dme-mir-2490- Best orthologs

dme-mir-2490	chr2LHet:27336-27410 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mature strand at position 27344-27366
   star strand at position 27382-27402
   mutations
   read mismatches

Notes: The reads that map to sechelia and yakuba are not uniquely mapped reads.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2LHet:27321-27425 +		1	ACAATCGTACGTTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGC--TTTGCT----------------CTTACTTTATCGCTTAAACTCGCAACTCGCTT--------------------------------------------------------------------------CGCT-----CTCA
droSim1	chr4:281112-281214 +	LASTZ	4	AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGC--TTTGCT----------------CTCGCTATATCGCTTGAGCTCGCAACTCGCTT--------------------------------------------------------------------------CGCT-------CA
droSec1	super_30:85009-85111 +	LASTZ	3	AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGC--TTTGCT----------------CTCGCTATATCGCTTGAGCTCGCAACTCGCTT--------------------------------------------------------------------------CGCT-------CA
droYak2	chrU:9061077-9061181 +	LASTZ	3	ACAATCGTACGCTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGC--TTTGCT----------------CTCGCTTTATCGCTTGAGCTCGCTACTCGCCT--------------------------------------------------------------------------CGCT-----CTCA
droEre2	scaffold_4784:23192819-23192904 -	LASTZ	4	ACTATCAGACGCTCTGAGCGAGTTGCAGCGATAATGCAGGTTGCAAACTGTTCTCT-------------------------------------CGCTTGAGCTCGCAACTCGTTT--------------------------------------------------------------------------CGCT-----CTCA
droEug1	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBia1	scf7180000301391:7073-7197 -	LASTZ	0	ACTTTTGTAGCTTCTGCAGGCATTTGG----CTGTGTAGATTGTATGGTCTCCGAT-------------------------------------AAGTAGTAGTCGAAAGTCCCT--------------CACGATGACAACGTTTGTAACG--------TACCAGGGGAGCTCGAATGCTCGCCG-----A--G-------CT
droTak1	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEle1	scf7180000490727:38228-38321 -	LASTZ	0	AGAA-CTTACGTTTTGATTAAGTTCAAGCGATAAAGCAAGTTCAAAACTGATCTCTTTC--TTTGCC----------------CTCAATTTTTCGCTTCGTT----------TTT--------------------------------------------------------------------------CGCA-----GCCA
droRho1	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droFic1	scf7180000453955:804345-804445 -	LASTZ	0	AAAATTTTTCGATCGG-----G--------------CTCCCCCCAAAATTTTTTCTGCG--TCCGC-----------------------------------------CCCTGACTG------------------------GCTTGTGACC--------TACCAGGGAAGCCCGGATGCCCGTCG-----A--GCAGCACGTG
droKik1	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396710:138523-138625 +	LASTZ	0	ACAATCGAACGCTCTGAGCGAGTTGAAGCGATGAAGCTGGTTGCAAACTGCTCTCTC----TTTCCT----------------CCCGCTTTATCGCTTGAACTCGCAACTCGCTT--------------------------------------------------------------------------CGGT-----TTTA
dp4	chr4_group4:3101286-3101457 +	LASTZ	0	AGCAT-GAGCG---TCCACGAGATCAAGCGATAAGACATTTGCAAAGCTACTCTCTTGC--TTCGCTTGCACTCGTTGCTGTCTTCGCTATAA-------------------CTTGTTTCCCGCTCTTCACTGTAAATCGTTTTGCACTCTTCGCTCAAACTAGCCGCGCTGCTCTCTTCGCTTATCTTTGCT-----CTCA
droPer1	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181143:687820-687924 +	LASTZ	0	ACACACGTATAACAGCAGCTGGATGAAGCGATAAAGCGA-TTCAGAATCGCTTTCTCGCAACTCGCT-----------------TCAACTTGTCGCTTTGGCTCTCTTCTCGCTT--------------------------------------------------------------------------CGCT-----TGCA
droVir3	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6498:432956-433055 +	LASTZ	0	AACAC---ACTTTAT-CATGCGATTAAGCGAGAAAGCGA-TTCAGGAATGCTTTCTCGC--AACTCG----------------CTTAACTTCTCGCTTTGGGTCTCTTCTCGCTT--------------------------------------------------------------------------CGCT-----TGCA
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	ACAATCGTACGTTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGCTTTGCTCTTACTTTATCGCTTAAACTCGCAACTCGCTTCGCTCTCA
droSim1	AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGCTTTGCTCTCGCTATATCGCTTGAGCTCGCAACTCGCTTCGCT--CA
droSec1	AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGCTTTGCTCTCGCTATATCGCTTGAGCTCGCAACTCGCTTCGCT--CA
droYak2	ACAATCGTACGCTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGCTTTGCTCTCGCTTTATCGCTTGAGCTCGCTACTCGCCTCGCTCTCA
droEre2	ACTATCAGACGCTCTGAGCGAGTTGCAGCGATAATGCAGGTTGCAAACTGTTCTCT-------------------CGCTTGAGCTCGCAACTCGTTTCGCTCTCA

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		None		None
UNAFold Image						None		None		None		None	None			None		None		None

Small RNA-seq read pileup

Species

Alignment

droSim1

AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGC--TTTGCT----------------CTCGCTATATCGCTTGAGCTCGCAACTCGCTT--------------------------------------------------------------------------CGCT-------CA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..AATCGTACGCTCTGAGCGA.....................................................................................................................................................................................	19	13	0.08	0.00	0.00	0.08	0.00
..........................................................................................TATCGCTTGAGCTCGCAACTC...........................................................................................	21	11	0.09	0.00	0.09	0.00	0.00
..AATCGTACGCTCTGAGCGG.....................................................................................................................................................................................	19	13	0.08	0.00	0.00	0.08	0.00
..AATCGTACGCTCTGAGCGAGTTAAAGC.............................................................................................................................................................................	27	10	0.10	0.00	0.00	0.10	0.00

droSec1

AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGC--TTTGCT----------------CTCGCTATATCGCTTGAGCTCGCAACTCGCTT--------------------------------------------------------------------------CGCT-------CA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................TTGAAGCAATAAAGCAGGTTG...............................................................................................................................................................	21	2	1.00	0.00	0.00	1.00
.......................TGAAGCAATAAAGCAGGTTGCA.............................................................................................................................................................	22	2	0.50	0.00	0.00	0.50
.........................AAGCGATAAAGCAGGTTGCAAACTG........................................................................................................................................................	25	5	0.20	0.00	0.00	0.20

droYak2

ACAATCGTACGCTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGC--TTTGCT----------------CTCGCTTTATCGCTTGAGCTCGCTACTCGCCT--------------------------------------------------------------------------CGCT-----CTCA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...............................................................TGCT----------------CTCGCTTAATCGCTTGAGA....................................................................................................	23	7	0.14	0.00	0.00	0.00	0.14	0.00
.....................GTTGAAGCGATAAAGCAGGTTGCA.............................................................................................................................................................	24	10	0.10	0.00	0.00	0.10	0.00	0.00
.......................TGAAGCGATAAAGCAGGTTGCA.............................................................................................................................................................	22	10	0.10	0.10	0.00	0.00	0.00	0.00
.....................GTTGAAGCGATAAAGCAGGTTGC..............................................................................................................................................................	23	10	0.10	0.00	0.00	0.10	0.00	0.00
.......................TGAAGCGATAAAGCAGGTTGCC.............................................................................................................................................................	22	11	0.09	0.09	0.00	0.00	0.00	0.00

droEre2

ACTATCAGACGCTCTGAGCGAGTTGCAGCGATAATGCAGGTTGCAAACTGTTCTCT-------------------------------------CGCTTGAGCTCGCAACTCGTTT--------------------------------------------------------------------------CGCT-----CTCA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

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

Size

Hit Count

Total Norm

droBia1

ACTTTTGTAGCTTCTGCAGGCATTTGG----CTGTGTAGATTGTATGGTCTCCGAT-------------------------------------AAGTAGTAGTCGAAAGTCCCT--------------CACGATGACAACGTTTGTAACG--------TACCAGGGGAGCTCGAATGCTCGCCG-----A--G-------CT

Size

Hit Count

Total Norm

droTak1

Size

Hit Count

Total Norm

droEle1

AGAA-CTTACGTTTTGATTAAGTTCAAGCGATAAAGCAAGTTCAAAACTGATCTCTTTC--TTTGCC----------------CTCAATTTTTCGCTTCGTT----------TTT--------------------------------------------------------------------------CGCA-----GCCA

Size

Hit Count

Total Norm

droRho1

Size

Hit Count

Total Norm

droFic1

AAAATTTTTCGATCGG-----G--------------CTCCCCCCAAAATTTTTTCTGCG--TCCGC-----------------------------------------CCCTGACTG------------------------GCTTGTGACC--------TACCAGGGAAGCCCGGATGCCCGTCG-----A--GCAGCACGTG

Size

Hit Count

Total Norm

droKik1

Size

Hit Count

Total Norm

droAna3

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

ACAATCGAACGCTCTGAGCGAGTTGAAGCGATGAAGCTGGTTGCAAACTGCTCTCTC----TTTCCT----------------CCCGCTTTATCGCTTGAACTCGCAACTCGCTT--------------------------------------------------------------------------CGGT-----TTTA

Size

Hit Count

Total Norm

dp4

AGCAT-GAGCG---TCCACGAGATCAAGCGATAAGACATTTGCAAAGCTACTCTCTTGC--TTCGCTTGCACTCGTTGCTGTCTTCGCTATAA-------------------CTTGTTTCCCGCTCTTCACTGTAAATCGTTTTGCACTCTTCGCTCAAACTAGCCGCGCTGCTCTCTTCGCTTATCTTTGCT-----CTCA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................CTTGCACTCGTTTCGGTC.......................................................................................................................	18	1	3.00	0.00	0.00	0.00	3.00
..................................................................TTGCACTCGTTTCGGTCT......................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....................................................................GCACTCGTTGCTGTTGTCGC..................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.................................................................CTTGCACTCGTTTCGGTCT......................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

ACACACGTATAACAGCAGCTGGATGAAGCGATAAAGCGA-TTCAGAATCGCTTTCTCGCAACTCGCT-----------------TCAACTTGTCGCTTTGGCTCTCTTCTCGCTT--------------------------------------------------------------------------CGCT-----TGCA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........................................TTCAGAATCGCTTTCTCGCAACTCGCT-----------------......................................................................................................................	27	13	0.31	0.00	0.31	0.00	0.00
........................................TTCAGAATCGCTTTCTCGCAACTCGCT-----------------T.....................................................................................................................	28	13	0.15	0.00	0.15	0.00	0.00
..........................................................................................TGTCGCTTTGGCTCTCTTCTCGCTT--------------------------------------------------------------------------.............	25	16	0.13	0.00	0.13	0.00	0.00
..........................................................................................TGTCGCTTTGGCTCTCTTCTC...........................................................................................	21	16	0.06	0.00	0.06	0.00	0.00
..........AAACGCAGCTGGATGAAG..............................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................TGTCGCTTTGGCTCTCTTCTCGCT........................................................................................	24	16	0.06	0.00	0.06	0.00	0.00
...............................................................CGCT-----------------TCAACTTGTCGCTTTGGCTCT.................................................................................................	25	15	0.07	0.00	0.07	0.00	0.00
...............................................TCGCTTTCTCGCAACTCGCT-----------------TCAAC.................................................................................................................	25	14	0.07	0.00	0.07	0.00	0.00
................................................CGCTTTCTCGCAACTCGCT-----------------TCAAC.................................................................................................................	24	14	0.07	0.00	0.07	0.00	0.00
................................................CGCTTTCTCGCAACTCACT-----------------TCAACT................................................................................................................	25	13	0.08	0.00	0.08	0.00	0.00
.........................................TCAGAATCGCTTTCTCGCAACTCACT-----------------......................................................................................................................	26	14	0.07	0.00	0.07	0.00	0.00
..........................................CAGAATCGCTTTCTCGCAACTCGCT-----------------T.....................................................................................................................	26	14	0.07	0.00	0.07	0.00	0.00
.........................................TCAGAATCGCTTTCTCGCAACTCGCT-----------------......................................................................................................................	26	13	0.08	0.00	0.08	0.00	0.00
...........................................................AACTCGCT-----------------TCAACTTGTCGCTTTTGCTC..................................................................................................	28	15	0.07	0.00	0.07	0.00	0.00
...............................................................CGCT-----------------TCAACTTGTCGCTTTGGCT...................................................................................................	23	15	0.07	0.00	0.07	0.00	0.00
.....................................................TCTCGCAACTCGCT-----------------TCAACTTGTCG...........................................................................................................	25	15	0.07	0.00	0.07	0.00	0.00
....................................................................................TCAACTTGTCGCTTTGGCTCTCTTCT............................................................................................	26	15	0.07	0.00	0.07	0.00	0.00
...........................GCGATAAAGCGA-TTCAGAATCG........................................................................................................................................................	22	13	0.08	0.00	0.08	0.00	0.00
.............................................................................................CGCTTTGGCTCTCTTCTCGCTT--------------------------------------------------------------------------CGC..........	25	16	0.06	0.00	0.06	0.00	0.00
.............................................................................................CGCTTTGTCTCTCTTCTCGCTT--------------------------------------------------------------------------CGCT-----....	26	16	0.06	0.00	0.06	0.00	0.00

droVir3

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

AACAC---ACTTTAT-CATGCGATTAAGCGAGAAAGCGA-TTCAGGAATGCTTTCTCGC--AACTCG----------------CTTAACTTCTCGCTTTGGGTCTCTTCTCGCTT--------------------------------------------------------------------------CGCT-----TGCA

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 05:14:36 EDT

dme-mir-2490

chr2LHet:27336-27410 +

Known_mirbase

antisense_to_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