dme-mir-983-1-as- Best orthologs

dme-mir-983-1-as	chrX:4262342-4262432 +	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 4262358-4262379
   star strand at position 4262396-4262416
   mutations
   read mismatches

Notes: This is in a cluster with 983-2 and 983-1. Looks like a genuine loss event

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:4262327-4262447 +		1	TAC-GCCAGCGAGTTGAATGTTTACAACAACTAGATAATG---------------------------------------CGTAACTACCTAATGAATGA---ACTGAAAAT-CATTAGTTC----------GAA----------AC-GTATTATTTAATTATTGCAATATAAT------------AGCATATG---------------------------CATAT
droSim1	chrX:3277334-3277447 +	LASTZ	1	TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATA---------------------------------------CCTGACGAACTCATGAATGA----CTGAAAAT-CATGTGTTC----------GAA----------AG-GTATTACTAAATTACTGCAAGATATC---------------ATAT------------------------------GCA
droSec1	super_4:2462215-2462328 -	LASTZ	1	TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATA---------------------------------------CCTAACGAACTCATGAATGA----CTGAAAAT-CATATGTTC----------GAA----------AG-GTATTACTAAATTACTGCAACATATC---------------ATAT------------------------------GCA
droYak2	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4690:1633112-1633231 +	LASTZ	1	CAC-GCCAACGAGTTGAATGTTAACAATAACTTAATAATC---------------------------------------CGTTTCGCATTTATGAATGA----TTAAAGCA-CATAACTTC----------GAA----------TC-GAATTATTAAATCACTGTAACATAAT------------ATCACACA---------------------------ATTCC
droEug1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBia1	scf7180000301703:495454-495597 -	LASTZ	0	AAA-TCCGACACG----------------------------------TACTATTTGTT-TTTAAACCGAGCAAATAGTACGTAACGAACTTTCTAATGA----TTGGAAA----TGCGTTT----------GAA----------AC-A-------------CTACACACA---ATTTAAGATGGCAATATGTACCCTTAATTTAATAATGAAAAACCTTTTATAA
droTak1	scf7180000415394:1160785-1160887 -	LASTZ	0	GA------------TGTTTGTTAACAATAATTGAATAATCCGAAACGCACTACTGCATTTTCAAAATAAGCAC-----------------------------------------TAAGAAC----------GAA----------TC-GGACTATTAAATGATTGGAAATTTC-------------------------------------------------CTTT
droEle1	scf7180000491011:2112374-2112507 -	LASTZ	0	GAC-A-------------------------------------ATGCGAACAAGTTGATTTTAAAAAGGAGTGCATA---GTCAACAAAATGTTAAAAGAGAACTTGAAAATTCACTTGTTTTTATATCTATTCA----------CT-TTATTATATATTTTTTGTAATATGTA------------TGTATGTA---------------------------TGTCG
droRho1	scf7180000779334:415671-415796 -	LASTZ	0	CTA-AGCAGTGTGCTATTTATTAATTCGAACTATTTTAAT---------------------------------------ATTGATTAGGTAATAGATAT----CTAAAACT-AATATTTTA----------GGAGCAACTTATGAT-ATGTTACTATACAACTACACAAC---TTTT-------------AAG---------------------------CAGAT
droFic1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6540:31109889-31110001 +	LASTZ	0	TATCATGAGCTTTTCAAGTACTTAA---AGCTAGATAACA---------------------------------------AATTT------CGTTTATTG----ATTAAATT-GATAGGTTT----------TGG----------TTTTAATTATTTAGTTATTTTAATATAGT------------AACATACG---------------------------TTGTT
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	TACGCCAGCGAGTTGAATGTTTACAACAACTAGATAATGCGTAACTACCTAATGAATGAACTGAAAATCATTAGTTCGAAACGTATTATTTAATTATTGCAATATAATAGCATATGCATAT
droSim1	TCCGCCAGCGAGTTGAATGTTTACAATAACTAGATAATACCTGACGAACTCATGAATGA-CTGAAAATCATGTGTTCGAAAGGTATTACTAAATTACTGCAAGATA---TCATATGCA---
droSec1	TCCGCCAGCGAGTTGAATGTTTACAATAACTAGATAATACCTAACGAACTCATGAATGA-CTGAAAATCATATGTTCGAAAGGTATTACTAAATTACTGCAACATA---TCATATGCA---
droEre2	CACGCCAACGAGTTGAATGTTAACAATAACTTAATAATCCGTTTCGCATTTATGAATGA-TTAAAGCACATAACTTCGAATCGAATTATTAAATCACTGTAACATAATATCACACAATTCC

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

Small RNA-seq read pileup

Species

Alignment

droSim1

TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATA---------------------------------------CCTGACGAACTCATGAATGA----CTGAAAAT-CATGTGTTC----------GAA----------AG-GTATTACTAAATTACTGCAAGATATC---------------ATAT------------------------------GCA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................AGATAATA---------------------------------------CCTGACGAACTCA.....................................................................................................................................	21	4	1.25	0.00	1.00	0.25	0.00
...................................................................................................................GTGTTC----------GAA----------AG-GTATTACT......................................................................	19	3	0.67	0.00	0.67	0.00	0.00
..................................................................................................................TGTGTTC----------GAA----------AG-GTATTACT......................................................................	20	3	0.33	0.00	0.00	0.33	0.00
..............................................................................................................................................................TTAATGCAAGATATC---------------ATAT------------------------------GA.	21	3	0.33	0.33	0.00	0.00	0.00
................................AGATAATA---------------------------------------CCTGACGGACTCA.....................................................................................................................................	21	4	0.25	0.00	0.25	0.00	0.00

droSec1

TCC-GCCAGCGAGTTGAATGTTTACAATAACTAGATAATA---------------------------------------CCTAACGAACTCATGAATGA----CTGAAAAT-CATATGTTC----------GAA----------AG-GTATTACTAAATTACTGCAACATATC---------------ATAT------------------------------GCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..................................................................................................................TATGTTC----------GAA----------AG-GTATTACTAA....................................................................	22	3	0.33	0.00	0.33	0.00

droYak2

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

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

CAC-GCCAACGAGTTGAATGTTAACAATAACTTAATAATC---------------------------------------CGTTTCGCATTTATGAATGA----TTAAAGCA-CATAACTTC----------GAA----------TC-GAATTATTAAATCACTGTAACATAAT------------ATCACACA---------------------------ATTCC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................................................................................ACTTC----------GAA----------TC-GAATTATTAAAT..................................................................	22	3	5.67	0.33	0.00	0.00	5.33
....................................................................................................................ACTTC----------GAA----------TC-GAATTATTA.....................................................................	19	3	1.00	0.00	0.00	0.00	1.00
..................................................................................................................TAACTTC----------GAA----------TC-GAATTATT......................................................................	20	3	0.33	0.00	0.00	0.00	0.33
..................................................................................................................TAACTTC----------GAA----------TC-GAATTATTAA....................................................................	22	3	0.33	0.00	0.00	0.00	0.33
....................................................................................................................ACTTC----------GAA----------TC-GAATTATT......................................................................	18	3	0.33	0.00	0.00	0.00	0.33
................................TAATAATC---------------------------------------CGTTTCGCATTTATG...................................................................................................................................	23	3	0.33	0.00	0.00	0.00	0.33
....................................................................................................................ACTTC----------GAA----------TC-GAATTATTAAAC..................................................................	22	3	0.33	0.00	0.33	0.00	0.00
....................................................................................................................ACTTC----------GAA----------TC-GAATTATTAAATG.................................................................	23	3	0.33	0.00	0.00	0.00	0.33

droEug1

Size

Hit Count

Total Norm

droBia1

AAA-TCCGACACG----------------------------------TACTATTTGTT-TTTAAACCGAGCAAATAGTACGTAACGAACTTTCTAATGA----TTGGAAA----TGCGTTT----------GAA----------AC-A-------------CTACACACA---ATTTAAGATGGCAATATGTACCCTTAATTTAATAATGAAAAACCTTTTATAA

Size

Hit Count

Total Norm

droTak1

GA------------TGTTTGTTAACAATAATTGAATAATCCGAAACGCACTACTGCATTTTCAAAATAAGCAC-----------------------------------------TAAGAAC----------GAA----------TC-GGACTATTAAATGATTGGAAATTTC-------------------------------------------------CTTT

Size

Hit Count

Total Norm

droEle1

GAC-A-------------------------------------ATGCGAACAAGTTGATTTTAAAAAGGAGTGCATA---GTCAACAAAATGTTAAAAGAGAACTTGAAAATTCACTTGTTTTTATATCTATTCA----------CT-TTATTATATATTTTTTGTAATATGTA------------TGTATGTA---------------------------TGTCG

Size

Hit Count

Total Norm

droRho1

CTA-AGCAGTGTGCTATTTATTAATTCGAACTATTTTAAT---------------------------------------ATTGATTAGGTAATAGATAT----CTAAAACT-AATATTTTA----------GGAGCAACTTATGAT-ATGTTACTATACAACTACACAAC---TTTT-------------AAG---------------------------CAGAT

Size

Hit Count

Total Norm

droFic1

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

Size

Hit Count

Total Norm

dp4

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

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

TATCATGAGCTTTTCAAGTACTTAA---AGCTAGATAACA---------------------------------------AATTT------CGTTTATTG----ATTAAATT-GATAGGTTT----------TGG----------TTTTAATTATTTAGTTATTTTAATATAGT------------AACATACG---------------------------TTGTT

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 05:21:53 EDT

dme-mir-983-1-as

chrX:4262342-4262432 +

Novel

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