dme-mir-4975- Best orthologs

dme-mir-4975	chr2R:2594667-2594778 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 2594732-2594752
   star strand at position 2594680-2594706
   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:2594652-2594793 -		1	T-AGAACTGGAAATCTGGGCAAATAAAG--CACGTTGCTCCCTGTTTACTTGGGTTTTCTGT-TCAT------------------------------------TTCGCCTATCGAACGTTGAACTTAA------AAAG-----------CCACGATCAGTTGTTTAACAT-----------ACAGATA--------TCTCTGT------AC----ACAAGAAGATTCA------------------------
droSim1	chr2R:1414726-1414867 -	LASTZ	5	T-AGAACTGAAAGTCTCGGCAAATAGAG--CACGTTGCTCCCTGTTTACTCAGGTTCCCTGT-TCAT------------------------------------TTCGCCTATCGAACGTTGAACTTCA------AGAG-----------CCACGATCAGTTGGTAAAGAT-----------ACAGATA--------TCTCTGT------AT----ACTAGAAGATACA------------------------
droSec1	super_1:259050-259190 -	LASTZ	5	T-AGAACTGGAAGTCTCGGCAAATAAAG--CACGTTGCTCCCTGTTTACTCAGGTTCCCTGT-TCAG------------------------------------TTCGCCTATCGAACGTTGAACTTCA------AGAG-----------CCACGATCAGTTGGT-AGGAT-----------ACAGATA--------TCTCTGT------AT----ACTAGAAGATACA------------------------
droYak2	chr2L:15337545-15337682 -	LASTZ	5	T-AGAAATGAAAATCTCGGCAAGTAAAG--CACGTTGCTCCATGTTTACTCAGGTTTGCTGT-TTAT------------------------------------ATCGCCTATCAAACGTTGAACTTGA---------A-----------TCACGATCAGTTGGTCAACAT-----------ACATATA--------TTTGT-C------AC----ACTAGGTGATCCA------------------------
droEre2	scaffold_4929:19950710-19950840 +	LASTZ	5	T-AGGACTGCAGATCCCGGCAACTAAAG--CACGTTGCTCCCAGTTTACTCAGGTTCGCTGT-TTAT------------------------------------ATCGCCTATCGAGCGTTGAACTTGA------GGAG-----------CCACGATCAGTTGGTCAGCAT-----------ACATATA-----------------------------AAGATGATCCA------------------------
droEug1	scf7180000409447:268824-268959 -	LASTZ	0	A--GAACCGGCAAACCGGGCAAATACTG--CACGTATTTAATTCAATGCCCGGATTTTTTGT-TACC---A-GCTGGCATATACGTACATAT--------------ACAAATATAGCATAGAACATGCC----------------------TCAA-----------------------------------T------------TGGTGG--CCATT-----------------------AAAATGCATAAAT
droBia1	scf7180000302292:3556325-3556502 +	LASTZ	0	TCAAAACTGAAAATCTCGCCAATTAAAACAAATGCCGCTCCGTATTTACTCGAGCTCTCTGT-TCA----G-CCCGGAATATACGAGCGTTTTAATCGC----TTCGCCTATCGAACGTTGAACTTGGCCATTCGCAG-----------CCTCAAGCTATTGGCCAACGT-----------GTG--C-ATT-------TGA-T------ACACTTA-TTGTAGATCCA------------------------
droTak1	scf7180000413887:7090-7270 +	LASTZ	0	T-AGAACTGAAAATCTCGGCAAATAAAG--CATGCCGCTCCTTGTTTACTCGACTTCTCTGTTCGGTTTAG-CCTGCAATATACGAGCGTTTTAATCAC----CTCGCCTATCGAACGTTGAACTTGGCCATTCGCAG-----------GCACATTCT------------GTATTTACTGAATA--T-ACT------------TGATAG--CTTCC-----------------------TTGATGATTAGAG
droEle1	scf7180000491217:416541-416721 +	LASTZ	0	T-AAAACTGAAAATCTCGGAAAATAAAA--CACGCCGTTTACTGTTTACTTAGGCTCTCTGC-TAA----G-CGTGCAATACACGAGTATTTTAATCGC----TTCGCTTATCGATCGTTGAACTTGTCCGTTTACAA-----------CCACGTTCACTTGGTCT-------------------------------------------TT----ATTGGATGTTCCATTCAGAAGGTGGACTCGAGCGTCC
droRho1	scf7180000766409:482949-483059 -	LASTZ	0	T-AAAACTGAAAATCTCGGCAATTAAAG--CTCAG-------------------------------------CGTGCAATATACGAGCATTATAATCTC----TTCCCCTATCGAACGTTGAACTTGGCCGTTCACAA-----------CCACGTTGATATAG--------------------------------------------------------------TCT------------------------
droFic1	scf7180000453955:706562-706716 +	LASTZ	0	T-AGAACTGAAAATCTCAGCAAATACAG--CCCGTCGCTCCTTGTTTACTTGGGTTCTCTGT-TAA----G-CCCGCGGTATACGATCGTTTTAATCAC----TTCGCCTATCGAACGTTGAACTTGGC-----------------------CGATCAGTTGGTCAATGTGCACTTAGC--ACAGATC--------T---------------------------GTCA------------------------
droKik1	scf7180000302470:157289-157421 -	LASTZ	0	T-----CTGAAAATCTCGGCACTCACT----------------TTCCACA------------------------TGAAATGT----ACATTTTAATCA----------GTGTCGTACGTTGGTGATAT------TGCCCCCCATTCAAGTCTTA-------AAT-CAAAT-----------ACAAATTATTTGGCCTCCCTC-------TT----ACGAGATCCTGCA------------------------
droAna3	scaffold_13266:18414789-18414883 +	LASTZ	0	A-AGTCT----AATTTCGGT------------------GCCTTGTTTACTTCGCTCTCCGGC-GGA----GAGCTGCAGTGCACGAGGTGTCTAATCGG----CCAGCCCATAGAGCAATGAACTT------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396735:1686720-1686820 +	LASTZ	0	T-GGAAGTGG-AATCTCAGT------------------GCCTTGTTTACTTGG-TTCTCCGC-CGG--A-GAGCTGCAGTGCACGAGGTTTCTAATCGCGTGGTCGGTCTATCGAGCAATGAACTT------------------------------------------------------------------------------------------------------------------------------
dp4	chr3:859167-859237 -	LASTZ	0	T-AGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTTTC-TGTTTACGTTACTTCTCGTC-CCGT------------------------------------CCCGTCT----------------------------------------------------------------------------------------------------------------------------------------------
droPer1	super_2:1035040-1035110 -	LASTZ	0	T-AGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTTTC-TGTTTACGTTACTTCTCGTC-CCGT------------------------------------CCCGTCT----------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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	TAGAACTGGAAATCTGGGCAAATAAAGCACGTTGCTCCCTGTTTACTTGGGTTTTCTGTTCATTTCGCCTATCGAACGTTGAACTTAAAAAGCCACGATCAGTTGTTTAACATACAGATATCTCTGTACACAAGAAGATTCA
droSim1	TAGAACTGAAAGTCTCGGCAAATAGAGCACGTTGCTCCCTGTTTACTCAGGTTCCCTGTTCATTTCGCCTATCGAACGTTGAACTTCAAGAGCCACGATCAGTTGGTAAAGATACAGATATCTCTGTATACTAGAAGATACA
droSec1	TAGAACTGGAAGTCTCGGCAAATAAAGCACGTTGCTCCCTGTTTACTCAGGTTCCCTGTTCAGTTCGCCTATCGAACGTTGAACTTCAAGAGCCACGATCAGTTGGT-AGGATACAGATATCTCTGTATACTAGAAGATACA
droYak2	TAGAAATGAAAATCTCGGCAAGTAAAGCACGTTGCTCCATGTTTACTCAGGTTTGCTGTTTATATCGCCTATCAAACGTTGAACTTGA---ATCACGATCAGTTGGTCAACATACATATATTTGT-CACACTAGGTGATCCA
droEre2	TAGGACTGCAGATCCCGGCAACTAAAGCACGTTGCTCCCAGTTTACTCAGGTTCGCTGTTTATATCGCCTATCGAGCGTTGAACTTGAGGAGCCACGATCAGTTGGTCAGCATACATATA-----------AAGATGATCCA

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
UNAFold Image																	None	None	None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

T-AGAACTGAAAGTCTCGGCAAATAGAG--CACGTTGCTCCCTGTTTACTCAGGTTCCCTGT-TCAT------------------------------------TTCGCCTATCGAACGTTGAACTTCA------AGAG-----------CCACGATCAGTTGGTAAAGAT-----------ACAGATA--------TCTCTGT------AT----ACTAGAAGATACA------------------------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......CGGAAAATCTCGGCAAAT....................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

T-AGAACTGGAAGTCTCGGCAAATAAAG--CACGTTGCTCCCTGTTTACTCAGGTTCCCTGT-TCAG------------------------------------TTCGCCTATCGAACGTTGAACTTCA------AGAG-----------CCACGATCAGTTGGT-AGGAT-----------ACAGATA--------TCTCTGT------AT----ACTAGAAGATACA------------------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................................CA------AGAG-----------CGACGATCAGCT...........................................................................................	18	1	1.00	0.00	1.00	0.00
.....................................................................................................................GTTGAACTTCA------AGAG-----------CCACGATCA..............................................................................................	24	1	1.00	0.00	1.00	0.00

droYak2

T-AGAAATGAAAATCTCGGCAAGTAAAG--CACGTTGCTCCATGTTTACTCAGGTTTGCTGT-TTAT------------------------------------ATCGCCTATCAAACGTTGAACTTGA---------A-----------TCACGATCAGTTGGTCAACAT-----------ACATATA--------TTTGT-C------AC----ACTAGGTGATCCA------------------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................GTAAAG--xACGTTGCTCCATGC...............................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................GTTTACTCAGGATAGCTG...............................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

T-AGGACTGCAGATCCCGGCAACTAAAG--CACGTTGCTCCCAGTTTACTCAGGTTCGCTGT-TTAT------------------------------------ATCGCCTATCGAGCGTTGAACTTGA------GGAG-----------CCACGATCAGTTGGTCAGCAT-----------ACATATA-----------------------------AAGATGATCCA------------------------

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

A--GAACCGGCAAACCGGGCAAATACTG--CACGTATTTAATTCAATGCCCGGATTTTTTGT-TACC---A-GCTGGCATATACGTACATAT--------------ACAAATATAGCATAGAACATGCC----------------------TCAA-----------------------------------T------------TGGTGG--CCATT-----------------------AAAATGCATAAAT

Size

Hit Count

Total Norm

droBia1

TCAAAACTGAAAATCTCGCCAATTAAAACAAATGCCGCTCCGTATTTACTCGAGCTCTCTGT-TCA----G-CCCGGAATATACGAGCGTTTTAATCGC----TTCGCCTATCGAACGTTGAACTTGGCCATTCGCAG-----------CCTCAAGCTATTGGCCAACGT-----------GTG--C-ATT-------TGA-T------ACACTTA-TTGTAGATCCA------------------------

Size

Hit Count

Total Norm

droTak1

T-AGAACTGAAAATCTCGGCAAATAAAG--CATGCCGCTCCTTGTTTACTCGACTTCTCTGTTCGGTTTAG-CCTGCAATATACGAGCGTTTTAATCAC----CTCGCCTATCGAACGTTGAACTTGGCCATTCGCAG-----------GCACATTCT------------GTATTTACTGAATA--T-ACT------------TGATAG--CTTCC-----------------------TTGATGATTAGAG

Size

Hit Count

Total Norm

droEle1

T-AAAACTGAAAATCTCGGAAAATAAAA--CACGCCGTTTACTGTTTACTTAGGCTCTCTGC-TAA----G-CGTGCAATACACGAGTATTTTAATCGC----TTCGCTTATCGATCGTTGAACTTGTCCGTTTACAA-----------CCACGTTCACTTGGTCT-------------------------------------------TT----ATTGGATGTTCCATTCAGAAGGTGGACTCGAGCGTCC

Size

Hit Count

Total Norm

droRho1

T-AAAACTGAAAATCTCGGCAATTAAAG--CTCAG-------------------------------------CGTGCAATATACGAGCATTATAATCTC----TTCCCCTATCGAACGTTGAACTTGGCCGTTCACAA-----------CCACGTTGATATAG--------------------------------------------------------------TCT------------------------

Size

Hit Count

Total Norm

droFic1

T-AGAACTGAAAATCTCAGCAAATACAG--CCCGTCGCTCCTTGTTTACTTGGGTTCTCTGT-TAA----G-CCCGCGGTATACGATCGTTTTAATCAC----TTCGCCTATCGAACGTTGAACTTGGC-----------------------CGATCAGTTGGTCAATGTGCACTTAGC--ACAGATC--------T---------------------------GTCA------------------------

Size

Hit Count

Total Norm

droKik1

T-----CTGAAAATCTCGGCACTCACT----------------TTCCACA------------------------TGAAATGT----ACATTTTAATCA----------GTGTCGTACGTTGGTGATAT------TGCCCCCCATTCAAGTCTTA-------AAT-CAAAT-----------ACAAATTATTTGGCCTCCCTC-------TT----ACGAGATCCTGCA------------------------

Size

Hit Count

Total Norm

droAna3

A-AGTCT----AATTTCGGT------------------GCCTTGTTTACTTCGCTCTCCGGC-GGA----GAGCTGCAGTGCACGAGGTGTCTAATCGG----CCAGCCCATAGAGCAATGAACTT------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

T-GGAAGTGG-AATCTCAGT------------------GCCTTGTTTACTTGG-TTCTCCGC-CGG--A-GAGCTGCAGTGCACGAGGTTTCTAATCGCGTGGTCGGTCTATCGAGCAATGAACTT------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

dp4

T-AGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTTTC-TGTTTACGTTACTTCTCGTC-CCGT------------------------------------CCCGTCT----------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

T-AGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTTTC-TGTTTACGTTACTTCTCGTC-CCGT------------------------------------CCCGTCT----------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..........................................TGATTACGTTACTTCTCTT...............................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

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

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 05:15:26 EDT

dme-mir-4975

chr2R:2594667-2594778 -

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