ID:

dsi_229

Coordinate:

2L:1683143-1683180 +

Confidence:

Candidate

Type:

Unknown

[View on UCSC Genome Browser {Cornell Mirror}]

Legend:

mature

star

mismatch in alignment

mismatch in read

Predicted structure

-28.2	-27.5	-27.5

Flybase annnotation

intergenic

Repeatable elements

Name	Class	Family
(CA)n	Simple_repeat	Simple_repeat

Sense Strand Reads

ACCAATGCAAACACCCACACAAGCACACGCACGCGCCCCACACAAGCACACACACACACACATTGCTTGTGTATGTGGGTGTGTGTGTGTATACAAGGCATACGAACGCAAGCTGCAAAAGTGCGTTCGGAAACAGAA *********************************..((......((((((((((((.(((((.((....))))))).))))))))))))......)).....*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	O001 Testis
..................................................CACACACACACATTGCTT......................................................................	18	0	4	3.00	12	12
................................................................GCTTGTGTATGTGGGTGT........................................................	18	0	1	1.00	1	1
..........................ACGCCCGGGCCCCACA................................................................................................	16	2	18	0.06	1	0
.......................................................................TATGTTGGTGTGTGTGTG.................................................	18	1	20	0.05	1	0
.................................................................................................................TGCAAAAGTGCGTTTGTA.......	18	2	20	0.05	1	0

Anti-sense strand reads

TTCTGTTTCCGAACGCACTTTTGCAGCTTGCGTTCGTATGCCTTGTATACACACACACACCCACATACACAAGCAATGTGTGTGTGTGTGTGCTTGTGTGGGGCGCGTGCGTGTGCTTGTGTGGGTGTTTGCATTGGT *********************************.....((......((((((((((((.(((((((....)).))))).))))))))))))......))..*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total
...................................................................................................GGGGCGCCTGCGTGT........................	15	1	6	0.17	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droSim3	2L:1683093-1683230 +	dsi_229	ACCAATGCAAACAC----------CCA------------------------------------------CACAAGCAC-A------------------------------CGCACGCGCCCCACA------CAAGCACAC--ACACACAC--ACATTGCTTGTG--------TAT-------------------GTGGGTGTGTGT-----GTG--TATAC-A-AGGCATACGAACGCAAGCTGCAAAAGTGCGTTCGG---AAACAGAA
droSec2	scaffold_14:1591786-1591921 +		ACCAATGCAAACAC----------CCA------------------------------------------CACAAGCAC-A------------------------------CGCACGCGCCCCACA------CAAGCACAC--ACACACAC----ATTGTTTGTG--------TAT-------------------GTGTGTGTGTGT-----GTG--TATAC-A-AGGCATACGAACGCAAGCTGCAAAAGTGCGTTCGG---AAACAGAA
dm3	chr2L:1649067-1649196 +		ACCAATGCAAACAC----------CCA------------------------------------------CACAACCAC-A------------------------------CGCACGCGCCCCACA------CAAGCACAC--ACACACAGAC------GTTGTGTGTAT--GTG----------------------------------CGTGTG--TATAC-A-AGGCATACGAACGCAAGCTGCAAAAGTGCGTTCGG---AAACAGAA
droEre2	scaffold_4929:1698469-1698600 +		ACCAATGCAAACAC----------CCA------------------------------------------CACAACCAC-A------------------------------CGCACGCGCCCCACA------CAAGCACAC--ACACACACACGCACTCATTGTG----T--GTG----------------------------------GGTGTG--TATAC-A-AGGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA
droYak3	2L:1624156-1624289 +		ACCAATGCAAACAC----------CCA------------------------------------------CACAACCAC-A------------------------------CGCACGCGCCCCACA------CAAGCACAC--ACACACACACACATTGA----GTGTATGTGGG----------------------------------TGTGTG--TATAC-A-AGGCATACAAACGCAAGCTGCAGAAGTGCGTTCGA---AAACAGAA
droEug1	scf7180000407252:136371-136508 -		ACCAATGCAAACAC--------ACCCA------------------------------------------CACAACCACAA------------------------------CGCACGCGCCCCACACAC----AAATA----------C--AAGGAATGTCTGTG--------TGT-------------------GTGCTTGAGTTTGT---GTT--TATAC-AAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA
droBia1	scf7180000302188:160512-160641 -		ACCAATGCAAACAC----------CCA------------------------------------------CACAACCACAA------------------------------CGCACGCGCCCCACACAC--------------AGATAC------AGAGTTTGCG--------GGA-------------------GTGTGTGTGTCG-----CTG--TATAC-AAAGGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA
droTak1	scf7180000415779:57497-57619 +		ACCAATGCAAACAC----------CCA------------------------------------------CACAATCAC-A------------------------------CGCACGCGCCCCACA------C----------ACACAGATACGGTGCGATTGT--------GTG----------------------------------TGTGTG--TATAC-AAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA
droEle1	scf7180000491273:1727164-1727287 -		ACCAATGCAAACAC----------ACA------------------------------------------CACAAGCGCAA------------------------------CGCACGCGCCCCACA------CAAATACAT--AGACACAC----AGTATC------------TG----------------------------------TGTGTA--TATGG-AAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCAA---AAACAGAA
droRho1	scf7180000767698:404-525 +		ACCAATGCAAACAC----------ACA-------------------------------C-----ACACACACAACAGCAA------------------------------CGCACGCGCCCCACA------CAAATACA----------------GTATCT----------GTG----------------------------------TGTGTA--TATAG-AAGAGCATACAAACGCAAGCTGCAAAAGTGCGTTCAA---AAACAGAA
droFic1	scf7180000448848:123-246 +		ACCAATGCAAACACTCGCACTCACGCA------------------------------------------CACAACCGCAA------------------------------CGCACGCGCCCCACA------CAAACACAC--GTACACA------------------------------------------------------------GTGTG--TATAC-AAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA
droKik1	scf7180000302643:882873-882990 -		ACCAATGCAAACAC----------ACA-------------------------------AATACAACACACACATACAT-A------------------------------CGCACGCGCCGCACTCAC------ATACC--------C------------------------------------------------------------C--GTA--TATACTAAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCGAA--AAACAGAA
droBip1	scf7180000396572:1957527-1957660 -		ACCAATACAAACAC----------ATA------------------------------------------GA-------------------CGCACAAAAACCAATACAAACGCACGCGCCCCACA------CAAACACCC--GAACATACA---------------------TAT--------ATAGTAAGCCC--------------AGTACA--TATAC---AAATATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AA------
dp5	4_group2:543412-543591 -		ACCAATACACA--------------GGCAAAAGTAAGGGCGCGTGTCGCACACAAACG-----------CGCACACAC-CTACACATAGACTCATACATACTCATATTTTCGTACATACCATACATAC-------------------------------ATATG--------TATGTACATACATA----------------------CATACA--TACAT-ACATATATACAAACGCAAGCTGCAAAAGTGCGTTCCCCATAGAGAATG
droPer2	scaffold_8:3347445-3347612 +		ACCAATACACA--------------GGCAAAAGTAAGGGCGCGTGTCGCACACAAACG-----------CACACACAC-CTACACATAGACTCATACATACTCATATATTCGTACATACCATACATAC--------ATAT--G-----------------------------TA----------------------------------CATACA--TACAT-ACATATATACAAACGCAAGCTGCAAAAGTGCGTTCCCCATAGAGAATG
droWil2	scf2_1100000004521:3509227-3509329 +		AC----------AC----------ACA------------------------------------------CACAAACAA-A------------------------------CGCACGCGCCCCACACACACATATACGCAC--ACACACACACGCACA--------------------------------------------CATTT-----ATGTAT-----------ATACAAGCGCAAGCTGCAAAAGTGCGTTC-------------
droVir3	scaffold_12970:10205657-10205743 +		TCCAGT----------------------------------------CGCATACACACA-----------CGCACACAC-GCACACACGCACA---------------------------CCTACA------CACACACAC--AC------ACACATAGCCTGTG--------TGC-------------------GTGTGTGTGCCT-----G----------------------------------------------------------
droMoj3	scaffold_6500:27080503-27080633 +		ACACACACACACAC----------ACA------------------------------------------CACACACAC-A------------------------------CACACACAC---A--------CACACACACACACACAC--ACACAATACATGTG--------TGT-------------------ATGTATAT---------GTG--TATAT-AAAGATATATATACATATG-TACATAAGTACGCCCAC---ATACACAG
droGri2	scaffold_15110:13283685-13283783 +		ACTAACGCACACAC----------ACA------------------------------------------CCAACACAC-ACACACGG-----------------------------AGACACACA------CACACGCAC--ACACACATACTCACTACTTGTG--------TGT-------------------GTGTGTGTGTGT-------------------------------------------GTGTGTGCGA-----------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSim3

ACCAATGCAAACAC----------CCA------------------------------------------CACAAGCAC-A------------------------------CGCACGCGCCCCACA------CAAGCACAC--ACACACAC--ACATTGCTTGTG--------TAT-------------------GTGGGTGTGTGT-----GTG--TATAC-A-AGGCATACGAACGCAAGCTGCAAAAGTGCGTTCGG---AAACAGAA	Size	Hit Count	Total Norm	Total	V044 Embryo	M023 Head	M024 Male-body	M025 Embryo	O001 Testis	O002 Head	M053 Female-body	SRR553485 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553488 Ovary	SRR618934 Ovary
...........................................................................................................................................C--ACACACAC--ACATTGCTT.............................................................................................................	18	4	3.00	12	0	0	0	0	12	0	0	0	0	0	0	0
.............................................................................................................................................................GCTTGTG--------TAT-------------------GTGGGTGT....................................................................	18	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0

droSec2

ACCAATGCAAACAC----------CCA------------------------------------------CACAAGCAC-A------------------------------CGCACGCGCCCCACA------CAAGCACAC--ACACACAC----ATTGTTTGTG--------TAT-------------------GTGTGTGTGTGT-----GTG--TATAC-A-AGGCATACGAACGCAAGCTGCAAAAGTGCGTTCGG---AAACAGAA	Size	Hit Count	Total Norm	Total	V113 Male-body	V114 Embryo	V115 Head	M054 Female-body
No Reads

droEre2

ACCAATGCAAACAC----------CCA------------------------------------------CACAACCAC-A------------------------------CGCACGCGCCCCACA------CAAGCACAC--ACACACACACGCACTCATTGTG----T--GTG----------------------------------GGTGTG--TATAC-A-AGGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA	Size	Hit Count	Total Norm	Total	V040 Embryo	V060 Head	V107 Male-body	V108 Head	M055 Female-body	M057 Embryo
No Reads

droYak3

ACCAATGCAAACAC----------CCA------------------------------------------CACAACCAC-A------------------------------CGCACGCGCCCCACA------CAAGCACAC--ACACACACACACATTGA----GTGTATGTGGG----------------------------------TGTGTG--TATAC-A-AGGCATACAAACGCAAGCTGCAGAAGTGCGTTCGA---AAACAGAA	Size	Hit Count	Total Norm	Total	V046 Embryo	V052 Head	V120 Male-body	V058 Head	M026 Head	M043 Female-body	M056 Embryo
No Reads

droEug1

ACCAATGCAAACAC--------ACCCA------------------------------------------CACAACCACAA------------------------------CGCACGCGCCCCACACAC----AAATA----------C--AAGGAATGTCTGTG--------TGT-------------------GTGCTTGAGTTTGT---GTT--TATAC-AAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA	Size	Hit Count	Total Norm	Total
No Reads

droBia1

ACCAATGCAAACAC----------CCA------------------------------------------CACAACCACAA------------------------------CGCACGCGCCCCACACAC--------------AGATAC------AGAGTTTGCG--------GGA-------------------GTGTGTGTGTCG-----CTG--TATAC-AAAGGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

ACCAATGCAAACAC----------CCA------------------------------------------CACAATCAC-A------------------------------CGCACGCGCCCCACA------C----------ACACAGATACGGTGCGATTGT--------GTG----------------------------------TGTGTG--TATAC-AAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA	Size	Hit Count	Total Norm	Total
No Reads

droEle1

ACCAATGCAAACAC----------ACA------------------------------------------CACAAGCGCAA------------------------------CGCACGCGCCCCACA------CAAATACAT--AGACACAC----AGTATC------------TG----------------------------------TGTGTA--TATGG-AAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCAA---AAACAGAA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

ACCAATGCAAACAC----------ACA-------------------------------C-----ACACACACAACAGCAA------------------------------CGCACGCGCCCCACA------CAAATACA----------------GTATCT----------GTG----------------------------------TGTGTA--TATAG-AAGAGCATACAAACGCAAGCTGCAAAAGTGCGTTCAA---AAACAGAA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

ACCAATGCAAACACTCGCACTCACGCA------------------------------------------CACAACCGCAA------------------------------CGCACGCGCCCCACA------CAAACACAC--GTACACA------------------------------------------------------------GTGTG--TATAC-AAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AAACAGAA	Size	Hit Count	Total Norm	Total
No Reads

droKik1

ACCAATGCAAACAC----------ACA-------------------------------AATACAACACACACATACAT-A------------------------------CGCACGCGCCGCACTCAC------ATACC--------C------------------------------------------------------------C--GTA--TATACTAAAAGCATACAAACGCAAGCTGCAAAAGTGCGTTCGAA--AAACAGAA	Size	Hit Count	Total Norm	Total
No Reads

droBip1

ACCAATACAAACAC----------ATA------------------------------------------GA-------------------CGCACAAAAACCAATACAAACGCACGCGCCCCACA------CAAACACCC--GAACATACA---------------------TAT--------ATAGTAAGCCC--------------AGTACA--TATAC---AAATATACAAACGCAAGCTGCAAAAGTGCGTTCGA---AA------	Size	Hit Count	Total Norm	Total
No Reads

dp5

ACCAATACACA--------------GGCAAAAGTAAGGGCGCGTGTCGCACACAAACG-----------CGCACACAC-CTACACATAGACTCATACATACTCATATTTTCGTACATACCATACATAC-------------------------------ATATG--------TATGTACATACATA----------------------CATACA--TACAT-ACATATATACAAACGCAAGCTGCAAAAGTGCGTTCCCCATAGAGAATG	Size	Hit Count	Total Norm	Total	V112 Male-body	V043 Embryo	V051 Head	M022 Male-body	M040 Female-body	M059 Embryo	M062 Head
No Reads

droPer2

ACCAATACACA--------------GGCAAAAGTAAGGGCGCGTGTCGCACACAAACG-----------CACACACAC-CTACACATAGACTCATACATACTCATATATTCGTACATACCATACATAC--------ATAT--G-----------------------------TA----------------------------------CATACA--TACAT-ACATATATACAAACGCAAGCTGCAAAAGTGCGTTCCCCATAGAGAATG	Size	Hit Count	Total Norm	Total	V111 Male-body	V042 Embryo	V050 Head	V057 Head	M021 Embryo	M042 Female-body
...........................................................................CAC-CTACACATAGACTCATAC.............................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0

droWil2

AC----------AC----------ACA------------------------------------------CACAAACAA-A------------------------------CGCACGCGCCCCACACACACATATACGCAC--ACACACACACGCACA--------------------------------------------CATTT-----ATGTAT-----------ATACAAGCGCAAGCTGCAAAAGTGCGTTC-------------	Size	Hit Count	Total Norm	Total	V117 Male-body	V118 Embryo	V119 Head	M020 Head	M045 Female-body
No Reads

droVir3

TCCAGT----------------------------------------CGCATACACACA-----------CGCACACAC-GCACACACGCACA---------------------------CCTACA------CACACACAC--AC------ACACATAGCCTGTG--------TGC-------------------GTGTGTGTGCCT-----G----------------------------------------------------------	Size	Hit Count	Total Norm	Total	V116 Male-body	V053 Head	V047 Embryo	M027 Male-body	M028 Head	M047 Female-body	M061 Embryo	SRR060654 Ovary	SRR060655 Testis	SRR060656 Ovary	SRR060657 Testis	SRR060658 Ovary	SRR060659 Testis	SRR060660 Ovary	SRR060661 Embryo	SRR060662 Embryo	SRR060663 Embryo	SRR060664 Male-body	SRR060665 Female-body	SRR060666 Male-body	SRR060667 Female-body	SRR060668 Male-body	SRR060669 Female-body	SRR060670 Testis	SRR060671 Male-body	SRR060672 Female-body	SRR060673 Ovary	SRR060674 Ovary	SRR060675 Ovary	SRR060676 Ovary	SRR060677 Ovary	SRR060678 Testis	SRR060679 Testis	SRR060680 Testis	SRR060681 Testis	SRR060682 Embryo	SRR060683 Testis	SRR060684 Embryo	SRR060685 Embryo	SRR060686 Embryo	SRR060687 Embryo	SRR060688 Ovary	SRR060689 Testis
.....T----------------------------------------CGCATACACACA-----------CGCACAC..................................................................................................................................................................................................	20	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................................................................TGTG--------TGC-------------------GTGTGTGTGCC.................................................................	18	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................CACAC-GCACACACGCACA---------------------------C......................................................................................................................................................	19	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0

droMoj3

ACACACACACACAC----------ACA------------------------------------------CACACACAC-A------------------------------CACACACAC---A--------CACACACACACACACAC--ACACAATACATGTG--------TGT-------------------ATGTATAT---------GTG--TATAT-AAAGATATATATACATATG-TACATAAGTACGCCCAC---ATACACAG	Size	Hit Count	Total Norm	Total	V110 Male-body	V056 Head	V049 Head	V041 Embryo	M046 Female-body	M060 Embryo
No Reads

droGri2

ACTAACGCACACAC----------ACA------------------------------------------CCAACACAC-ACACACGG-----------------------------AGACACACA------CACACGCAC--ACACACATACTCACTACTTGTG--------TGT-------------------GTGTGTGTGTGT-------------------------------------------GTGTGTGCGA-----------	Size	Hit Count	Total Norm	Total	V109 Male-body	M041 Female-body
.......CACACAC----------ACA------------------------------------------CCAACACAC-A..............................................................................................................................................................................................	20	20	0.05	1	0	1

Generated: 12/06/2013 at 02:35 PM