ATATCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TGCAC--------CGCAAAAAAAA-----------AT-------------
droGri2	scaffold_15110:607074-607202 -	LASTZ	4	TCATTTTTAGTCCCCGACAGCAGCCTTGTTGCTTTGATCCATTTGTACACCTAACCTCTCATAGGCTATGTCTGATTGA-ATTGAAAAAGTGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAA----------------------------------------------------

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	TCCGTTTT------------------CGCTGATTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAGAAGGAAA-CTATA--------G-TTAAAGAAC-----------GG-------------
droSim1	TCCGTTTT------------------CGCTGATTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-CTTTA--------G-TTTAAGAAC-----------GG-------------
droSec1	TCCGTTTT------------------CGCTGATTGTTCACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-CTTTA--------T-TTTAAGAAC-----------GG-------------
droYak2	TCCGTTTT------------------CGCTGATTTTTCACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGTA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-CTGAT--A-TAACGGATATAGAAC-----------GA-------------
droEre2	TCCGTTTT------------------CGCTGCTTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTTGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-CTGTG--------G-TGATAGAAC-----------GA-------------
droEug1	TCCGTTTT------------------TGCTGACTTTTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTAGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTC--------G-GTGTATAAC-----------GG-------------
droBia1	TCCGATTC------------------CGATGATTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG--TTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-TCTGC----------ACTTAGAAG-----------GGTAC----------
droTak1	TCCGTTTTC-----------------TGATGATTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGA-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGTAGATTG-CAGATTCTCG-ATTTAGAAT-----------GG-------------
droEle1	GCCGTTTT------------------TGATGCTTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTT--------G-AGTTAGAAC-----------AG-------------
droRho1	TCCGTTTT------------------TGCTGATTTTTCGCCTTTGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTATT--------G-GATTAGAAC-----------GG-------------
droFic1	GCCCTCTT------------------CGCTGCTCTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAGA-TTCTC--------G-G-CCAGAAC-----------GG-------------
droKik1	TCCGCCTTT-----------------CGCTGCACATTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-ATTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTC--------GGATTCAGAAC-----------GG-------------
droAna3	TCCGTTTTTG----------------TGATGTCTTGTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGA-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAA-TTTTC-GATTTTCG-AATTAGAAC-----------GGCCA----------
droBip1	TCCGTTTTAA----------------TGATGACT-TTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATC--------GAA--AACACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAA-TTTTC--------G-ATTTAGAACGTAGAGCATATTGCCACGCCCACACG
dp4	TCCGCTTT------------------TGATGCATTTCTTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA----------------------------------------------------
droPer1	TCCGCTTT------------------TGATGCATTTCTTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA----------------------------------------------------
droWil1	T--------------------------GTTGTATTTTCTCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGAA------TCCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGATA-TATTA-ATATT------ACATAAA-----GGAA--AA-------------
droVir3	--CGCCCT------------------CGCTGCTT-GTCCCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGACCGT-ATATCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTT--------------GTCGGAC-----------GC-------------
droMoj3	TCT----C------------------TGCTGTT-TGACCCCTTGCTACACCTAACCTCTCATAGGCTATGTCTGATCTT-ATATCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TGCAC--------CGCAAAAAAAA-----------AT-------------
droGri2	TCATTTTTAGTCCCCGACAGCAGCCTTGTTGCTTTGATCCATTTGTACACCTAACCTCTCATAGGCTATGTCTGATTGA-ATTGAAAAAGTGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAA----------------------------------------------------

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

Small RNA-seq read pileup

Species

Alignment

droSim1

TCCGTTTT------------------CGCTGATTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-CTTTA--------G-TTTAAGAAC-----------GG-------------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................................CCTCTTCTAGGCTTTGTCT.............................................................................................................	19	4	0.25	0.00	0.00	0.25	0.00

droSec1

TCCGTTTT------------------CGCTGATTGTTCACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-CTTTA--------T-TTTAAGAAC-----------GG-------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................A--TACAAAGACAAAGCCTA...........................................................................	18	2	0.50	0.00	0.50	0.00

droYak2

TCCGTTTT------------------CGCTGATTTTTCACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGTA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-CTGAT--A-TAACGGATATAGAAC-----------GA-------------

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TCCGTTTT------------------CGCTGCTTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTTGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-CTGTG--------G-TGATAGAAC-----------GA-------------

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

TCCGTTTT------------------TGCTGACTTTTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTAGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTC--------G-GTGTATAAC-----------GG-------------

Size

Hit Count

Total Norm

droBia1

TCCGATTC------------------CGATGATTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG--TTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-TCTGC----------ACTTAGAAG-----------GGTAC----------

Size

Hit Count

Total Norm

droTak1

TCCGTTTTC-----------------TGATGATTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGA-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGTAGATTG-CAGATTCTCG-ATTTAGAAT-----------GG-------------

Size

Hit Count

Total Norm

droEle1

GCCGTTTT------------------TGATGCTTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTT--------G-AGTTAGAAC-----------AG-------------

Size

Hit Count

Total Norm

droRho1

TCCGTTTT------------------TGCTGATTTTTCGCCTTTGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTATT--------G-GATTAGAAC-----------GG-------------

Size

Hit Count

Total Norm

droFic1

GCCCTCTT------------------CGCTGCTCTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAGA-TTCTC--------G-G-CCAGAAC-----------GG-------------

Size

Hit Count

Total Norm

droKik1

TCCGCCTTT-----------------CGCTGCACATTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-ATTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTC--------GGATTCAGAAC-----------GG-------------

Size

Hit Count

Total Norm

droAna3

TCCGTTTTTG----------------TGATGTCTTGTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGA-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAA-TTTTC-GATTTTCG-AATTAGAAC-----------GGCCA----------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...................................................TAGCCTCTTATAGGCTTTGTCT.............................................................................................................	22	4	0.25	0.00	0.00	0.25	0.00

droBip1

TCCGTTTTAA----------------TGATGACT-TTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATC--------GAA--AACACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAA-TTTTC--------G-ATTTAGAACGTAGAGCATATTGCCACGCCCACACG

Size

Hit Count

Total Norm

dp4

TCCGCTTT------------------TGATGCATTTCTTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA----------------------------------------------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
......................................................................................AA--TGCAATGACAAAGCCTA...........................................................................	19	2	0.50	0.00	0.50	0.00	0.00
...................................................TAGCCTCTTATAGGCTTTGTCT.............................................................................................................	22	4	0.25	0.00	0.25	0.00	0.00
......................................................................................AA--TACAAAGACAAAGCCTAG..........................................................................	20	2	0.50	0.00	0.50	0.00	0.00

droPer1

TCCGCTTT------------------TGATGCATTTCTTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA----------------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
............................................................................................CAATGACAAAGCCTAGTAG.......................................................................	19	2	0.50	0.00	0.50	0.00	0.00	0.00

droWil1

T--------------------------GTTGTATTTTCTCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGAA------TCCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGATA-TATTA-ATATT------ACATAAA-----GGAA--AA-------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........................................................................................................................TTATACGGATA-TATTT-AT..........................................	18	3	27.33	0.00	19.33	0.67	7.33
........................................................................................................................TTATAAGGATA-TATTT-ATT.........................................	19	2	1.00	0.00	1.00	0.00	0.00
........................................................................................................................TTATACGGATA-TATTA-TT..........................................	18	2	1.00	0.50	0.50	0.00	0.00
.......................................................................................................................TTTAGAAGAATA-TATTA-AT..........................................	19	2	0.50	0.00	0.00	0.00	0.50
.......................................................................................A--TACAAAGACAAAGCCTA...........................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droVir3

--CGCCCT------------------CGCTGCTT-GTCCCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGACCGT-ATATCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTT--------------GTCGGAC-----------GC-------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TCT----C------------------TGCTGTT-TGACCCCTTGCTACACCTAACCTCTCATAGGCTATGTCTGATCTT-ATATCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TGCAC--------CGCAAAAAAAA-----------AT-------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....................................................ACCTCTCATAGGCTATGTCTGA...........................................................................................................	22	2	1.50	0.00	0.50	0.50	0.50
.....................................................ACCTCTCATAGGCTATGTCTG............................................................................................................	21	2	1.00	0.50	0.00	0.00	0.50
.....................................................ACCTCTCATAGGCTATGTCT.............................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
.....................................................ACCTCTCATAGGCTATGTCTGT...........................................................................................................	22	2	0.50	0.00	0.00	0.00	0.50
.......................................................CTCTAATAGGCTTTGTCT.............................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25

droGri2

TCATTTTTAGTCCCCGACAGCAGCCTTGTTGCTTTGATCCATTTGTACACCTAACCTCTCATAGGCTATGTCTGATTGA-ATTGAAAAAGTGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAA----------------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:27:39 EDT

dme-mir-282-as

chr3L:3251022-3251118 -

Candidate

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