dme-mir-2492- Best orthologs

dme-mir-2492	chrX:11441455-11441530 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 11441502-11441523
   star strand at position 11441463-11441484
   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:11441440-11441545 +		1	ACAAAATTCACACTCGAATT-TTTT-TGGGATCTC-------TTTATAAAGCGTTTATTA---TTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAAATT---------C--AGA------------AGACAACAACGCA
droSim1	chrX_random:3203326-3203430 +	LASTZ	1	ACAAAATTCACACTCGAATT-TTTT-G-GGATCTC-------TTTATAAAGCGTTTATTATTATTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAAAGT---------C--AGA------------AGA---CAACGCA
droSec1	super_36:155641-155745 +	LASTZ	1	ATAAAATTCACTCTCGAATT-TTTT-G-GGATCTC-------TTTATAAAGCATTTATTATTATTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAAAGC---------C--AGA------------AGA---CAACGCA
droYak2	chrX:10720999-10721105 -	LASTZ	4	ACAAAATTCACACTCGAATT-TTTT-GGCAATCTG-------TTTATAAAGCGTTTATTA---TTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAATACA--------A--CAA------------AATAGGAAAAAAA
droEre2	scaffold_4690:3720646-3720750 -	LASTZ	4	ACAAAATTCACACTCGAATT-T--TGG-GTATCTC-------TTTATAAAGCGTTTATTA---TTTATTTATTATGTTTT-GTCGAGAGCTTAAAAAAAAT----------ATGAAA------------AGACAACAACCAA
droEug1	scf7180000408176:611267-611357 +	LASTZ	5	ACAGAATTCACACTCGTTTT-T--T-G-GCATC---------TCTATAAAGCGTTTATTA---TTTATTTATTATGCTTGCTTTGAGAGCTTTCAAAGAGA----------C------------------------AAAAAT
droBia1	scf7180000301760:529098-529183 +	LASTZ	5	ACAAAATTCACACTCGAATT-TTTT-G-GCATC---------TCTATAAAGCGTTTATTA---TTTGTTTATTGTGTTGT-GTCGAGAGCTTTCAAAAGAGC----------------------------------------
droTak1	scf7180000415843:399035-399133 +	LASTZ	5	ACAAAATTCACACTCAAATT-T--T-G-GGACCTC-------TCTATAAAGCGTTTATTA---CTTATTTATTTTGTTAA-GTCGAGAGCTTTCAAAAGA-----------C--AAA------------AAAAACC--AAAA
droEle1	scf7180000491193:278928-279018 -	LASTZ	5	ACAAAATTCACACTCGATTT-TTTT-TTTTTTTTTTATTCTTGCTATAAAGACTTTATTA---TTTATTTATTATGTTTT-GTTGAGAGCTTTCAAA---------------------------------------------
droRho1	scf7180000779986:444043-444125 +	LASTZ	5	ACAAAATTCACACTCGAATTTT--T-G-GGATC---------TCTATAAAGCGTTTATTA---TTCATTTATTATGTTTT-GTCGAGAGCTTTCAAATGA------------------------------------------
droFic1	scf7180000453872:274536-274622 +	LASTZ	5	ACAAAATTCACACTCGAATT-T--C-G-GGAAC---------TCAATAAAGTGTTTATTA---TTTAATTATTATGTTTT-GTAAAGAGCTTTTAAAGAT-------------------------------------ACACA
droKik1	scf7180000302344:177104-177194 +	LASTZ	5	ACAAAATTCACACTCGAATT-T--G-G-AGATC---------TCTATAAAGCGTTTATTT---TTTGGTATTTGTATACCCTTCAAGAGGGTATTAAATAC----------T------------------------TTTAAG
droAna3	scaffold_13047:188962-189053 +	LASTZ	0	ACAAAATTCACACTCGCTTT-T--G-G-CCAAC---------TCCATAAAGCGTTAATTA---TCTGGC---------------------ATTCTGAGAGC----------C--AAAAGCTAAATCAAATTCGATCGGAGCG
droBip1	scf7180000396425:338388-338489 +	LASTZ	0	ACAAAATTCACACTCGCTTT-T--G-G-CCAACTC-------TCCATAAAGCGTTAATTA---TTTAAC---------------------ATTCTAAAAGCCGAAAAGCGGC----AAATGAATTCAAATTGAAGCAAAGCC
dp4	chrXL_group1e:1762210-1762257 +	LASTZ	0	ACAAAATTCACACTCGAATT-T--G-G-GGATC---------GCG----------------------------------T-AGCGAGGGGGGG---------------------------------------------GCAA
droPer1	super_18:601670-601716 +	LASTZ	0	ACAAAATTCACACTCGAATT-T--G-G-GGATC---------GCG----------------------------------T-AGCAAGGGGGGGCA----------------------------------------------A
droWil1	scaffold_180777:122952-122984 +	LASTZ	0	ATAAACTCAATACACGAATT-TGGT-ACTGATTTC-----------------------------------------------------------------------------------------------------------
droVir3	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:22511787-22511827 +	LASTZ	0	TCCGT------------------------------------------------------------------------------CAATCATCTCCTTAAAACT---------C--TAA------------AGCAAACCAAGCA
droGri2	scaffold_15203:463820-463836 -	LASTZ	0	GTGAAATTCACACTCGA-----------------------------------------------------------------------------------------------------------------------------

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	ACAAAATTCACACTCGAATTTTTTTGGG-ATCTCT---------TTATAAAGCGTTTATT---ATTTATTTATTATGTTTTG-TCGAGAGCTTTCAAAAAATT-CAGAAG----ACA--ACAACGCA
droSim1	ACAAAATTCACACTCGAATTTTTT-GGG-ATCTCT---------TTATAAAGCGTTTATTATTATTTATTTATTATGTTTTG-TCGAGAGCTTTCAAAAAAGT-CAGAAG----ACA--A---CGCA
droSec1	ATAAAATTCACTCTCGAATTTTTT-GGG-ATCTCT---------TTATAAAGCATTTATTATTATTTATTTATTATGTTTTG-TCGAGAGCTTTCAAAAAAGC-CAGAAG----ACA--A---CGCA
droYak2	ACAAAATTCACACTCGAATTTTTT-GGCAATCTGT---------TTATAAAGCGTTTATT---ATTTATTTATTATGTTTTG-TCGAGAGCTTTCAAAAATAC-AACAAAATAGGAA--A---AAAA
droEre2	ACAAAATTCACACTCGAATTT--T-GGGTATCTCT---------TTATAAAGCGTTTATT---ATTTATTTATTATGTTTTG-TCGAGAGCTTAAAAAAAATATGAAAAG----ACA--ACAACCAA
droEug1	ACAGAATTCACACTCGT--TTTTT-GGC-AT--CT---------CTATAAAGCGTTTATT---ATTTATTTATTATGCTTGCTTTGAGAGCTTTCAAAGAGAC-------------A--AA---AAT
droBia1	ACAAAATTCACACTCGAATTTTTT-GGC-AT--CT---------CTATAAAGCGTTTATT---ATTTGTTTATTGTGTTGTG-TCGAGAGCTTTCAAAAGAGC------------------------
droTak1	ACAAAATTCACACTCAAATTT--T-GGG-ACCTCT---------CTATAAAGCGTTTATT---ACTTATTTATTTTGTTAAG-TCGAGAGCTTTCAAAAGACA---AAAA----AAACCA----AAA
droEle1	ACAAAATTCACACTCGATTTTTTT-TTT-TT-TTTTTATTCTTGCTATAAAGACTTTATT---ATTTATTTATTATGTTTTG-TTGAGAGCTTTCAAA-----------------------------
droRho1	ACAAAATTCACACTCGAATTT-TT-GGG-AT--CT---------CTATAAAGCGTTTATT---ATTCATTTATTATGTTTTG-TCGAGAGCTTTCAAATGA--------------------------
droFic1	ACAAAATTCACACTCGAATTT--C-GGG-AA--CT---------CAATAAAGTGTTTATT---ATTTAATTATTATGTTTTG-TAAAGAGCTTTTAAAGATA---------------------CACA
droKik1	ACAAAATTCACACTCGAATTT--G-GAG-AT--CT---------CTATAAAGCGTTTATT---TTTTGGTATTTGTATACCCTTCAAGAGGGTATTAAATACT-TTT-----------------AAG

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		None

Small RNA-seq read pileup

Species

Alignment

droSim1

ACAAAATTCACACTCGAATT-TTTT-G-GGATCTC-------TTTATAAAGCGTTTATTATTATTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAAAGT---------C--AGA------------AGA---CAACGCA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................................................TTATGTTTT-GTCGAGAGCTTTC................................................	22	1	1.00	0.00	0.00	0.00	1.00
............................................................................TTTT-GTCGAGAGCTTTCAAA.............................................	20	1	1.00	0.00	1.00	0.00	0.00

droSec1

ATAAAATTCACTCTCGAATT-TTTT-G-GGATCTC-------TTTATAAAGCATTTATTATTATTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAAAGC---------C--AGA------------AGA---CAACGCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................T-G-GGATCTC-------TTTATAAAGCAT........................................................................................	21	1	2.00	0.00	1.00	1.00
..........................................................................TGTTTT-GTCGAGAGCTTTCAA..............................................	21	1	1.00	0.00	1.00	0.00
............................................................................TTTT-CTCGAGAGCTTTCAAAA............................................	21	1	1.00	0.00	1.00	0.00
..............................................................................TT-GTCGAGAGCTTTCAAA.............................................	18	1	1.00	0.00	1.00	0.00
..............................................................ATTTATTTATTATGTTTC-GTCGAGA......................................................	25	1	1.00	0.00	1.00	0.00
........................T-G-GGATCTC-------TTTATAAAGCATT.......................................................................................	22	1	1.00	1.00	0.00	0.00
...................................................................................TGAGAGCTCTCAAAAAAG.........................................	18	1	1.00	0.00	1.00	0.00
............................................................................TTTT-GTCxxGAGCTTTCAAAA............................................	19	1	1.00	0.00	1.00	0.00
............................................................................TTTT-GTCGAGAGCTTTCAAAA............................................	21	1	1.00	0.00	1.00	0.00

droYak2

ACAAAATTCACACTCGAATT-TTTT-GGCAATCTG-------TTTATAAAGCGTTTATTA---TTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAATACA--------A--CAA------------AATAGGAAAAAAA

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

ACAAAATTCACACTCGAATT-T--TGG-GTATCTC-------TTTATAAAGCGTTTATTA---TTTATTTATTATGTTTT-GTCGAGAGCTTAAAAAAAAT----------ATGAAA------------AGACAACAACCAA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................................TTTAGTT---TTTATTTATTA....................................................................	18	3	1.00	0.00	0.00	0.00	1.00
......................................................................ATTTTGxTTT-GTCGAGAGC....................................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

ACAGAATTCACACTCGTTTT-T--T-G-GCATC---------TCTATAAAGCGTTTATTA---TTTATTTATTATGCTTGCTTTGAGAGCTTTCAAAGAGA----------C------------------------AAAAAT

Size

Hit Count

Total Norm

droBia1

ACAAAATTCACACTCGAATT-TTTT-G-GCATC---------TCTATAAAGCGTTTATTA---TTTGTTTATTGTGTTGT-GTCGAGAGCTTTCAAAAGAGC----------------------------------------

Size

Hit Count

Total Norm

droTak1

ACAAAATTCACACTCAAATT-T--T-G-GGACCTC-------TCTATAAAGCGTTTATTA---CTTATTTATTTTGTTAA-GTCGAGAGCTTTCAAAAGA-----------C--AAA------------AAAAACC--AAAA

Size

Hit Count

Total Norm

droEle1

ACAAAATTCACACTCGATTT-TTTT-TTTTTTTTTTATTCTTGCTATAAAGACTTTATTA---TTTATTTATTATGTTTT-GTTGAGAGCTTTCAAA---------------------------------------------

Size

Hit Count

Total Norm

droRho1

ACAAAATTCACACTCGAATTTT--T-G-GGATC---------TCTATAAAGCGTTTATTA---TTCATTTATTATGTTTT-GTCGAGAGCTTTCAAATGA------------------------------------------

Size

Hit Count

Total Norm

droFic1

ACAAAATTCACACTCGAATT-T--C-G-GGAAC---------TCAATAAAGTGTTTATTA---TTTAATTATTATGTTTT-GTAAAGAGCTTTTAAAGAT-------------------------------------ACACA

Size

Hit Count

Total Norm

droKik1

ACAAAATTCACACTCGAATT-T--G-G-AGATC---------TCTATAAAGCGTTTATTT---TTTGGTATTTGTATACCCTTCAAGAGGGTATTAAATAC----------T------------------------TTTAAG

Size

Hit Count

Total Norm

droAna3

ACAAAATTCACACTCGCTTT-T--G-G-CCAAC---------TCCATAAAGCGTTAATTA---TCTGGC---------------------ATTCTGAGAGC----------C--AAAAGCTAAATCAAATTCGATCGGAGCG

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

ACAAAATTCACACTCGCTTT-T--G-G-CCAACTC-------TCCATAAAGCGTTAATTA---TTTAAC---------------------ATTCTAAAAGCCGAAAAGCGGC----AAATGAATTCAAATTGAAGCAAAGCC

Size

Hit Count

Total Norm

dp4

ACAAAATTCACACTCGAATT-T--G-G-GGATC---------GCG----------------------------------T-AGCGAGGGGGGG---------------------------------------------GCAA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

ACAAAATTCACACTCGAATT-T--G-G-GGATC---------GCG----------------------------------T-AGCAAGGGGGGGCA----------------------------------------------A	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................A-G-GGATC---------GGG----------------------------------T-AGCAAGGG.....................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

ATAAACTCAATACACGAATT-TGGT-ACTGATTTC-----------------------------------------------------------------------------------------------------------

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

TCCGT------------------------------------------------------------------------------CAATCATCTCCTTAAAACT---------C--TAA------------AGCAAACCAAGCA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

GTGAAATTCACACTCGA-----------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:16:33 EDT

dme-mir-2492

chrX:11441455-11441530 +

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