dme-mir-305-as- Best orthologs

dme-mir-305-as	chr2L:7425972-7426044 -	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 7425979-7426001
   star strand at position 7426016-7426036
   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	chr2L:7425957-7426059 -		1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droSim1	chr2L:7217527-7217627 -	LASTZ	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAGCATGTGCCGGGTTACGA-GACACACCAGAGCA-CTGATGAAGTACAATAGACATGGGAGACAGT-G--------ATAC------------------------------------------
droSec1	super_3:2941418-2941520 -	LASTZ	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droYak2	chr2L:5473614-5473716 +	LASTZ	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droEre2	scaffold_4929:16344683-16344785 -	LASTZ	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-ACCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droEug1	scf7180000409463:614863-614965 -	LASTZ	4	GT----------------ATGCAAATCACCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droBia1	scf7180000302422:9125681-9125783 -	LASTZ	4	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTCG--------ATAC------------------------------------------
droTak1	scf7180000415604:142269-142370 +	LASTZ	4	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACG--GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droEle1	scf7180000491028:1624701-1624808 +	LASTZ	4	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACTT-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATACACAAC-------------------------------------
droRho1	scf7180000766421:7519-7621 +	LASTZ	4	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACTT-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droFic1	scf7180000454115:155833-155935 -	LASTZ	4	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTGCGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droKik1	scf7180000302384:54674-54769 +	LASTZ	4	AT----------------TTGGAAATCACCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAG---------------ATAC------------------------------------------
droAna3	scaffold_12916:15334141-15334251 -	LASTZ	1	GT----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-TGGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACATATTTCTCAAAAATAC------------------------------------------
droBip1	scf7180000396572:1689256-1689352 +	LASTZ	4	GA----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-TAGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACATT--------------------------------------------------------
dp4	chr4_group1:4175881-4175974 -	LASTZ	4	GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGAC-----------------------------------------------------------
droPer1	super_5:1086315-1086408 +	LASTZ	1	GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGAC-----------------------------------------------------------
droWil1	scaffold_180772:5257378-5257513 +	LASTZ	1	------------------ATGAAGATCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAAACGGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAA--------------C--AACAATAAATTAAAAATGCCAATAAAAAAAAAAGAGAATC
droVir3	scaffold_12963:15419827-15419927 +	LASTZ	1	AA----------------ATGCAAATCAACGCATATTGAGTGTACTTCAACATGTGCCGGGTTACAA-GTCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACA--TG--------AAAC------------------------------------------
droMoj3	scaffold_6500:18399247-18399346 +	LASTZ	1	GC--------------AACTGCAAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTTCCA-CTGACACCAGAGCACCTGATGAAGTACAATAGACATGGGGGA-----G--------ACAC------------------------------------------
droGri2	scaffold_15126:5008541-5008648 -	LASTZ	1	TTAATTAAAACGCAGCAAATGCCAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GTGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAG-------------------------------------------------------------

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	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droSim1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAGCATGTGCCGGGTTACGA-GACACACCAGAGCA-CTGATGAAGTACAATAGACATGGGAGACAGT-G--------ATAC------------------------------------------
droSec1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droYak2	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droEre2	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-ACCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droEug1	GT----------------ATGCAAATCACCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droBia1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTCG--------ATAC------------------------------------------
droTak1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACG--GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droEle1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACTT-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATACACAAC-------------------------------------
droRho1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACTT-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droFic1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTGCGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droKik1	AT----------------TTGGAAATCACCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAG---------------ATAC------------------------------------------
droAna3	GT----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-TGGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACATATTTCTCAAAAATAC------------------------------------------
droBip1	GA----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-TAGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACATT--------------------------------------------------------
dp4	GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGAC-----------------------------------------------------------
droPer1	GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGAC-----------------------------------------------------------
droWil1	------------------ATGAAGATCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAAACGGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAA--------------C--AACAATAAATTAAAAATGCCAATAAAAAAAAAAGAGAATC
droVir3	AA----------------ATGCAAATCAACGCATATTGAGTGTACTTCAACATGTGCCGGGTTACAA-GTCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACA--TG--------AAAC------------------------------------------
droMoj3	GC--------------AACTGCAAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTTCCA-CTGACACCAGAGCACCTGATGAAGTACAATAGACATGGGGGA-----G--------ACAC------------------------------------------
droGri2	TTAATTAAAACGCAGCAAATGCCAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GTGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAG-------------------------------------------------------------

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

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAGCATGTGCCGGGTTACGA-GACACACCAGAGCA-CTGATGAAGTACAATAGACATGGGAGACAGT-G--------ATAC------------------------------------------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................ATTGTACTTCATCATGTGC.................................................................................................................	19	2	1.50	0.00	1.50	0.00	0.00
......................................................................................ATGAAGxACAATAGGCATG.................................................................	18	2	0.50	0.00	0.50	0.00	0.00
......................................ATTGTACTTCATCATGTGCC................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00

droSec1

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................................................................CAGAGCACCTGATGAAGTACAAT........................................................................	23	2	10.00	6.00	0.00	4.00
...........................................................................CAGAGCACCTGATGAAGTACA..........................................................................	21	2	3.00	2.00	0.00	1.00
...........................................................................CAGAGCACCTGATGAAGTACAA.........................................................................	22	2	1.50	1.00	0.50	0.00
............................................................................AGAGCACCTGATGAAGTACAAT........................................................................	22	2	1.00	0.00	0.50	0.50
............................................................................AGAGCACCTGTTGAAGTACAAT........................................................................	22	2	0.50	0.00	0.00	0.50
...........................................................................CAGAGCACCTGATGAAGTTCAAT........................................................................	23	2	0.50	0.50	0.00	0.00
...........................................................................CAGAGCACCTGATGAAGTACAAA........................................................................	23	2	0.50	0.00	0.00	0.50
...........................................................................CAGAGCACCTGATGAAGTA............................................................................	19	2	0.50	0.00	0.00	0.50

droYak2

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................................................................CAGAGCACCTGATGAAGTACA..........................................................................	21	2	3.00	0.00	0.00	1.50	1.00	0.50
...........................................................................CAGAGCACCTGATGAAGTACAAT........................................................................	23	2	2.00	0.00	0.00	1.50	0.50	0.00
...........................................................................CAGAGCACCTGATGAAGTACAA.........................................................................	22	2	1.00	0.00	0.00	1.00	0.00	0.00
...........................................................................CAGAGCACCTGATGAAGTAC...........................................................................	20	2	0.50	0.00	0.00	0.00	0.50	0.00

droEre2

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-ACCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...........................................................................CAGAGCACCTGATGAAGTACAAT........................................................................	23	2	2.00	0.00	0.00	0.00	2.00
...........................................................................CAGAGCACCTGATGAAGTACA..........................................................................	21	2	1.00	0.00	0.00	0.00	1.00
......................................ATTGTACTTCATCATGTGC.................................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25
...........................................................................CATAGCACCTGATGAAGTAC...........................................................................	20	2	0.50	0.00	0.00	0.00	0.50
...........................................................................CAGAGCACCTGATGAAGTAC...........................................................................	20	2	0.50	0.00	0.00	0.00	0.50
...........................................................................CAGAGCACCTGATGAGGTA............................................................................	19	2	0.50	0.00	0.00	0.00	0.50
......................................ATTGTACTTCATCATGTG..................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25

droEug1

GT----------------ATGCAAATCACCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------

Size

Hit Count

Total Norm

droBia1

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTCG--------ATAC------------------------------------------

Size

Hit Count

Total Norm

droTak1

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACG--GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------

Size

Hit Count

Total Norm

droEle1

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACTT-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATACACAAC-------------------------------------

Size

Hit Count

Total Norm

droRho1

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACTT-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------

Size

Hit Count

Total Norm

droFic1

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTGCGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------

Size

Hit Count

Total Norm

droKik1

AT----------------TTGGAAATCACCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAG---------------ATAC------------------------------------------

Size

Hit Count

Total Norm

droAna3

GT----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-TGGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACATATTTCTCAAAAATAC------------------------------------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................CAGAGCACCTGATGAAGTACA..........................................................................	21	2	0.50	0.00	0.50	0.00	0.00

droBip1

GA----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-TAGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACATT--------------------------------------------------------

Size

Hit Count

Total Norm

dp4

GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGAC-----------------------------------------------------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.......................................GTGTACTTCAACCTGGGC.................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50

droPer1

GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGAC-----------------------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........................................................................CAGAGCACCTGATGAAGTACA..........................................................................	21	2	0.50	0.50	0.00	0.00	0.00	0.00
...........................................................................CAGAGCACCTGATGAAGTACAAT........................................................................	23	2	0.50	0.50	0.00	0.00	0.00	0.00

droWil1

------------------ATGAAGATCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAAACGGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAA--------------C--AACAATAAATTAAAAATGCCAATAAAAAAAAAAGAGAATC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........................................................................CAGAGCACCTGATGAAGTACAAT........................................................................	23	2	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................TCAATAAAAGAAAAAGAGA...	19	4	0.25	0.00	0.25	0.00	0.00
....................GAAGATCxCGACATATTGAGT.................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
......................................................................................................................................................AAAAAAAAAAAAAGAGAA..	18	32	0.03	0.03	0.00	0.00	0.00
................................................................................................................................................AATGTTAATAAAAAAAAA........	18	15	0.07	0.00	0.07	0.00	0.00
..............................................................................................................................................AAAATGACATTAAAAAAAA.........	19	3	0.33	0.00	0.33	0.00	0.00

droVir3

AA----------------ATGCAAATCAACGCATATTGAGTGTACTTCAACATGTGCCGGGTTACAA-GTCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACA--TG--------AAAC------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
........................................TGTACTTCAACATGTGCCGGGT............................................................................................................	22	2	0.50	0.00	0.00	0.00	0.50	0.00
.................................................................AA-GTCACACCAGAGCACCTGA...................................................................................	21	2	0.50	0.50	0.00	0.00	0.00	0.00
......................................AGTGTACTTCATCAGGTG..................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00	0.00

droMoj3

GC--------------AACTGCAAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTTCCA-CTGACACCAGAGCACCTGATGAAGTACAATAGACATGGGGGA-----G--------ACAC------------------------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...........................................................................CAGAGCACCTGATGAAGTACA..........................................................................	21	2	0.50	0.50	0.00	0.00	0.00

droGri2

TTAATTAAAACGCAGCAAATGCCAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GTGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAG-------------------------------------------------------------	Size	Hit Count	Total Norm	V109 Male body
............................................................................AGAGCACCTGATGAAGTACAAT........................................................................	22	2	0.50	0.50

Generated: 04/20/2012 at 05:19:04 EDT

dme-mir-305-as

chr2L:7425972-7426044 -

Novel

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