sblock103084- Best orthologs

sblock103084	chr3L:11689515-11689577 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_5pUTR

Legend:

   mature strand at position 11689556-11689575
   star strand at position 11689521-11689541
   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	chr3L:11689500-11689592 +		1	CGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGC-------------CGTTTG--GCTGCTGCACA-----------AA-TTTTGGTC
droSim1	chr3L:11059386-11059485 +	LASTZ	4	CGG---------------------------------------------------ATCGTGCGATACCTTTATCAGTTGGACGTTAG------ACGCCGTCTG---AA---T------TTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droSec1	super_0:3875908-3876007 +	LASTZ	4	AGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ATGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droYak2	chr3L:11719778-11719883 +	LASTZ	4	CGG---------------------------------------------------AACGCTCGATACCTTTATCAGTTGGCCGTTGG------ACGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGCTGTTTGCCGTTGGCGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droEre2	scaffold_4784:11672204-11672298 +	LASTZ	1	CGG---------------------------------------------------ACAGTTCAATA-CTTTATCAGTTGGCCGTTAG------ACGCCGTCTG---AGGAGT------TTCAGGGGTTGCGTTTGG-------------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droEug1	scf7180000409711:3565307-3565407 +	LASTZ	4	CGG---------------------------------------------------A-CGTTCGATACCTTTATCAGTTGGACGTTAG------ACACTGTCTG---AATGGTTTCAACTTCAGGGGTTGCGTTTTG-------------TGTTTG--GCTGCTGCACA-----------AA-AATTGGTC
droBia1	scf7180000302334:131835-131925 +	LASTZ	4	CGG---------------------------------------------------ACGGTTCGATACCTTTGTCAGTTGGACGTTAG------ACGCAGTCTG---AC----------TTCAGGGGTTGCGATTCG-------------CGTTTG--GCTGCTGCA-A-----------GA-AATTGGTC
droTak1	scf7180000414445:514999-515100 -	LASTZ	4	GTGCG--------------------------GATTG----GG------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCTGTCTG---AA---T------TTCAGGGGTTGCGTTTCG-------------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droEle1	scf7180000490993:2107331-2107434 -	LASTZ	4	GGA---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTCAG------ACGCTGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------CGTTTG--GCTGCTGCACAGAAACAACATAGA-AATTGGTC
droRho1	scf7180000767448:131229-131349 -	LASTZ	4	ACACAAACTGCGA------------------GATTG----GA------------TTCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCGGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------TGTTTG--GCTGCTGCACAGAAACAACACAGA-AATTGGTC
droFic1	scf7180000454113:3011634-3011728 -	LASTZ	4	CGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGAACGTTAG------ACGCGGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------CCTTTG--GCTGCTGCACG---------CAGA-AATTGGTC
droKik1	scf7180000302391:1149742-1149835 -	LASTZ	4	TTG---------------------------------------------------ATCGTTCAACTTCTTTATCAGTTAAACGTTAG------ACGCCGTCTG---AT---T-CCGA-GTCTAGGGGTGTGTTTT--------------CGTTTG--GCTGCTGCA-------------GA-AATTGGTC
droAna3	scaffold_13337:5952676-5952761 +	LASTZ	4	CGG---------------------------------------------------ATCGTTCGACACCTTTATCAGTTGGACGTTAG------ACGCCTTCTG---AC----------TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA-----------GA-AATTGGTC
droBip1	scf7180000396518:16786-16877 +	LASTZ	4	TGTTT-----------------------------TG----GC------------ATCGTTCGACACCTTTATCAGTTGGACGTTAG------ACGCCTACTG---AC----------TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA-----------GA-AATTGGTC
dp4	chrXR_group6:10003251-10003350 -	LASTZ	5	CAAAC--------------------------GAGTG----CC------------AACTTCTAGCTTCTATGCCGCGTGAACGTTAA------GTGCTGTCTG---GG----------TTCGGGGGTTGCGCCTGC-------------TGCT----GCTGCTGCACA-----------GAAAATTGGTC
droPer1	super_61:283689-283791 -	LASTZ	5	CAAAC--------------------------GAGTG----CC------------AACTTCTAGCTTCTATGCCGCGTGAACGTTAA------GTGCTGTCTG---GG----------TTCGGGGGTTGCGCCTGC-------------TGCT-GCTGCTGCTGCACA-----------GAAAATTGGTC
droWil1	scaffold_180949:2659355-2659454 -	LASTZ	5	CAGAC--------------------------TCCG----------------------GTTTATTTCTAATTTCGACTCGACGTTATCAGGTTGAACTGTCTGCTTG----C------TTCAGGGGTTGCACT-A--------------CAATTG--GTT-TTGTTTC------------G-ATTTGGTC
droVir3	scaffold_13049:23903492-23903589 -	LASTZ	5	CTGCT-----CGAAAT---AATATTTGCAATTAATGACTGTC----------------TAC------GAAAACAGTTCAAATTTAA------ATGCTGCTTG---C-----------CTCAGGGGTTG-----------------------------CTGTTGCACG-----------AA-AATTGGTC
droMoj3	scaffold_6680:18531558-18531638 -	LASTZ	5	GCAAT--------------------------TAGTT----G-------------------CTGCCTCGCTAACAGTTCAAATTTAA------ATGCGG-CTA---TG----------CTCAGGGGTTGCAGT-----------------------------TGCACT---------ACGG-AATTGGTC
droGri2	scaffold_15110:9775660-9775767 +	LASTZ	5	CGTTTATCTG---GCTGTGTGTGTTTGCG---TGTGATTTTCAATTAAAACATATTCGTTCGA--------------AAATGTTGA------ATACTGCTTG---G-----------TTCGAGGGTTG-----------------------------CCGTTGCACT-----------AA-AATTGGTC

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	CGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGC-------------CGTTTG--GCTGCTGCACA-----------AA-TTTTGGTC
droSim1	CGG---------------------------------------------------ATCGTGCGATACCTTTATCAGTTGGACGTTAG------ACGCCGTCTG---AA---T------TTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droSec1	AGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ATGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droYak2	CGG---------------------------------------------------AACGCTCGATACCTTTATCAGTTGGCCGTTGG------ACGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGCTGTTTGCCGTTGGCGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droEre2	CGG---------------------------------------------------ACAGTTCAATA-CTTTATCAGTTGGCCGTTAG------ACGCCGTCTG---AGGAGT------TTCAGGGGTTGCGTTTGG-------------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droEug1	CGG---------------------------------------------------A-CGTTCGATACCTTTATCAGTTGGACGTTAG------ACACTGTCTG---AATGGTTTCAACTTCAGGGGTTGCGTTTTG-------------TGTTTG--GCTGCTGCACA-----------AA-AATTGGTC
droBia1	CGG---------------------------------------------------ACGGTTCGATACCTTTGTCAGTTGGACGTTAG------ACGCAGTCTG---AC----------TTCAGGGGTTGCGATTCG-------------CGTTTG--GCTGCTGCA-A-----------GA-AATTGGTC
droTak1	GTGCG--------------------------GATTG----GG------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCTGTCTG---AA---T------TTCAGGGGTTGCGTTTCG-------------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droEle1	GGA---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTCAG------ACGCTGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------CGTTTG--GCTGCTGCACAGAAACAACATAGA-AATTGGTC
droRho1	ACACAAACTGCGA------------------GATTG----GA------------TTCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCGGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------TGTTTG--GCTGCTGCACAGAAACAACACAGA-AATTGGTC
droFic1	CGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGAACGTTAG------ACGCGGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------CCTTTG--GCTGCTGCACG---------CAGA-AATTGGTC
droKik1	TTG---------------------------------------------------ATCGTTCAACTTCTTTATCAGTTAAACGTTAG------ACGCCGTCTG---AT---T-CCGA-GTCTAGGGGTGTGTTTT--------------CGTTTG--GCTGCTGCA-------------GA-AATTGGTC
droAna3	CGG---------------------------------------------------ATCGTTCGACACCTTTATCAGTTGGACGTTAG------ACGCCTTCTG---AC----------TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA-----------GA-AATTGGTC
droBip1	TGTTT-----------------------------TG----GC------------ATCGTTCGACACCTTTATCAGTTGGACGTTAG------ACGCCTACTG---AC----------TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA-----------GA-AATTGGTC
dp4	CAAAC--------------------------GAGTG----CC------------AACTTCTAGCTTCTATGCCGCGTGAACGTTAA------GTGCTGTCTG---GG----------TTCGGGGGTTGCGCCTGC-------------TGCT----GCTGCTGCACA-----------GAAAATTGGTC
droPer1	CAAAC--------------------------GAGTG----CC------------AACTTCTAGCTTCTATGCCGCGTGAACGTTAA------GTGCTGTCTG---GG----------TTCGGGGGTTGCGCCTGC-------------TGCT-GCTGCTGCTGCACA-----------GAAAATTGGTC
droWil1	CAGAC--------------------------TCCG----------------------GTTTATTTCTAATTTCGACTCGACGTTATCAGGTTGAACTGTCTGCTTG----C------TTCAGGGGTTGCACT-A--------------CAATTG--GTT-TTGTTTC------------G-ATTTGGTC
droVir3	CTGCT-----CGAAAT---AATATTTGCAATTAATGACTGTC----------------TAC------GAAAACAGTTCAAATTTAA------ATGCTGCTTG---C-----------CTCAGGGGTTG-----------------------------CTGTTGCACG-----------AA-AATTGGTC
droMoj3	GCAAT--------------------------TAGTT----G-------------------CTGCCTCGCTAACAGTTCAAATTTAA------ATGCGG-CTA---TG----------CTCAGGGGTTGCAGT-----------------------------TGCACT---------ACGG-AATTGGTC
droGri2	CGTTTATCTG---GCTGTGTGTGTTTGCG---TGTGATTTTCAATTAAAACATATTCGTTCGA--------------AAATGTTGA------ATACTGCTTG---G-----------TTCGAGGGTTG-----------------------------CCGTTGCACT-----------AA-AATTGGTC

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

CGG---------------------------------------------------ATCGTGCGATACCTTTATCAGTTGGACGTTAG------ACGCCGTCTG---AA---T------TTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................................................................................................................GCGTTTGC------CGTTTG--GCTG.............................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

AGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ATGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

CGG---------------------------------------------------AACGCTCGATACCTTTATCAGTTGGCCGTTGG------ACGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGCTGTTTGCCGTTGGCGTTTG--GCTGCTGCACA-----------GA-AATTGGTC

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

CGG---------------------------------------------------ACAGTTCAATA-CTTTATCAGTTGGCCGTTAG------ACGCCGTCTG---AGGAGT------TTCAGGGGTTGCGTTTGG-------------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
............................................................................................................AGT------ATCAGGGGGTGCGTT.........................................................	18	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................TTGCGTTTGG-------------CGTTTG--TT...............................	18	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................TG---AGGAGx------TTCAGGGGTTC.............................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................GTTTGCGTTTxG-------------CGTTTG--GCTG.............................	21	1	1.00	0.00	0.00	0.00	1.00

droEug1

CGG---------------------------------------------------A-CGTTCGATACCTTTATCAGTTGGACGTTAG------ACACTGTCTG---AATGGTTTCAACTTCAGGGGTTGCGTTTTG-------------TGTTTG--GCTGCTGCACA-----------AA-AATTGGTC

Size

Hit Count

Total Norm

droBia1

CGG---------------------------------------------------ACGGTTCGATACCTTTGTCAGTTGGACGTTAG------ACGCAGTCTG---AC----------TTCAGGGGTTGCGATTCG-------------CGTTTG--GCTGCTGCA-A-----------GA-AATTGGTC

Size

Hit Count

Total Norm

droTak1

GTGCG--------------------------GATTG----GG------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCTGTCTG---AA---T------TTCAGGGGTTGCGTTTCG-------------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC

Size

Hit Count

Total Norm

droEle1

GGA---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTCAG------ACGCTGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------CGTTTG--GCTGCTGCACAGAAACAACATAGA-AATTGGTC

Size

Hit Count

Total Norm

droRho1

ACACAAACTGCGA------------------GATTG----GA------------TTCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCGGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------TGTTTG--GCTGCTGCACAGAAACAACACAGA-AATTGGTC

Size

Hit Count

Total Norm

droFic1

CGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGAACGTTAG------ACGCGGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------CCTTTG--GCTGCTGCACG---------CAGA-AATTGGTC

Size

Hit Count

Total Norm

droKik1

TTG---------------------------------------------------ATCGTTCAACTTCTTTATCAGTTAAACGTTAG------ACGCCGTCTG---AT---T-CCGA-GTCTAGGGGTGTGTTTT--------------CGTTTG--GCTGCTGCA-------------GA-AATTGGTC

Size

Hit Count

Total Norm

droAna3

CGG---------------------------------------------------ATCGTTCGACACCTTTATCAGTTGGACGTTAG------ACGCCTTCTG---AC----------TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA-----------GA-AATTGGTC

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

TGTTT-----------------------------TG----GC------------ATCGTTCGACACCTTTATCAGTTGGACGTTAG------ACGCCTACTG---AC----------TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA-----------GA-AATTGGTC

Size

Hit Count

Total Norm

dp4

CAAAC--------------------------GAGTG----CC------------AACTTCTAGCTTCTATGCCGCGTGAACGTTAA------GTGCTGTCTG---GG----------TTCGGGGGTTGCGCCTGC-------------TGCT----GCTGCTGCACA-----------GAAAATTGGTC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CAAAC--------------------------GAGTG----CC------------AACTTCTAGCTTCTATGCCGCGTGAACGTTAA------GTGCTGTCTG---GG----------TTCGGGGGTTGCGCCTGC-------------TGCT-GCTGCTGCTGCACA-----------GAAAATTGGTC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................................................................................................C-------------TGCT-GCAGCTGCTGAAC.......................	18	22	0.09	0.00	0.00	0.00	0.00	0.09
..............................................................................................................................TGCGCCGGA-------------TGCT-GCTGCTG.............................	20	11	0.09	0.00	0.00	0.00	0.09	0.00
............................................................................................GTGCTGxCTG---GG----------ATCGGGG.................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

CAGAC--------------------------TCCG----------------------GTTTATTTCTAATTTCGACTCGACGTTATCAGGTTGAACTGTCTGCTTG----C------TTCAGGGGTTGCACT-A--------------CAATTG--GTT-TTGTTTC------------G-ATTTGGTC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.............................................................ATTTCGAATTTCGGCTCG..............................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.............................................................ATTTCTAATTTCGAGTTGA.............................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................................................................ACTTTATCAGGTTGAAGT............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

CTGCT-----CGAAAT---AATATTTGCAATTAATGACTGTC----------------TAC------GAAAACAGTTCAAATTTAA------ATGCTGCTTG---C-----------CTCAGGGGTTG-----------------------------CTGTTGCACG-----------AA-AATTGGTC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...........................................................................................................................GGTTG-----------------------------CGGTTGCAAG-----------AA-AA......	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

GCAAT--------------------------TAGTT----G-------------------CTGCCTCGCTAACAGTTCAAATTTAA------ATGCGG-CTA---TG----------CTCAGGGGTTGCAGT-----------------------------TGCACT---------ACGG-AATTGGTC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....................................................................TAACAGTTTAAAGTTAA------A................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droGri2

CGTTTATCTG---GCTGTGTGTGTTTGCG---TGTGATTTTCAATTAAAACATATTCGTTCGA--------------AAATGTTGA------ATACTGCTTG---G-----------TTCGAGGGTTG-----------------------------CCGTTGCACT-----------AA-AATTGGTC

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:35:37 EDT

sblock103084

chr3L:11689515-11689577 +

Candidate

antisense_to_5pUTR

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