ID:

dvi_14681

Coordinate:

scaffold_13042:4118160-4118310 +

Confidence:

Candidate

Type:

Unknown

[View on UCSC Genome Browser {Cornell Mirror}]

Legend:

mature

star

mismatch in alignment

mismatch in read

Predicted structure

-18.8	-18.8	-18.8	-18.3

Flybase annnotation

CDS [Dvir\GJ15991-cds]; exon [dvir_GLEANR_16415:2]; intron [Dvir\GJ15991-in]

Repeatable elements

Name	Class	Family	Strand
Helitron-2N1_DVir	RC	Helitron	-

mature

star

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------################################################## GAGCTATAGAGCTAAGGCAGTGTTAGGACTCGGCTCAGATGTAGGCATCCTTCCTATTGCAGCTATATGATATAGTGCTTCGATGTGGACAATCTTGGAGATAATAGTAAAACTTTTAAATTCTGAGTTTGTTTAAGATATCTTGATAAACAAGAAAGCTTTCCTACTTGTCGACCGATTCCTTTTATGTATATTATATAGTCGTCCGATCCGGCAGACATATGGCCTGCATCGGAAAGATGGACCCAAGC ***************************************************************...((..............((.(((((....(((((....................(((..(((((.(((((....)))))))))).)))....)))))...))))).))....))********************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	GSM1528803 follicle cells	M028 head	SRR060689 160x9_testes_total	V116 male body	SRR060681 Argx9_testes_total	M047 female body	SRR060668 160x9_males_carcasses_total
............................................................................................................................................................AGCTTTCCTACTTGTCGACCGATTC......................................................................	25	0	1	1.00	1	1	0	0	0	0	0	0
............................................................................................................................................................AGCTTTCCTACTTGTCGAACGATTC......................................................................	25	1	1	1.00	1	1	0	0	0	0	0	0
.........................................................................AGTTCTTCGATGTGGACACTCT............................................................................................................................................................	22	2	2	0.50	1	0	1	0	0	0	0	0
.................................................................TATGATATAGTGCTTCGATGTGGACAA...............................................................................................................................................................	27	0	2	0.50	1	0	0	1	0	0	0	0
........................AGGACTGGGCTGAGATGT.................................................................................................................................................................................................................	18	2	3	0.33	1	0	0	0	1	0	0	0
..........................................................................GTTCTTCGATGTGGACACT..............................................................................................................................................................	19	2	6	0.17	1	0	0	0	0	1	0	0
......................................................................................GGGAAATCTTGGAGATAATC.................................................................................................................................................	20	3	20	0.05	1	0	0	0	0	0	1	0
......................................................................................................................................................CAAGGAAGCCTTCCAACTT..................................................................................	19	3	20	0.05	1	0	0	0	0	0	0	1

Anti-sense strand reads

CTCGATATCTCGATTCCGTCACAATCCTGAGCCGAGTCTACATCCGTAGGAAGGATAACGTCGATATACTATATCACGAAGCTACACCTGTTAGAACCTCTATTATCATTTTGAAAATTTAAGACTCAAACAAATTCTATAGAACTATTTGTTCTTTCGAAAGGATGAACAGCTGGCTAAGGAAAATACATATAATATATCAGCAGGCTAGGCCGTCTGTATACCGGACGTAGCCTTTCTACCTGGGTTCG ********************************************************************...((..............((.(((((....(((((....................(((..(((((.(((((....)))))))))).)))....)))))...))))).))....))***************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060679 140x9_testes_total	SRR060678 9x140_testes_total	SRR060659 Argentina_testes_total	V047 embryo	V053 head	SRR060680 9xArg_testes_total	SRR060681 Argx9_testes_total
....................................TCTACATCCGTAGGAAGGATAACGT..............................................................................................................................................................................................	25	0	2	1.00	2	1	1	0	0	0	0	0
.............................................GTAGGAAGGATAACGTCGATA.........................................................................................................................................................................................	21	0	2	0.50	1	0	0	1	0	0	0	0
........................................................................................TGGTACAACCTCTATCATCA...............................................................................................................................................	20	3	5	0.20	1	0	0	0	1	0	0	0
..............................................GAGGTAGGATAACGTCAATATACTAT...................................................................................................................................................................................	26	3	20	0.10	2	1	0	0	0	0	1	0
....................................................GGATAACGTCGATATACTAT...................................................................................................................................................................................	20	0	20	0.10	2	2	0	0	0	0	0	0
..............................................................................................................CTGAAGATTTAAGACTCA...........................................................................................................................	18	2	13	0.08	1	0	0	0	0	1	0	0
................................................GGTAGGATAACGTCAATATACTATA..................................................................................................................................................................................	25	2	20	0.05	1	0	1	0	0	0	0	0
...................................................AGGATAACGTCGATATACTA....................................................................................................................................................................................	20	0	20	0.05	1	0	0	0	0	0	0	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_13042:4118110-4118360 +	dvi_14681	GAGCTATAGAGC---TAA-------GGCAGTGTTAGGA-----------------------CTCGGCTCAGATGTAG--GCATCCTTCCTATTGCAGCTATATGATATAGTGCTTCGATGTGGACAATCTTG--------------------------------------GAGATA--A-TAGTAAAACTTTT----------AAATTCTGAGTTTGTTTAAGATA------------------------TCTTGATAAACAAGAAAGCT----------TTCCTAC------------TTGTCGACCGATTCCTTTTAT-----GTATATTATATAGTCGTCCGATCCGGCA----------GACATATGG-CCTGCATCGGAAA----GATGGACCCAAGC
droGri2	scaffold_15203:8268556-8268731 -		AT---------------------------------------------------------------------------------TGTTCCTATGGCAGCTATATAATATAGTAGTCCGATGTGACTGATTTTT------------------------------------TGTCCATGTGTG---CAGCACATAATTGAACGCATATTCATTAAGTTTGGTTCGAATA------------------------TTTTGTTA--------------------------CAAGAACTC------ACTTTCACCGATCATTCCTATGGCATCTATATGATACAGTTATCCGATCCGAC---------------------------------------------------
droWil2	scf2_1100000004866:27812-28048 -		AG-TTATTGACA---AAA-------GTCACTG---------------------------------------TTTTCGACCGATCGTTCCTCTGGGAGCTATATGATATAGTCACCCGACCTTGATCAAATTT------------------------------------GGCAGAGGCGTATAAT-AAACTCTC----------CAATATTAAATTTCATGAGAATA------------------------GCTCAGAAAATAACGAAGTT----------ATTGAGAAAAGTCACTG-TTAGTGACATTGCCGTTTGTATGGGAGGTATATGATATAGTGGTCCGATCCGGCT----------GATATAGTGGTCTACA------------------------
droAna3	scaffold_13417:3829579-3829785 -		--------------------------------------------------------------------------------------TTCTATGACGGCTATAGGATATAGTCGGCAGATCCTTATACAATTT------------------------------------TTCAGATA--A-GAT-----ATCTT----AAATTTAACTTGTGTGCAAAGTCCCTCTA------------------------GCTCGAAAAACACCAAAGTT----------ATGAC-------------ATTTCCGATCAATCAGTTATATGGCATATATATGATATAGTCGACCGATCCGACT----------TATATACTA-CCTGCAAGGAAAA----AAAGGATGTGTGC
droBip1	scf7180000395214:8332-8531 -		AT---------------------------------------------------------------------------------TTTTGCTATGACAGCTGTATGATATAGTTTTCCGATTTGGACTATATTT------------------------------------GGCAA--------------------------GCATAGTTTGTATGTTAGGTTTACATA------------------------TCTTGAAAAACAAAAAATTT----------TTTCCTACTATATACTT-ATTTCTATCCTATCGTTCCTATGGCAGCTATATGATATAGTCGTACGATATGGCC----------AATTTTTTT-ACTGCATTTCAAA----TAT----------
droKik1	scf7180000301587:13299-13604 -		GTTC-------C---TAT-------GGCAGCTATAAGATATAGTCGTCCGATTTACATAAAATTTATACAAAAATTC--CGATCATTCCTATGGCAGCTATAAGATATAGTGGTCCGATTTTCATAAAATTTTAAACAAAATTCTGGAATAATATAAAATGGCTATATCTCAAAGATGA-TG--------------------------------------AAATAA------------------------TATTGAAAAACAGCCAAGTTATAATTTTTTT-TCCAA------------AAATTTATCGAACATTTGTATGGCAGCTATATGATATAGTCGTCCGATCTGGCCCGTTCCGACATATATAGCA-GTGAGAGTATATA-GAAGACGGACAGACGG
droFic1	scf7180000449205:49213-49408 +		AT---------------------------------------------------------------------------------TTTTGCTATGGCAGCTGTATGATATAGTTTTCCGATTTGGACTATATTT------------------------------------GGCAAGTATATA---TAAAACTGGTCCAGGCGTACAATCTGTAAGTTTGGTTTACATA------------------------TCTTGAAAAACAAAAAAGTT----------TTTCATACTATATACT--ATTTTTATCCTATCGTTCCTATGGCAGCTATATGATATAGGCGTACGATGTGGC---------------------------------------------------
droEle1	scf7180000491315:14317-14542 -		AT---------------------------------------------------------------------------------TGTTCCTATGGGAGCTATATGATATAATCGTCCGATTTTGATGAAATTTAAACCGTAATTCTGAAATATTTAACTAATCCTATATGTCTAAGAAG-------------------------------------------------------------------------TAAGATAAAAATTAAATTT----------T-TTTAT----------T-TATTTTTCCGATTGTTGCTATGGGAGCTATATGATATAGTCGTCCGATCCGGCTCGTTCCGACTTGTATACTA-CCTGCAATAGAAATAAAGATGGACGGAAAG
droRho1	scf7180000769384:24388-24586 -		AT-----------------------------------------------------------------------TTTG--ACATCGTTTCTATGACAGCTATATGATATAGTTGTTCGATTTTAATTTAATTAAAACCGTAATTCCATATTATCTAAAGATATCTATCTGTA-------------------------------------------------------------------------------------TA---------T----------TCT-TAAAT----------T-GTTTTTTGCGATTATTCCTATGGGAGCTATATGATATAGTCGCCCGATCCGGCT----------TATATACTA-CCTGCAATAGAAA----GACAACTTTTGAG
droBia1	scf7180000302049:53383-53636 +		CC------------------------------------------------------------------CTAATTTTG--TCATCGTTCCTATGGCAGCTATATGATATAGTCGTCCGATTTTGAAAAAATTTAATTTGAAATTCAGAACTAATTAAGAAATGTTATTTCTAAGCTTAGA-AG--------------------------------------GTAATA------------------------TGTTAAAAAGTACCGAAGATATAATTTTTTT-TAAGT------------TTTTCCTCCGATAGTTCCTATGGGAGCTATAAGATATAGTTGTCCGATCCGGCTGGTCCCGACTTGTACACTA-CCTGCAACAGAAA----GAAGGCCTTTGGA
droTak1	scf7180000415786:41288-41570 +		AATTTACAAATCGCAAAAATGTTAAT--TTTCCTATTA-----------------------TTTCTCATTAATTTTG--CGTTCGTTTCAATGGCAGCTATATGATATAGTAGTTCGATTTTGATAAA-------------------------------------TATCCTAGAGTAGA-AG--------------------------------------AAAATACAATAAAAACCAACGAATGTTATAGGTTCAAAAACACCCAAGATATAATTTTTTT-TACAT----------T-TTTTTTCCCGATTGTTCCTTTGAGAGCTATATGATATAGTTGTCCGATCCGGCTCGTTCCGACTTATATATTA-CCTGCAATAGAAA----GAAGACTTTTGGA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

GAGCTATAGAGC---TAA-------GGCAGTGTTAGGA-----------------------CTCGGCTCAGATGTAG--GCATCCTTCCTATTGCAGCTATATGATATAGTGCTTCGATGTGGACAATCTTG--------------------------------------GAGATA--A-TAGTAAAACTTTT----------AAATTCTGAGTTTGTTTAAGATA------------------------TCTTGATAAACAAGAAAGCT----------TTCCTAC------------TTGTCGACCGATTCCTTTTAT-----GTATATTATATAGTCGTCCGATCCGGCA----------GACATATGG-CCTGCATCGGAAA----GATGGACCCAAGC	Size	Hit Count	Total Norm	Total	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	SRR1106712 embryo_0-2h	SRR1106713 embryo_0-2h	SRR1106714 embryo_2-4h	SRR1106715 embryo_4-6h	SRR1106716 embryo_4-6h	SRR1106717 embryo_6-8h	SRR1106718 embryo_6-8h	SRR1106719 embryo_8-10h	SRR1106720 embryo_8-10h	SRR1106721 embryo_10-12h	SRR1106722 embryo_10-12h	SRR1106723 embryo_12-14h	SRR1106724 embryo_12-14h	SRR1106725 embryo_14-16h	SRR1106726 embryo_14-16h	SRR1106727 larvae	SRR1106728 larvae	SRR1106729 mixed whole adult body	SRR1106730 embryo_16-30h	V047 Embryo	V053 Head	V116 Male-body	GSM1528803 follicle cells
..........................................................................................................................................................................................................................................................................AGCT----------TTCCTAC------------TTGTCGACCGATTC..........................................................................................	25	1	1.00	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	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
....................................................................................................TATGATATAGTGCTTCGATGTGGACAA....................................................................................................................................................................................................................................................................................	27	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	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

droGri2

AT---------------------------------------------------------------------------------TGTTCCTATGGCAGCTATATAATATAGTAGTCCGATGTGACTGATTTTT------------------------------------TGTCCATGTGTG---CAGCACATAATTGAACGCATATTCATTAAGTTTGGTTCGAATA------------------------TTTTGTTA--------------------------CAAGAACTC------ACTTTCACCGATCATTCCTATGGCATCTATATGATACAGTTATCCGATCCGAC---------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

AG-TTATTGACA---AAA-------GTCACTG---------------------------------------TTTTCGACCGATCGTTCCTCTGGGAGCTATATGATATAGTCACCCGACCTTGATCAAATTT------------------------------------GGCAGAGGCGTATAAT-AAACTCTC----------CAATATTAAATTTCATGAGAATA------------------------GCTCAGAAAATAACGAAGTT----------ATTGAGAAAAGTCACTG-TTAGTGACATTGCCGTTTGTATGGGAGGTATATGATATAGTGGTCCGATCCGGCT----------GATATAGTGGTCTACA------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.............................................................................................................................................................................................................................................................................T----------ATTGAGAAAAGTCACTG-TTAGTG...................................................................................................	24	12	0.08	1	0	1	0	0	0

droAna3

--------------------------------------------------------------------------------------TTCTATGACGGCTATAGGATATAGTCGGCAGATCCTTATACAATTT------------------------------------TTCAGATA--A-GAT-----ATCTT----AAATTTAACTTGTGTGCAAAGTCCCTCTA------------------------GCTCGAAAAACACCAAAGTT----------ATGAC-------------ATTTCCGATCAATCAGTTATATGGCATATATATGATATAGTCGACCGATCCGACT----------TATATACTA-CCTGCAAGGAAAA----AAAGGATGTGTGC	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
....................................................................................................................................................................................................................................................................................................................................................GACCGATCCGACT----------TATATACTA-CCTGC.........................	27	1	1.00	1	1	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................TTTCCGATCAATCAGTTATATGGCAT..............................................................................	26	20	0.35	7	0	7	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................CGATCCGACT----------TATATACTA-CCTGC.........................	24	6	0.17	1	0	1	0	0	0	0
................................................................................................GCTATAGGATATAGTCGGCAGATCCT.........................................................................................................................................................................................................................................................................................	26	18	0.11	2	0	2	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................................................CCTGCAAGGAAAA----AAAGGATGTGTG.	25	20	0.10	2	1	0	1	0	0	0
...........................................................................................................................................................................................................................................................................................................................................................................TATATACTA-CCTGCAAGGAAAA----AAAGG........	27	20	0.05	1	0	1	0	0	0	0
........................................................................................................................................................................................................................................................................................................................................TATGATATAGTCGACCGATCC......................................................	21	20	0.05	1	0	0	1	0	0	0
..................................................................................................TATAGGATATAGTCGGCAGA.............................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
..........................................................................................................................................................................................................................................................................................GAC-------------ATTTCCGATCAATCAGTT.......................................................................................	21	20	0.05	1	0	0	0	0	0	1
.............................................................................................................................................................................................................................................................................................................................................................GACT----------TATATACTA-CCTGCAAGGAAA..................	25	20	0.05	1	0	1	0	0	0	0
.................................................................................................CTATAGGATATAGTCGGCAGATCCT.........................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................................A-CCTGCAAGGAAAA----AAAGGATGTGTGC	27	20	0.05	1	0	1	0	0	0	0

droBip1

AT---------------------------------------------------------------------------------TTTTGCTATGACAGCTGTATGATATAGTTTTCCGATTTGGACTATATTT------------------------------------GGCAA--------------------------GCATAGTTTGTATGTTAGGTTTACATA------------------------TCTTGAAAAACAAAAAATTT----------TTTCCTACTATATACTT-ATTTCTATCCTATCGTTCCTATGGCAGCTATATGATATAGTCGTACGATATGGCC----------AATTTTTTT-ACTGCATTTCAAA----TAT----------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

GTTC-------C---TAT-------GGCAGCTATAAGATATAGTCGTCCGATTTACATAAAATTTATACAAAAATTC--CGATCATTCCTATGGCAGCTATAAGATATAGTGGTCCGATTTTCATAAAATTTTAAACAAAATTCTGGAATAATATAAAATGGCTATATCTCAAAGATGA-TG--------------------------------------AAATAA------------------------TATTGAAAAACAGCCAAGTTATAATTTTTTT-TCCAA------------AAATTTATCGAACATTTGTATGGCAGCTATATGATATAGTCGTCCGATCTGGCCCGTTCCGACATATATAGCA-GTGAGAGTATATA-GAAGACGGACAGACGG	Size	Hit Count	Total Norm	Total
No Reads

droFic1

AT---------------------------------------------------------------------------------TTTTGCTATGGCAGCTGTATGATATAGTTTTCCGATTTGGACTATATTT------------------------------------GGCAAGTATATA---TAAAACTGGTCCAGGCGTACAATCTGTAAGTTTGGTTTACATA------------------------TCTTGAAAAACAAAAAAGTT----------TTTCATACTATATACT--ATTTTTATCCTATCGTTCCTATGGCAGCTATATGATATAGGCGTACGATGTGGC---------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AT---------------------------------------------------------------------------------TGTTCCTATGGGAGCTATATGATATAATCGTCCGATTTTGATGAAATTTAAACCGTAATTCTGAAATATTTAACTAATCCTATATGTCTAAGAAG-------------------------------------------------------------------------TAAGATAAAAATTAAATTT----------T-TTTAT----------T-TATTTTTCCGATTGTTGCTATGGGAGCTATATGATATAGTCGTCCGATCCGGCTCGTTCCGACTTGTATACTA-CCTGCAATAGAAATAAAGATGGACGGAAAG	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AT-----------------------------------------------------------------------TTTG--ACATCGTTTCTATGACAGCTATATGATATAGTTGTTCGATTTTAATTTAATTAAAACCGTAATTCCATATTATCTAAAGATATCTATCTGTA-------------------------------------------------------------------------------------TA---------T----------TCT-TAAAT----------T-GTTTTTTGCGATTATTCCTATGGGAGCTATATGATATAGTCGCCCGATCCGGCT----------TATATACTA-CCTGCAATAGAAA----GACAACTTTTGAG	Size	Hit Count	Total Norm	Total
No Reads

droBia1

CC------------------------------------------------------------------CTAATTTTG--TCATCGTTCCTATGGCAGCTATATGATATAGTCGTCCGATTTTGAAAAAATTTAATTTGAAATTCAGAACTAATTAAGAAATGTTATTTCTAAGCTTAGA-AG--------------------------------------GTAATA------------------------TGTTAAAAAGTACCGAAGATATAATTTTTTT-TAAGT------------TTTTCCTCCGATAGTTCCTATGGGAGCTATAAGATATAGTTGTCCGATCCGGCTGGTCCCGACTTGTACACTA-CCTGCAACAGAAA----GAAGGCCTTTGGA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

AATTTACAAATCGCAAAAATGTTAAT--TTTCCTATTA-----------------------TTTCTCATTAATTTTG--CGTTCGTTTCAATGGCAGCTATATGATATAGTAGTTCGATTTTGATAAA-------------------------------------TATCCTAGAGTAGA-AG--------------------------------------AAAATACAATAAAAACCAACGAATGTTATAGGTTCAAAAACACCCAAGATATAATTTTTTT-TACAT----------T-TTTTTTCCCGATTGTTCCTTTGAGAGCTATATGATATAGTTGTCCGATCCGGCTCGTTCCGACTTATATATTA-CCTGCAATAGAAA----GAAGACTTTTGGA	Size	Hit Count	Total Norm	Total
No Reads

Generated: 05/16/2015 at 08:48 PM