dme-mir-3643- Best orthologs

dme-mir-3643	chr2R:13653898-13653965 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	tailed_mirtron

Legend:

   mature strand at position 13653944-13653965
   star strand at position 13653910-13653931
   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:13653883-13653980 -		1	GAATCCAAGCTGAACGTGAGTTTATC-TA--AATATG-CCCA-------------TTTATCAATAGTCATA--CTTATTTATG----------C--------T-----CCTTTAACTCCTTGCAGAGCTTCGAAAAAGAC
droSim1	chr2R:12393703-12393800 -	LASTZ	5	GAGTCCAAGCTGAACGTGGGTTTATC-TA--GATACG-CCCA-------------TTTATCATTGGTCATA--CTTATTTATG----------T--------T-----CCTTTAACTCCTTGCAGAGCTTCGAAAAAGAC
droSec1	super_1:11152590-11152687 -	LASTZ	5	GAGTCCAAGCTGAACGTGGGTTTATC-TA--TTTACG-CCCA-------------TTTATCATTGGTCATA--CTTATTTATG----------T--------T-----CCTTTAACGCCTTGCAGAGCTTCGAAAAAGAC
droYak2	chr2R:15527673-15527770 +	LASTZ	5	GAATCCAAGCTGAACGTGGGTTCATC-TA--GATACT-TCCA-------------TATATCAAAAGCCGTA--CTTATTTATG----------T--------T-----ATTTAAACTGCTTGCAGAGCTTCGAAAAAGAC
droEre2	scaffold_4845:7883019-7883116 -	LASTZ	5	GAATCCAAGCTGAACGTGGGTTTTTC-TA--GATACG-CCCA-------------TTTATCAATGGCCCTA--CTTATTTATG----------C--------A-----TTTTAAACTCCTTGCAGAGCTTCGAAAAAGAC
droEug1	scf7180000409672:1451984-1452077 +	LASTZ	5	GAATCCAAGCTGAACGTGAGTTCTTC-TA--TATACG-CCCA-------------CATGTCGGTACCTC------TTCTTATG----------C--------T-----TCCTTTACGTTTCGTAGAGTTTTGAAAAGGAC
droBia1	scf7180000301754:2921050-2921150 +	LASTZ	5	GAATCCAAGCTGAACGTGCGTCTCTT-AAAACACACG-CCCA-------------TTTATCTGTATCCC------TACTTACGCTC-------G--------TC---CTTTTTTACTGATTGTAGAGCTTCGAGAAGGAC
droTak1	scf7180000415313:36259-36358 +	LASTZ	5	GAATCCAAGCTGAACGTGGGTTCTGTCTA-ACATACG-CCGA-------------AATATATGTATCCC------TACTTATGCTA-----C-T--------C-----CTTTTGACTCCTTGCAGAGCTTCGAAAAGGAC
droEle1	scf7180000491214:594780-594873 +	LASTZ	5	GAATCCAAGCTAAACGTGGGTTCTCC-CA--TATACG-CCCA-------------TTTGCCTGTACCC------CTATTTATG----------C--------T-----CCATTGACTTTTTGCAGAGCTTCGAAAAGGAC
droRho1	scf7180000777956:135402-135495 +	LASTZ	5	GAATCCAAGCTGAACGTGGGTTCTCC-TA--TACACG-CCCA-------------TATGTCTGTACCCA------TGTTTATG----------C--------T-----CCTTTGACTCCTTGCAGAGCTTCGAAAAGGAC
droFic1	scf7180000453948:1793989-1794080 +	LASTZ	5	GAATCCAAGCTGAACGTATGTTTTTT-CT--CACACG-CCCA-------------TTTGT--GTATC------CCTATTTATG----------C--------T-----TCATTATCTCCTTGCAGAGCTTCGAAAAGGAC
droKik1	scf7180000302385:414803-414893 -	LASTZ	5	GAGTCCAAGCTGAACGTGGGTCCTTCCTA--GACACG-CCCA-------------TTTTT--------ACA--CGTATTAATA----------C--------T-----CCCTTAACTCCTTGCAGAGCTTCGAGAAGGAC
droAna3	scaffold_13266:10531972-10532067 +	LASTZ	5	GAATCCAAGCTGAACGTTAGTTACTT-GTGCAACTCG-TCCA-------------ATCGG---TT-C--AATAACTA--GATC----------C--------TC---CTTTACATCTCCTTGTAGGGCTTCGAGAAGGAC
droBip1	scf7180000396428:953655-953755 +	LASTZ	5	GAATCCAAGCTGAACGTTAGTTAATT-AC--TACACC-CCTC-------------TAAAACCTGTGCAATA--ACTA--GACC----------A--------TCCATCTTTCCATCTTCTTGTAGAGCTTCGAGAAGGAC
dp4	chr3:16466931-16467019 -	LASTZ	5	GAATCCAAGCTGAACGTAAGTGCTTA-G---CAAATG-TTCACTGAACCTTGAAT------------------------CAT---------TGC--------C-----TTTGTTCTCGGTTCCAGAGCTTCGAAAAGGAC
droPer1	super_4:295271-295359 +	LASTZ	5	GAATCCAAGCTGAACGTAAGTGCTTA-G---CAAATG-TTCACTGAACCTTGAAT------------------------CAT---------TGC--------C-----TTTGTTCTCGGTTCCAGAGCTTCGAAAAGGAC
droWil1	scaffold_181141:4609865-4609965 +	LASTZ	5	GAATCAAAATTGAATGTAAGCTGA----------------------AAATTTAA-TTTATATTTTGT------TTTCTCCTAT---TTACA--TACCACGTGT-----CCTTCACTCAATTACAGAGCTTCGAAAAGGAT
droVir3	scaffold_12875:16919908-16919994 -	LASTZ	5	GAATCCAAACTAAATGTGAGTATCTC-CT--AAT-CGCCTCA-------------TCCA-----------A--TTCATTTTTG----------A--------C-----CCTTTGCCTACTTTTAGAACTTTGAAAAAGAC
droMoj3	scaffold_6496:11084070-11084155 +	LASTZ	5	GAATCTAAACTAAATGTAGGTATAGT-AA--TAGATG----AGTTTTTCTTTTAT------------------------TTT---------A-A--------C-----CTTTGGCCCGCTTGCAGAACTTTGAGAAGGAC
droGri2	scaffold_15245:16459236-16459327 -	LASTZ	5	GAATCCAAACTAAATGTGAGATACCTCTA-AAACAAA-T-CA-------------TAAA----GATTTTGA--TGTATTGAGA--------------------------TTATGTACATTTGCAGAACTTTGAGAAAGAC

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	GAATCCAAGCTGAACGTGAGTTTATC-TA--AATATG-CCCA-------------TTTATCAATAGTCATA--CTTATTTATG----------C--------T-----CCTTTAACTCCTTGCAGAGCTTCGAAAAAGAC
droSim1	GAGTCCAAGCTGAACGTGGGTTTATC-TA--GATACG-CCCA-------------TTTATCATTGGTCATA--CTTATTTATG----------T--------T-----CCTTTAACTCCTTGCAGAGCTTCGAAAAAGAC
droSec1	GAGTCCAAGCTGAACGTGGGTTTATC-TA--TTTACG-CCCA-------------TTTATCATTGGTCATA--CTTATTTATG----------T--------T-----CCTTTAACGCCTTGCAGAGCTTCGAAAAAGAC
droYak2	GAATCCAAGCTGAACGTGGGTTCATC-TA--GATACT-TCCA-------------TATATCAAAAGCCGTA--CTTATTTATG----------T--------T-----ATTTAAACTGCTTGCAGAGCTTCGAAAAAGAC
droEre2	GAATCCAAGCTGAACGTGGGTTTTTC-TA--GATACG-CCCA-------------TTTATCAATGGCCCTA--CTTATTTATG----------C--------A-----TTTTAAACTCCTTGCAGAGCTTCGAAAAAGAC
droEug1	GAATCCAAGCTGAACGTGAGTTCTTC-TA--TATACG-CCCA-------------CATGTCGGTACCTC------TTCTTATG----------C--------T-----TCCTTTACGTTTCGTAGAGTTTTGAAAAGGAC
droBia1	GAATCCAAGCTGAACGTGCGTCTCTT-AAAACACACG-CCCA-------------TTTATCTGTATCCC------TACTTACGCTC-------G--------TC---CTTTTTTACTGATTGTAGAGCTTCGAGAAGGAC
droTak1	GAATCCAAGCTGAACGTGGGTTCTGTCTA-ACATACG-CCGA-------------AATATATGTATCCC------TACTTATGCTA-----C-T--------C-----CTTTTGACTCCTTGCAGAGCTTCGAAAAGGAC
droEle1	GAATCCAAGCTAAACGTGGGTTCTCC-CA--TATACG-CCCA-------------TTTGCCTGTACCC------CTATTTATG----------C--------T-----CCATTGACTTTTTGCAGAGCTTCGAAAAGGAC
droRho1	GAATCCAAGCTGAACGTGGGTTCTCC-TA--TACACG-CCCA-------------TATGTCTGTACCCA------TGTTTATG----------C--------T-----CCTTTGACTCCTTGCAGAGCTTCGAAAAGGAC
droFic1	GAATCCAAGCTGAACGTATGTTTTTT-CT--CACACG-CCCA-------------TTTGT--GTATC------CCTATTTATG----------C--------T-----TCATTATCTCCTTGCAGAGCTTCGAAAAGGAC
droKik1	GAGTCCAAGCTGAACGTGGGTCCTTCCTA--GACACG-CCCA-------------TTTTT--------ACA--CGTATTAATA----------C--------T-----CCCTTAACTCCTTGCAGAGCTTCGAGAAGGAC
droAna3	GAATCCAAGCTGAACGTTAGTTACTT-GTGCAACTCG-TCCA-------------ATCGG---TT-C--AATAACTA--GATC----------C--------TC---CTTTACATCTCCTTGTAGGGCTTCGAGAAGGAC
droBip1	GAATCCAAGCTGAACGTTAGTTAATT-AC--TACACC-CCTC-------------TAAAACCTGTGCAATA--ACTA--GACC----------A--------TCCATCTTTCCATCTTCTTGTAGAGCTTCGAGAAGGAC
dp4	GAATCCAAGCTGAACGTAAGTGCTTA-G---CAAATG-TTCACTGAACCTTGAAT------------------------CAT---------TGC--------C-----TTTGTTCTCGGTTCCAGAGCTTCGAAAAGGAC
droPer1	GAATCCAAGCTGAACGTAAGTGCTTA-G---CAAATG-TTCACTGAACCTTGAAT------------------------CAT---------TGC--------C-----TTTGTTCTCGGTTCCAGAGCTTCGAAAAGGAC
droWil1	GAATCAAAATTGAATGTAAGCTGA----------------------AAATTTAA-TTTATATTTTGT------TTTCTCCTAT---TTACA--TACCACGTGT-----CCTTCACTCAATTACAGAGCTTCGAAAAGGAT
droVir3	GAATCCAAACTAAATGTGAGTATCTC-CT--AAT-CGCCTCA-------------TCCA-----------A--TTCATTTTTG----------A--------C-----CCTTTGCCTACTTTTAGAACTTTGAAAAAGAC
droMoj3	GAATCTAAACTAAATGTAGGTATAGT-AA--TAGATG----AGTTTTTCTTTTAT------------------------TTT---------A-A--------C-----CTTTGGCCCGCTTGCAGAACTTTGAGAAGGAC
droGri2	GAATCCAAACTAAATGTGAGATACCTCTA-AAACAAA-T-CA-------------TAAA----GATTTTGA--TGTATTGAGA--------------------------TTATGTACATTTGCAGAACTTTGAGAAAGAC

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

GAGTCCAAGCTGAACGTGGGTTTATC-TA--GATACG-CCCA-------------TTTATCATTGGTCATA--CTTATTTATG----------T--------T-----CCTTTAACTCCTTGCAGAGCTTCGAAAAAGAC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................................................................TGAACAGCTTCGAAAAAGA.	19	1	1.00	0.00	1.00	0.00	0.00

droSec1

GAGTCCAAGCTGAACGTGGGTTTATC-TA--TTTACG-CCCA-------------TTTATCATTGGTCATA--CTTATTTATG----------T--------T-----CCTTTAACGCCTTGCAGAGCTTCGAAAAAGAC

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

GAATCCAAGCTGAACGTGGGTTCATC-TA--GATACT-TCCA-------------TATATCAAAAGCCGTA--CTTATTTATG----------T--------T-----ATTTAAACTGCTTGCAGAGCTTCGAAAAAGAC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................................................................TATTTATA----------T--------T-----GTTTAAAC........................	18	6	0.17	0.00	0.00	0.00	0.17	0.00
........GTTGGACGTGGGTTCAT...................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
........GTTGAACGTGGGTTAATC-.................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................ATTTATG----------T--------T-----CTTGAAACT.......................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
........GCTGGACGTGGGTTCGTC-.................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

GAATCCAAGCTGAACGTGGGTTTTTC-TA--GATACG-CCCA-------------TTTATCAATGGCCCTA--CTTATTTATG----------C--------A-----TTTTAAACTCCTTGCAGAGCTTCGAAAAAGAC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......AAGCTGAACGAGAGTTTTT...................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00
.......AGCTGAACGAGAGTTTTT...................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
..ATCCAAGCTGAACGAGAG........................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

GAATCCAAGCTGAACGTGAGTTCTTC-TA--TATACG-CCCA-------------CATGTCGGTACCTC------TTCTTATG----------C--------T-----TCCTTTACGTTTCGTAGAGTTTTGAAAAGGAC

Size

Hit Count

Total Norm

droBia1

GAATCCAAGCTGAACGTGCGTCTCTT-AAAACACACG-CCCA-------------TTTATCTGTATCCC------TACTTACGCTC-------G--------TC---CTTTTTTACTGATTGTAGAGCTTCGAGAAGGAC

Size

Hit Count

Total Norm

droTak1

GAATCCAAGCTGAACGTGGGTTCTGTCTA-ACATACG-CCGA-------------AATATATGTATCCC------TACTTATGCTA-----C-T--------C-----CTTTTGACTCCTTGCAGAGCTTCGAAAAGGAC

Size

Hit Count

Total Norm

droEle1

GAATCCAAGCTAAACGTGGGTTCTCC-CA--TATACG-CCCA-------------TTTGCCTGTACCC------CTATTTATG----------C--------T-----CCATTGACTTTTTGCAGAGCTTCGAAAAGGAC

Size

Hit Count

Total Norm

droRho1

GAATCCAAGCTGAACGTGGGTTCTCC-TA--TACACG-CCCA-------------TATGTCTGTACCCA------TGTTTATG----------C--------T-----CCTTTGACTCCTTGCAGAGCTTCGAAAAGGAC

Size

Hit Count

Total Norm

droFic1

GAATCCAAGCTGAACGTATGTTTTTT-CT--CACACG-CCCA-------------TTTGT--GTATC------CCTATTTATG----------C--------T-----TCATTATCTCCTTGCAGAGCTTCGAAAAGGAC

Size

Hit Count

Total Norm

droKik1

GAGTCCAAGCTGAACGTGGGTCCTTCCTA--GACACG-CCCA-------------TTTTT--------ACA--CGTATTAATA----------C--------T-----CCCTTAACTCCTTGCAGAGCTTCGAGAAGGAC

Size

Hit Count

Total Norm

droAna3

GAATCCAAGCTGAACGTTAGTTACTT-GTGCAACTCG-TCCA-------------ATCGG---TT-C--AATAACTA--GATC----------C--------TC---CTTTACATCTCCTTGTAGGGCTTCGAGAAGGAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................................................................................T	20	2	0.50	0.50	0.00	0.00	0.00

droBip1

GAATCCAAGCTGAACGTTAGTTAATT-AC--TACACC-CCTC-------------TAAAACCTGTGCAATA--ACTA--GACC----------A--------TCCATCTTTCCATCTTCTTGTAGAGCTTCGAGAAGGAC

Size

Hit Count

Total Norm

dp4

GAATCCAAGCTGAACGTAAGTGCTTA-G---CAAATG-TTCACTGAACCTTGAAT------------------------CAT---------TGC--------C-----TTTGTTCTCGGTTCCAGAGCTTCGAAAAGGAC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GAATCCAAGCTGAACGTAAGTGCTTA-G---CAAATG-TTCACTGAACCTTGAAT------------------------CAT---------TGC--------C-----TTTGTTCTCGGTTCCAGAGCTTCGAAAAGGAC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

GAATCAAAATTGAATGTAAGCTGA----------------------AAATTTAA-TTTATATTTTGT------TTTCTCCTAT---TTACA--TACCACGTGT-----CCTTCACTCAATTACAGAGCTTCGAAAAGGAT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................................................................................TTACAGAGxTTCGACAAGG..	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................ACAGAGCCTCGAAAGGGA.	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................TTTATATTTTGT------TTTGTT.............................................................	18	22	0.05	0.00	0.05	0.00	0.00

droVir3

GAATCCAAACTAAATGTGAGTATCTC-CT--AAT-CGCCTCA-------------TCCA-----------A--TTCATTTTTG----------A--------C-----CCTTTGCCTACTTTTAGAACTTTGAAAAAGAC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GAATCTAAACTAAATGTAGGTATAGT-AA--TAGATG----AGTTTTTCTTTTAT------------------------TTT---------A-A--------C-----CTTTGGCCCGCTTGCAGAACTTTGAGAAGGAC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...........AAATTTAGATATAGT-AA--T............................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00

droGri2

GAATCCAAACTAAATGTGAGATACCTCTA-AAACAAA-T-CA-------------TAAA----GATTTTGA--TGTATTGAGA--------------------------TTATGTACATTTGCAGAACTTTGAGAAAGAC

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:17:45 EDT

dme-mir-3643

chr2R:13653898-13653965 -

Known_mirbase

tailed_mirtron

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