ID:

dmo_1609

Coordinate:

scaffold_6500:20614444-20614594 -

Confidence:

Candidate

Type:

Unknown

[View on UCSC Genome Browser {Cornell Mirror}]

Legend:

mature

star

mismatch in alignment

mismatch in read

Predicted structure

Flybase annnotation

exon [dmoj_GLEANR_793:7]; CDS [Dmoj\GI22737-cds]; intron [Dmoj\GI22737-in]

Repeatable elements

Name	Class	Family	Strand
(TTG)n	Simple_repeat	Simple_repeat	+

Sense Strand Reads

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- AACTAAATCAGCTGGAGAACAATAAGGAGACAGAGAACCTGCAATCATTGGTAAGTAATGCTTTTAATTAGATTGTTATGATGAATGATTCTTGAATCGGTGCTTATCAATGTGATTGTACATGCAGGCCGGCGACAGCGAGCCGCAGACATCTGCCCATGATTCATAGCCGACAACAACAAAGACATCTACAACAACACCCACAACAACAGCAATTGTTGTTCCCCTCGAAGCTGCTGAAGCCTAGCTTA ************************************************....((((((((((..........(((((((...(((............((((..((((...)))).)))).....(((..((....))..)))((((....)))).)))...)))))))..........)))).))).))).........************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body	V049 head	V110 male body
...........................................................................................................................................................GCCATGATGCATAGCCGAC.............................................................................	19	2	1	3.00	3	3	0	0
............................................................................................................................................................CCATGATGCATAGCCGAC.............................................................................	18	1	1	2.00	2	2	0	0
............................................................................................................................................................................................................................GTTCCCCTCGAAGCTGCTGA...........	20	0	1	1.00	1	1	0	0
...............................................TTGGTAAGTGATGCTTTTAATT......................................................................................................................................................................................	22	1	1	1.00	1	0	1	0
..................................................................................................................................................................................................................................CTCGAAGCTGCTGAACTCT......	19	2	4	0.25	1	1	0	0
...........................................................................................................................................................GCCATGATGCATAGCCGA..............................................................................	18	2	8	0.13	1	0	0	1
..............................................................................................................................................................................................................CAACATCAATTCTTGTTC...........................	18	2	14	0.07	1	1	0	0
...................................................................................ACTGAGTCTTGAATCGGG......................................................................................................................................................	18	3	20	0.05	1	0	1	0
..............................................................................................................................................................ATGATACGTAGCCGACCA...........................................................................	18	3	20	0.05	1	1	0	0
....................................................................................................................................................................................................................TAATTGCTGTTCCCCTTGAA...................	20	3	20	0.05	1	0	0	1
............................................................................................................................................................CAATGATACGTAGCCGAC.............................................................................	18	3	20	0.05	1	0	1	0

Anti-sense strand reads

TTGATTTAGTCGACCTCTTGTTATTCCTCTGTCTCTTGGACGTTAGTAACCATTCATTACGAAAATTAATCTAACAATACTACTTACTAAGAACTTAGCCACGAATAGTTACACTAACATGTACGTCCGGCCGCTGTCGCTCGGCGTCTGTAGACGGGTACTAAGTATCGGCTGTTGTTGTTTCTGTAGATGTTGTTGTGGGTGTTGTTGTCGTTAACAACAAGGGGAGCTTCGACGACTTCGGATCGAAT ************************************************....((((((((((..........(((((((...(((............((((..((((...)))).)))).....(((..((....))..)))((((....)))).)))...)))))))..........)))).))).))).........************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body	M060 embryo	V049 head	V110 male body
..........TGACCTCTTGTTATTCCTCT.............................................................................................................................................................................................................................	20	1	1	1.00	1	1	0	0	0
..................................CTTGGACCTTAGTAATCA.......................................................................................................................................................................................................	18	2	4	0.25	1	0	1	0	0
.............................................GTAACCATTCATCAGGAATA..........................................................................................................................................................................................	20	3	4	0.25	1	0	0	1	0
...................................................................................................................................................................................................TTGTGGGTTTTGTTATCGTCAA..................................	22	3	8	0.13	1	0	0	0	1
............................................................................................................................................................................................................TCGTTGTAGTTAAGAACAAG...........................	20	3	20	0.10	2	2	0	0	0
...................................................................................................................................................................................GTTCCTGTAGATGTTGTTC.....................................................	19	2	13	0.08	1	1	0	0	0

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6500:20614394-20614644 -	dmo_1609	AACTAAATCAGCT---GGAGAACAATAAGGAGACAGAGAACCTG----CAATCATTGGTAAGTAATGCTTTTAATTAGATTGTTATG-----AT--------------------------GAATGAT----------------------------------------TCTTGAATCGGTGCTTATCAATGTGATTG------TACATGCAGGCCGGCGACAGCGAGCCGCAGACATCTGCCCATGAT------TCATAGCCGACAACAAC---A------------------------------AAGACATCTACAACAACACCCACAACAACAGCAATT--------GTTGTTCCCCTCGA--AG---------------CTGCTGAAGCCTAGCTTA
droVir3	scaffold_12963:11911285-11911531 -	dvi_11427	AACTAAACGAGCT---AGAGAATAGTGGGGAGCAGGAGAAACAGCTTTTAACCGTAAGTAATTG----------------------------CATATATATTCAATTTAT-------------CGTA----------------------------------------TTCGA-GAGAGT-----------------TCTTATCAAATTCAGACCAACAAAAGTGAGCCCCAAACACCTGCCCACAGC------ACATAGCTGATAACGAC---A------------------------------ACAACTACAACAACAACAACAACAACAAAAACAACTTGCGACTTGTTAACCACCTCCG--AGC---------AGCCGCCGCTTAAGCATAGTTTA
droGri2	scaffold_15126:5455745-5456060 -		AACTGAAAACGCT---GGAAAGCAATCAGGAGCAACAGCACCAGATGCTTACAGTAAGTAAATG----------------------------TATAAATTAACAATTTATCGTATCTGATGAGTAATTATGTGTGTATTTATATACATATATATATATACCGATGTATACCACAAGAGTTCTTATCAAAATTCTT----TAACAAATGCAGCCCAGCAACAGCGAGTGCAAAGCACCAGCCCCCACA------ACACAGGCGATAACAAA---G------------------------------ACAACCACAACAACAACAATAACA---ACAACAACTTTCGACTAG------AGCCCAAAGAGTCGTTGGTTCCTCCCCTGCTTAAGCATAGTTTA
droAna3	scaffold_12916:7562689-7562911 -		AGTCCGAGCAGA---CCGAA------AAGGAGTATGAGAGTCTG---GCAGCTGTGAGTATCTGACGGTTTCAATTACAAAATAATC---------------------------------AAACGAT----------------------------------------TCCAATAACTGTC-ATATACATATGTCTGTCATATCAAATTCAGA------AAACCGATACGAAAACAGCTACCCAAACA------AAAGAGTACAAAGCCAA---A------------------------------ACGAAATCAACAACTAGAGGGGCAACTAGACCTA----CAACTAA------ACCTATAAC-----------------------------------
droBip1	scf7180000396554:179120-179335 -		AGTCGGACCAGAC---GGAA------AAGGAGTTCGAGAGCCAG---GTAGCTGTGAGTATCTGACGGTTTCGATTACAT-------------------------------------------CGAT----------------------------------------TCCAATAAACGT------------CTTTGTTATATGAAATGCAGA------AAACCGATACGAAAACAGCTACCCAAACA------AAAGAGTACAAAGCCAA---A------------------------------ACGAATTCAACAACTAGAGCTGCAACTAGACCAA----CAACACA------ACCTACAAC--A---------AAACCCACAACA----------A
droKik1	scf7180000302389:327510-327545 -		ACTAGAC-CGACA---GAGATCCAGCGAAGAGCTGAGGAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEle1	scf7180000491028:774945-775136 +		AGCAGAGT---G---CCGAG------AAGGAGCATAAACAAATG---GCGTGTGTGAGTATCTGACGCTTTCGATTACCCCGCAATT---------------------------------AAGCGAT----------------------------------------TCCAATAACCCC------------GGTTGTCATATCAAATGCAGA------AAGGCGATACGAAAATACCTACACTAAAA------AGGGAGCCCA---CCAAAGCCACCAAACCTCCTCCTGCAGTCACAGCAACAA------------------------------CA--------------------------------------------------------------
droRho1	scf7180000780250:1034-1223 -		GATCCGA------------G------CAGGAGCAAAAACAAATG---GCATGTGTGAGTATCTGACAGTTTCGATTACCGTGCAATT---------------------------------AAGTGAT----------------------------------------TCCAATAACCCC------------GGTTGTCATATCAAATGCAGA------AAAACGATACGAAAACACCTACCCCAAAG------AGGGAGCCCA---CCAAAGCAACCAAACCT---TCCGCAGCCACAGCTAAAA------------------------CAAAATCA-------------------------------------------------------------A
droBia1	scf7180000302261:1315899-1316093 +		AATCGAG-CAGAGATCCGAG------GAGGAGCGCAAGCAAATG---GCATGTGTGAGTATCTGACGGTTTCGATTACCCCGCAATT---------------------------------AGGCGAT----------------------------------------TCCAATAACACC------------GCTTGTCATACCAAATGCAGA------AAGGCGATGCGAAAACACCTTCCCAAACAAACACAAGGGAGCCCA---GCAAAGCCACCAAAATC---CCCACAGCCACGGCGA-------------------------------------------------------------------------------------------------
droSec2	scaffold_3:1523264-1523457 -		AGACATTCGA---------G------CAGAAGAAAAATCAAGTG---ACAATTGTGAGTATCTGACGGCTTTGATTGCATCGCAAGTAACCAAT--------------------------AACCGAT----------------------------------------TCCAATAACCCC------------GGTTGTCATATCAAATGCAGG------AATGCGATACGAAAACACCTTCCCAAACA------AGGAAGCCAA---CCAAAGCCACCAAAATC---CCGGGAGCCACGGCAAAAA------------------------------CA-------------------------------------------------------------A

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

AACTAAATCAGCT---GGAGAACAATAAGGAGACAGAGAACCTG----CAATCATTGGTAAGTAATGCTTTTAATTAGATTGTTATG-----AT--------------------------GAATGAT----------------------------------------TCTTGAATCGGTGCTTATCAATGTGATTG------TACATGCAGGCCGGCGACAGCGAGCCGCAGACATCTGCCCATGAT------TCATAGCCGACAACAAC---A------------------------------AAGACATCTACAACAACACCCACAACAACAGCAATT--------GTTGTTCCCCTCGA--AG---------------CTGCTGAAGCCTAGCTTA	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
...............................................................................................................................................................................................................................................................................................................................................................GTTCCCCTCGA--AG---------------CTGCTGA...........	20	1	1.00	1	1	0	0	0	0	0

droVir3

AACTAAACGAGCT---AGAGAATAGTGGGGAGCAGGAGAAACAGCTTTTAACCGTAAGTAATTG----------------------------CATATATATTCAATTTAT-------------CGTA----------------------------------------TTCGA-GAGAGT-----------------TCTTATCAAATTCAGACCAACAAAAGTGAGCCCCAAACACCTGCCCACAGC------ACATAGCTGATAACGAC---A------------------------------ACAACTACAACAACAACAACAACAACAAAAACAACTTGCGACTTGTTAACCACCTCCG--AGC---------AGCCGCCGCTTAAGCATAGTTTA	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
................................................................................................................................................................................................................................................................................................................................................AACTTGCGACTTGTTAACCACC.........................................	22	1	1.00	1	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	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
..............................AGCAGGAGAAACAGCTTTT..............................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................AACAACAAAAACAACTTGC........................................................	19	1	1.00	1	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	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
..............................................................................................................................................................................................................................................................................................................................................................TAACCACCTCCG--AGC---------AGCC...................	19	1	1.00	1	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................................AAAAACAACTTGCGACTTGTT................................................	21	1	1.00	1	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	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
................................................................................................................................................................................................................................................................................................................................CAACAACAACAAAAACAACTTGCGACTT...................................................	28	1	1.00	1	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	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
.....................................................GTAAGTAATTG----------------------------CATATATATTCAATTTA..................................................................................................................................................................................................................................................................................................	28	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	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
AACTAAACGAGCT---AGAGAATAGT.....................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................AACTACAACAACAACAACAAC........................................................................	21	20	0.15	3	0	0	1	2	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
..................................................................................................................................................................................................................................................................................................................AACTACAACAACAACAACAACAA......................................................................	23	20	0.05	1	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	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
...................................................................................................................................................................................................................................................................................................................ACTACAACAACAACAACAACA.......................................................................	21	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	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

droGri2

AACTGAAAACGCT---GGAAAGCAATCAGGAGCAACAGCACCAGATGCTTACAGTAAGTAAATG----------------------------TATAAATTAACAATTTATCGTATCTGATGAGTAATTATGTGTGTATTTATATACATATATATATATACCGATGTATACCACAAGAGTTCTTATCAAAATTCTT----TAACAAATGCAGCCCAGCAACAGCGAGTGCAAAGCACCAGCCCCCACA------ACACAGGCGATAACAAA---G------------------------------ACAACCACAACAACAACAATAACA---ACAACAACTTTCGACTAG------AGCCCAAAGAGTCGTTGGTTCCTCCCCTGCTTAAGCATAGTTTA	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
.......................................................................................................................................................................................................................................................................................................................................................................CAAAGAGTCGTTGGTTCCT.....................	19	1	1.00	1	1	0

droAna3

AGTCCGAGCAGA---CCGAA------AAGGAGTATGAGAGTCTG---GCAGCTGTGAGTATCTGACGGTTTCAATTACAAAATAATC---------------------------------AAACGAT----------------------------------------TCCAATAACTGTC-ATATACATATGTCTGTCATATCAAATTCAGA------AAACCGATACGAAAACAGCTACCCAAACA------AAAGAGTACAAAGCCAA---A------------------------------ACGAAATCAACAACTAGAGGGGCAACTAGACCTA----CAACTAA------ACCTATAAC-----------------------------------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.................................................................................................................................................................................................................................................................................A------------------------------ACGAAATCAACAACTAGAGGGGCAAC.....................................................................	27	1	1.00	1	0	1	0	0	0	0

droBip1

AGTCGGACCAGAC---GGAA------AAGGAGTTCGAGAGCCAG---GTAGCTGTGAGTATCTGACGGTTTCGATTACAT-------------------------------------------CGAT----------------------------------------TCCAATAAACGT------------CTTTGTTATATGAAATGCAGA------AAACCGATACGAAAACAGCTACCCAAACA------AAAGAGTACAAAGCCAA---A------------------------------ACGAATTCAACAACTAGAGCTGCAACTAGACCAA----CAACACA------ACCTACAAC--A---------AAACCCACAACA----------A	Size	Hit Count	Total Norm	Total
No Reads

droKik1

ACTAGAC-CGACA---GAGATCCAGCGAAGAGCTGAGGAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AGCAGAGT---G---CCGAG------AAGGAGCATAAACAAATG---GCGTGTGTGAGTATCTGACGCTTTCGATTACCCCGCAATT---------------------------------AAGCGAT----------------------------------------TCCAATAACCCC------------GGTTGTCATATCAAATGCAGA------AAGGCGATACGAAAATACCTACACTAAAA------AGGGAGCCCA---CCAAAGCCACCAAACCTCCTCCTGCAGTCACAGCAACAA------------------------------CA--------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GATCCGA------------G------CAGGAGCAAAAACAAATG---GCATGTGTGAGTATCTGACAGTTTCGATTACCGTGCAATT---------------------------------AAGTGAT----------------------------------------TCCAATAACCCC------------GGTTGTCATATCAAATGCAGA------AAAACGATACGAAAACACCTACCCCAAAG------AGGGAGCCCA---CCAAAGCAACCAAACCT---TCCGCAGCCACAGCTAAAA------------------------CAAAATCA-------------------------------------------------------------A	Size	Hit Count	Total Norm	Total
No Reads

droBia1

AATCGAG-CAGAGATCCGAG------GAGGAGCGCAAGCAAATG---GCATGTGTGAGTATCTGACGGTTTCGATTACCCCGCAATT---------------------------------AGGCGAT----------------------------------------TCCAATAACACC------------GCTTGTCATACCAAATGCAGA------AAGGCGATGCGAAAACACCTTCCCAAACAAACACAAGGGAGCCCA---GCAAAGCCACCAAAATC---CCCACAGCCACGGCGA-------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droSec2

AGACATTCGA---------G------CAGAAGAAAAATCAAGTG---ACAATTGTGAGTATCTGACGGCTTTGATTGCATCGCAAGTAACCAAT--------------------------AACCGAT----------------------------------------TCCAATAACCCC------------GGTTGTCATATCAAATGCAGG------AATGCGATACGAAAACACCTTCCCAAACA------AGGAAGCCAA---CCAAAGCCACCAAAATC---CCGGGAGCCACGGCAAAAA------------------------------CA-------------------------------------------------------------A	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
..............................................................................................................................................................................................................................................................................AGCCACCAAAATC---CCGGGAGC.........................................................................................................	21	1	1.00	1	0	0	1	0

Generated: 05/18/2015 at 12:49 AM