dvi_21909

Name	Class	Family	Strand
Helitron1_Dmoj	RC	Helitron	-

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCAATTACTCAGAGCTTAAAATATGGAAGTGCAAATGATTCATTTATAAGTAAGTATACGTACACCCAAATGTATGTATATGGTATGTGCGCATTTTTAGGAGGGCTCAAAGAACAATATAGATCAATTTAAAAGTTCTGTTTTCTAGTTTGTCAACAAAGTAAAAAAAATAATTGGAGTTGTGCAATATCCGCTTTCTTGTCCCTTAGTCTGTCCGTCTTCGTTCCTTCCATCCTTGCGAATGAAAAAA ************************************************....(((((((((((......)))))))))))(((((.((((((.((((((((((((....(((((...................)))))))))))((.((((....)))).))..........)))))).))))))))))).........************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M047 female body	V116 male body	SRR060664 9_males_carcasses_total	SRR060687 9_0-2h_embryos_total	V047 embryo	SRR060666 160_males_carcasses_total	SRR060679 140x9_testes_total	SRR060657 140_testes_total	SRR060674 9x140_ovaries_total
......................................................................................TGTGCGCATTTTTAGGAGG..................................................................................................................................................	19	0	1	1.00	1	1	0	0	0	0	0	0	0	0
........CTCAGAGCGGAGAATATGGA...............................................................................................................................................................................................................................	20	3	4	0.50	2	0	1	0	1	0	0	0	0	0
...................................................................................................................................................................................................................CTATCTGGCTTCGTTCCTTC....................	20	3	4	0.25	1	0	0	1	0	0	0	0	0	0
........CTCAGAGCGGAAAATTTGGA...............................................................................................................................................................................................................................	20	3	11	0.18	2	0	2	0	0	0	0	0	0	0
.................................................................................................................................................................................................................GTCTGTCCTTCTTCGTTTC.......................	19	2	6	0.17	1	0	0	0	0	1	0	0	0	0
..............GCTTAAGAGATCGAAGTGCA.........................................................................................................................................................................................................................	20	3	15	0.13	2	0	0	0	0	0	1	1	0	0
....................................................................................................................................................................................................................................TTCCATCCTTGGGATTGTAAA..	21	3	12	0.08	1	0	0	0	0	1	0	0	0	0
........CTCAGAGCTGAGAATTTGGA...............................................................................................................................................................................................................................	20	3	15	0.07	1	0	1	0	0	0	0	0	0	0
........CTCAGAGCGGAGAATATGG................................................................................................................................................................................................................................	19	3	16	0.06	1	0	1	0	0	0	0	0	0	0
.....................................................................................................................................................TATGTCAACAAAGGAAAA....................................................................................	18	2	20	0.05	1	0	0	0	0	0	0	0	0	1
........................................................................................................................................................................................................................................ATCCTTGGGAATGAAGATA	19	3	20	0.05	1	0	0	0	0	0	0	0	1	0

GAGTTAATGAGTCTCGAATTTTATACCTTCACGTTTACTAAGTAAATATTCATTCATATGCATGTGGGTTTACATACATATACCATACACGCGTAAAAATCCTCCCGAGTTTCTTGTTATATCTAGTTAAATTTTCAAGACAAAAGATCAAACAGTTGTTTCATTTTTTTTATTAACCTCAACACGTTATAGGCGAAAGAACAGGGAATCAGACAGGCAGAAGCAAGGAAGGTAGGAACGCTTACTTTTTT ************************************************....(((((((((((......)))))))))))(((((.((((((.((((((((((((....(((((...................)))))))))))((.((((....)))).))..........)))))).))))))))))).........************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V116 male body	SRR060689 160x9_testes_total	SRR060664 9_males_carcasses_total
.................................................................................................................................................................................CTGAACACGTTATAGGCGGA......................................................	20	2	3	0.33	1	1	0	0
.....................................................................................................CTCCCGGGTTTCTAGCTATAT.................................................................................................................................	21	3	3	0.33	1	0	1	0
..............................................................................................AAAAATCCGCCCGAGGTT...........................................................................................................................................	18	2	15	0.07	1	0	0	1
.........................................................ATGCATGTGCGTGTACATA...............................................................................................................................................................................	19	2	20	0.05	1	1	0	0

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_13052:767149-767399 -	dvi_21909	CTCAATTACTCAGAGCTTAAAATATG------------------------------GAAGTGCAAATGATTCATTTA---------------TAAGTAAGTATACGTACACCC-AAATGTATGTATATGGTATGTGCGCAT---------TTTTAGGAGGGCTCAAAGAACAA-TATAGATCAATTTAAAAGTTCTGTTTTC-TAGTTTGTCAACAAAGTAAAAAAAATAATTGGAGTTGTGCAATATCCGCTTTCTTGTCCCTTAGTCTGTCCGTCT-TCGTTCCTTCCATCCTTGCGAATGAAAAAA
droMoj3	scaffold_6496:26618808-26619070 -		TCGAGAAA----------------TA------------------------------TAAATATAAATAATTTACACAAATTTATGTTTGAGACAAACAAATACCTGAACATTCGAGATATTTAGCTTTTGTACGTACGCGCACAATTATTATTTATAAAGTTTAAAAGTCCAAAAATATAAAAAGCCAAAAATACACTTTTTATACTCATTCACGAAAGTGAATCAGTATATTGGTTTTGTGCAATGTCCGTCTTGCTGTCCGTCCGTCTGTCCGTCTGTCCGTCCGTCCGTCTGTCCGTATGAACGCA
droGri2	scaffold_14822:175720-175776 +		ATCCACTTCGCAAAACTATAAAAACG------------------------------GGAATGTAAATGAGACATATC---------------TAAGTAAGTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil2	scf2_1100000004943:1184738-1184802 +		TACAAGTGCCCAATGCGCAA--AATG------------------------------GCAATGTGAATAAATCAAGCT---------------TGAGTAAGTACACATATATC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer2	scaffold_42:99448-99512 +		TTTAATCACCCTAAACGACAAACATG------------------------------GAAATTTGAATCATACAAATC---------------TAAGTAAGTATTTATATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droRho1	scf7180000779182:64809-64865 +		CAGGATTCCATATTAACACATTAATA------------------------------GAA-----AAATGTCCGGATA---------------TAAGTAAGTATACAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSim2	4:224377-224436 +		CATTTTAACACATTACCAGATTCCAG------------------------TAAGTATAAGTGCATATTGTTT---------------------AATT-------CATTTATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4512:1023561-1023641 -		CATAGCAATGC--------------TGGAGAGCAATTTAACACATTTACA------AAC-----AAATTCCTGGATT---------------CGAGTAAGTATATATGTA------------------------TGCATAT---------TTTT-----------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

CTCAATTACTCAGAGCTTAAAATATG------------------------------GAAGTGCAAATGATTCATTTA---------------TAAGTAAGTATACGTACACCC-AAATGTATGTATATGGTATGTGCGCAT---------TTTTAGGAGGGCTCAAAGAACAA-TATAGATCAATTTAAAAGTTCTGTTTTC-TAGTTTGTCAACAAAGTAAAAAAAATAATTGGAGTTGTGCAATATCCGCTTTCTTGTCCCTTAGTCTGTCCGTCT-TCGTTCCTTCCATCCTTGCGAATGAAAAAA	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
....................................................................................................................................TGTGCGCAT---------TTTTAGGAGG.....................................................................................................................................................	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

droMoj3

TCGAGAAA----------------TA------------------------------TAAATATAAATAATTTACACAAATTTATGTTTGAGACAAACAAATACCTGAACATTCGAGATATTTAGCTTTTGTACGTACGCGCACAATTATTATTTATAAAGTTTAAAAGTCCAAAAATATAAAAAGCCAAAAATACACTTTTTATACTCATTCACGAAAGTGAATCAGTATATTGGTTTTGTGCAATGTCCGTCTTGCTGTCCGTCCGTCTGTCCGTCTGTCCGTCCGTCCGTCTGTCCGTATGAACGCA	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
...............................................................................................................TCGAGATATTTAGCTTTTGTACGTAC............................................................................................................................................................................	26	1	2.00	2	0	1	0	0	1	0
.............................................................................................................ATTCGAGATATTTAGCTTTTGTACGT..............................................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0
.............................................................................................................ATTCGAGATATTTAGCTTTTGTACGTAC............................................................................................................................................................................	28	1	1.00	1	1	0	0	0	0	0
........................................................................................................................................................................................GCCAAAAATACACTTTTTATACTCA....................................................................................................	25	2	0.50	1	1	0	0	0	0	0
........................................................................................................................................................................................GCCAAAAATACACTTTTTATACT......................................................................................................	23	2	0.50	1	1	0	0	0	0	0
........................................................................................................................................................................................GCCAAAAATACACTTTTTATACTCAT...................................................................................................	26	2	0.50	1	1	0	0	0	0	0
.................................................................................................................................................................................................ACACTTTTTATACTCATTCACGAAA...........................................................................................	25	11	0.09	1	1	0	0	0	0	0
.............................................................................................................ATTCGAGATATTTAGCTTTTGTAC................................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
....................................................................................................................................................................................................................................................ATGTCCGTCTTGCTGTCCGTC............................................	21	20	0.05	1	0	0	0	0	1	0
............................................................................................................................................................................................................................................................................CTGTCCGTCTGTCCGTCCGT.....................	20	20	0.05	1	1	0	0	0	0	0

droGri2

ATCCACTTCGCAAAACTATAAAAACG------------------------------GGAATGTAAATGAGACATATC---------------TAAGTAAGTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

TACAAGTGCCCAATGCGCAA--AATG------------------------------GCAATGTGAATAAATCAAGCT---------------TGAGTAAGTACACATATATC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
No Reads

droPer2

TTTAATCACCCTAAACGACAAACATG------------------------------GAAATTTGAATCATACAAATC---------------TAAGTAAGTATTTATATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droRho1

CAGGATTCCATATTAACACATTAATA------------------------------GAA-----AAATGTCCGGATA---------------TAAGTAAGTATACAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droSim2

CATTTTAACACATTACCAGATTCCAG------------------------TAAGTATAAGTGCATATTGTTT---------------------AATT-------CATTTATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

Total

M023
Head

M024
Male-body

M025
Embryo

M053
Female-body

O001
Testis

O002
Head

SRR553485
Ovary

SRR553486
Ovary

SRR553487
Ovary

SRR553488
Ovary

SRR618934
Ovary

V044
Embryo

SRR902008
Ovary

SRR902009
Testis

SRR1275487
Male larvae

SRR1275485
Male prepupae

SRR1275483
Male prepupae

No Reads

droEre2

CATAGCAATGC--------------TGGAGAGCAATTTAACACATTTACA------AAC-----AAATTCCTGGATT---------------CGAGTAAGTATATATGTA------------------------TGCATAT---------TTTT-----------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
No Reads

dvi_21909

scaffold_13052:767199-767349 -

Candidate

Unknown

Predicted structure

Flybase annnotation

Repeatable elements

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-29.8	-29.2	-29.2