dmo_773

Name	Class	Family	Strand
Helitron1_Dmoj	RC	Helitron	+
AT_rich	Low_complexity	Low_complexity	+

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------################################################## ACGACAGTAGGGGCGTGGCAAATCGCGAAAAATGAATTTTCTACAATACTTAGCTTCTAAATTGCTGATGGGATGTGAATGAGTATTCCGCAGTCGGTAACGCCCGACTGCAACGTTCTTACTTGTTTTTATTTATTTTTATAAATAATTATTTATAATATAAATTAGTATGTTAATTAATTTGAAATTTTCGTTTTGCAGCAAATCTCAAACCTCGAGGACAATGACAAAATGTTTTTCGATGTGGAGGA **************************************************************.....((.(((..............((((((((......))))))))..))).))**********************************************************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body	V110 male body	M060 embryo	V041 embryo
..............................................................................................CGGTAACGCCCGACTGCAACGTTCT....................................................................................................................................	25	0	20	1.25	25	25	0	0	0
.............................................................................................................................................................................................................................CAATGACAAAATGTTTTTCGATGT......	24	0	1	1.00	1	1	0	0	0
........................................................................................................................................................................................................................GAGGACAATGACAAAATGT................	19	0	1	1.00	1	0	1	0	0
.......................................................................................................................................................................................................AGCAAATCTCAAACCTCGAGG...............................	21	0	1	1.00	1	0	0	1	0
............................................................................GAATGAGTATTCCGCAGTCGG..........................................................................................................................................................	21	0	20	0.75	15	15	0	0	0
................................................................CTGATGGGATGTGAATGAGTATTC...................................................................................................................................................................	24	0	20	0.55	11	0	0	0	11
................................................................CTGATGGGATGTGAATGAGTATT....................................................................................................................................................................	23	0	20	0.40	8	0	8	0	0
................................................................CTGATGGGATGTGAATGAGTATTCC..................................................................................................................................................................	25	0	20	0.25	5	0	0	5	0
................................................................................GAGTATTCCGCAGTCGGTAAC......................................................................................................................................................	21	0	20	0.25	5	5	0	0	0
................................................................CTGATGGGATGTGAATGAGTATTCCG.................................................................................................................................................................	26	0	20	0.20	4	4	0	0	0
...............................................................GCTGATGGGATGTGAATGAGTATTC...................................................................................................................................................................	25	0	20	0.15	3	0	3	0	0
................................................................CTGATGGGATGTGAATGAGTATTCCGC................................................................................................................................................................	27	0	20	0.15	3	0	0	0	3
...................................................................................TATTCCGCAGTCGGTAACGCCCGACTGC............................................................................................................................................	28	0	20	0.10	2	2	0	0	0
...............................................................GCTGATGGGATGTGAATGAGTATT....................................................................................................................................................................	24	0	20	0.10	2	1	1	0	0
...............................................................GCTGATGGGATGTGAATGAGTATTCCGC................................................................................................................................................................	28	0	20	0.10	2	2	0	0	0
....................................................................................................CGCCCGACTGCAACGTTCTTACTTG..............................................................................................................................	25	0	20	0.05	1	1	0	0	0
................................................................CGGTTGGGATGTGAATGAGTATTCC..................................................................................................................................................................	25	2	20	0.05	1	0	0	1	0
..........................................................AAATTGCTGATGGGATGTGAATGAGTA......................................................................................................................................................................	27	0	20	0.05	1	1	0	0	0
........................................................................................CGCAGTCGGTAACGCCCGA................................................................................................................................................	19	0	20	0.05	1	1	0	0	0
................................................................CTGATGGGATGTGAATAAGTATTCC..................................................................................................................................................................	25	1	20	0.05	1	0	0	0	1
.............................................................................AATGAGTATTCCGCAGTCGGTAACGC....................................................................................................................................................	26	0	20	0.05	1	1	0	0	0
.............................................................TTGCTGATGGGATGTGAATGAGTA......................................................................................................................................................................	24	0	20	0.05	1	0	0	1	0
.......................................................................................CCGCAGTCGGTAACGCCCGAC...............................................................................................................................................	21	0	20	0.05	1	0	0	1	0
........................................................................ATGTGAATGAGTATTCCGCAGTCGGTAA.......................................................................................................................................................	28	0	20	0.05	1	1	0	0	0

TGCTGTCATCCCCGCACCGTTTAGCGCTTTTTACTTAAAAGATGTTATGAATCGAAGATTTAACGACTACCCTACACTTACTCATAAGGCGTCAGCCATTGCGGGCTGACGTTGCAAGAATGAACAAAAATAAATAAAAATATTTATTAATAAATATTATATTTAATCATACAATTAATTAAACTTTAAAAGCAAAACGTCGTTTAGAGTTTGGAGCTCCTGTTACTGTTTTACAAAAAGCTACACCTCCT **********************************************************************************************************************************.....((.(((..............((((((((......))))))))..))).))**************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body
......................................................................................................................................TAAAAATATTTATTAATAA..................................................................................................	19	0	5	0.20	1	1
..................................................................CTACCCTACACTTACTCATAAGGCGTC..............................................................................................................................................................	27	0	20	0.05	1	1

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6473:13575415-13575665 +	dmo_773	ACGACAG-TAGGGGCGTGGCAAATCGCGAAAAATGAATTTTCTACAATACTTAGCTTCTAAATTGCTGATGGGATGTGAATGAGTATTC-CGCAGTCGGTAACGCCCGACTGCAACGTTCTT--------------------------ACTTGTTTTTATTTA--TTTTTATAAATAATTATTT----------ATAATATAAATTAGTATGTTAATTA---ATTTGAAATTTTCGTTTTGCAG------CAAATCTCAAACCT------------------CGAGGACAATGACAAAATGTTTTTCGATGTGGAG---GA
droVir3	scaffold_12963:16080411-16080583 +		ACGCCCGCTAGGGGCGTGGCAAATGAGGAAAAATGG--------CTATATTTGGC---------GGCATTGAACTGTGAACGAGTATCT-GTTAGTCGGTTACACCCGACTGCAATGTATTTGTGGTTGTTTTTCCGTTTCGTTTGGCAGTTGTTTAGAATTT--TCTT------------------------------------TAGT------------TATTTATTTTTTTTTTTT--TG------------------------------------------------------------------------------
droGri2	scaffold_15110:21148177-21148330 -		G---------------------------------------------------------------------------------AGTATTC-CGCAACCGGTTACACCCGACTGCAACGTTCTT--------------------------AATAGTTTTGAATTC--TTTTTAAAACT--TTGTTT----------AAA-AAGAAGTCAGTAAGTA---TACGTTCTCATTCTCTTTTTTT--CAGAAGAAGTAAATT-C--------------------------------------AAATTTTTTTTGGTGTCAAGAAAAA
droWil2	scf2_1100000004909:12136062-12136190 -		TTT---------------------------------------------------------------------------------TTCA-------------------------AATATTCAT--------------------------TCTAATTTTTGTTTTTGTTTTTCTCAATGTT-------------------------------------------------TTGTA--TTTTTGCAG------CAAATCACAAGTTTAGACGATGACCTTGACTTTGTGGAGAAAGACAATGTTATTTTGGATCGTGAG---AA
droSec2	scaffold_10:2193091-2193230 -		TTT---------------------------------------------------------------------------------TATTTATGTAATTGGATTTG----------TT----------------------------------------------------GTATATAGAATTATTTCCTTGCCTTCTTATTCTATACTAATATG---ATTT---AATCGTATCTCCCATTT--TAG------CAAATCTCAAATCTTGACGATGACCAAGATT---------------------TTATCCTGGCGGAT---GA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

ACGACAG-TAGGGGCGTGGCAAATCGCGAAAAATGAATTTTCTACAATACTTAGCTTCTAAATTGCTGATGGGATGTGAATGAGTATTC-CGCAGTCGGTAACGCCCGACTGCAACGTTCTT--------------------------ACTTGTTTTTATTTA--TTTTTATAAATAATTATTT----------ATAATATAAATTAGTATGTTAATTA---ATTTGAAATTTTCGTTTTGCAG------CAAATCTCAAACCT------------------CGAGGACAATGACAAAATGTTTTTCGATGTGGAG---GA	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
................................................................................................CGGTAACGCCCGACTGCAACGTTCT........................................................................................................................................................................................................	25	20	1.25	25	25	0	0	0	0	0
................................................................................................................................................................................................................................................................................................CAATGACAAAATGTTTTTCGATGT.........	24	1	1.00	1	1	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................GAGGACAATGACAAAATGT...................	19	1	1.00	1	0	0	0	0	0	1
..................................................................................................................................................................................................................................................AG------CAAATCTCAAACCT------------------CGAGG..................................	21	1	1.00	1	0	0	0	0	1	0
.............................................................................GAATGAGTATTC-CGCAGTCGG..............................................................................................................................................................................................................................	21	20	0.75	15	15	0	0	0	0	0
.................................................................CTGATGGGATGTGAATGAGTATTC-.......................................................................................................................................................................................................................................	24	20	0.55	11	0	11	0	0	0	0
.................................................................CTGATGGGATGTGAATGAGTATT.........................................................................................................................................................................................................................................	23	20	0.40	8	0	0	0	0	0	8
.................................................................CTGATGGGATGTGAATGAGTATTC-C......................................................................................................................................................................................................................................	25	20	0.25	5	0	0	0	0	5	0
.................................................................................GAGTATTC-CGCAGTCGGTAAC..........................................................................................................................................................................................................................	21	20	0.25	5	5	0	0	0	0	0
.................................................................CTGATGGGATGTGAATGAGTATTC-CG.....................................................................................................................................................................................................................................	26	20	0.20	4	4	0	0	0	0	0
................................................................GCTGATGGGATGTGAATGAGTATTC-.......................................................................................................................................................................................................................................	25	20	0.15	3	0	0	0	0	0	3
.................................................................CTGATGGGATGTGAATGAGTATTC-CGC....................................................................................................................................................................................................................................	27	20	0.15	3	0	3	0	0	0	0
....................................................................................TATTC-CGCAGTCGGTAACGCCCGACTGC................................................................................................................................................................................................................	28	20	0.10	2	2	0	0	0	0	0
................................................................GCTGATGGGATGTGAATGAGTATT.........................................................................................................................................................................................................................................	24	20	0.10	2	1	0	0	0	0	1
................................................................GCTGATGGGATGTGAATGAGTATTC-CGC....................................................................................................................................................................................................................................	28	20	0.10	2	2	0	0	0	0	0
......................................................................................................CGCCCGACTGCAACGTTCTT--------------------------ACTTG........................................................................................................................................................................	25	20	0.05	1	1	0	0	0	0	0
...........................................................AAATTGCTGATGGGATGTGAATGAGTA...........................................................................................................................................................................................................................................	27	20	0.05	1	1	0	0	0	0	0
..........................................................................................CGCAGTCGGTAACGCCCGA....................................................................................................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0
..............................................................................AATGAGTATTC-CGCAGTCGGTAACGC........................................................................................................................................................................................................................	26	20	0.05	1	1	0	0	0	0	0
..............................................................TTGCTGATGGGATGTGAATGAGTA...........................................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	0	1	0
........................................................................................C-CGCAGTCGGTAACGCCCGAC...................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0
.........................................................................ATGTGAATGAGTATTC-CGCAGTCGGTAA...........................................................................................................................................................................................................................	28	20	0.05	1	1	0	0	0	0	0

droVir3

ACGCCCGCTAGGGGCGTGGCAAATGAGGAAAAATGG--------CTATATTTGGC---------GGCATTGAACTGTGAACGAGTATCT-GTTAGTCGGTTACACCCGACTGCAATGTATTTGTGGTTGTTTTTCCGTTTCGTTTGGCAGTTGTTTAGAATTT--TCTT------------------------------------TAGT------------TATTTATTTTTTTTTTTT--TG------------------------------------------------------------------------------

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

No Reads

droGri2

G---------------------------------------------------------------------------------AGTATTC-CGCAACCGGTTACACCCGACTGCAACGTTCTT--------------------------AATAGTTTTGAATTC--TTTTTAAAACT--TTGTTT----------AAA-AAGAAGTCAGTAAGTA---TACGTTCTCATTCTCTTTTTTT--CAGAAGAAGTAAATT-C--------------------------------------AAATTTTTTTTGGTGTCAAGAAAAA	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

TTT---------------------------------------------------------------------------------TTCA-------------------------AATATTCAT--------------------------TCTAATTTTTGTTTTTGTTTTTCTCAATGTT-------------------------------------------------TTGTA--TTTTTGCAG------CAAATCACAAGTTTAGACGATGACCTTGACTTTGTGGAGAAAGACAATGTTATTTTGGATCGTGAG---AA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
............................................................................................................................................................................................................................................................................GATGACCTTGACTTTGTGGAGAA..............................	23	1	2.00	2	0	0	0	2	0
...........................................................................................................................................................................................................................................................................CGATGACCTTGACTTTGT....................................	18	1	2.00	2	0	0	0	2	0
........................................................................................................................................................................................................................................................................................................ATGTTATTTTGGATCGTGA......	19	1	2.00	2	0	0	0	2	0
......................................................................................................................................................................................................................................................................TTAGACGATGACCTTGAC.........................................	18	1	1.00	1	1	0	0	0	0
......................................................................................................................................................................................................................................................................TTAGACGATGACCTTGACTTTGT....................................	23	1	1.00	1	0	0	0	1	0
......................................................................................................................................................................................................................................................................TTAGACGATGACCTTGACTTTGC....................................	23	1	1.00	1	1	0	0	0	0
.............................................................................................................................................................................................................................................................................ATGACCTTGACTTTGTGGAGAAAGA...........................	25	1	1.00	1	0	0	1	0	0
.......................................................................................................................................................................................................................................................................................................AATGTTATTTTGGATCGTG.......	19	1	1.00	1	0	0	0	1	0
.......................................................................................................................................................................................................................................................................................................AATGTTATTTTGGATCGTGA......	20	1	1.00	1	0	0	0	1	0
.................................................................................................................................................................................................................................................................CAAGTTTAGACGATGACC..............................................	18	1	1.00	1	0	1	0	0	0
....................................................................................................................................................................................................................................................................................TGACTTTGTGGAGAAAGACAATGTTA...................	26	1	1.00	1	0	0	1	0	0
..........................................................................................................................................................................................................................................................................ACGATGACCTTGACTTTGT....................................	19	1	1.00	1	0	0	0	0	1
...............................................................................................................................................................................................................................................................CACAAGTTTAGACGATGACCT.............................................	21	1	1.00	1	0	0	0	1	0
.........................................................................................................................................................................................................................................................................................TTGTGGAGAAAGACAATGT.....................	19	1	1.00	1	0	0	1	0	0
....................................................................................................................................................................................................................................................................................TGACTTTGTGGAGAAAGACAATGT.....................	24	1	1.00	1	0	0	0	1	0
...........................................................................................................................................................................................................................................................................................GTGGAGAAAGACAATGTTATTTTG..............	24	1	1.00	1	0	0	0	1	0
...........................................................................................................................................................................................................................................................................................GTGGAGAAAGACAATGTTATTTTGG.............	25	1	1.00	1	0	0	0	1	0
........................................................................................................................................................................................................................................................................AGACGATGACCTTGACTTTGTGGA.................................	24	1	1.00	1	0	0	0	1	0
......................................................................................................................................................................................................................................................................................................CAATGTTATTTTGGATCGTGA......	21	1	1.00	1	0	0	0	1	0
...........................................................................................................................................................................................................................................................................CGATGACCTTGACTTTGTGGA.................................	21	1	1.00	1	0	0	0	1	0
.....................................................................................................................................................................................................................................................................TTTAGACGATGACCTTGAC.........................................	19	1	1.00	1	1	0	0	0	0
...............................................................................................................................................................................................................................................................CACAAGTTTAGACGATGACC..............................................	20	1	1.00	1	0	1	0	0	0

droSec2

TTT---------------------------------------------------------------------------------TATTTATGTAATTGGATTTG----------TT----------------------------------------------------GTATATAGAATTATTTCCTTGCCTTCTTATTCTATACTAATATG---ATTT---AATCGTATCTCCCATTT--TAG------CAAATCTCAAATCTTGACGATGACCAAGATT---------------------TTATCCTGGCGGAT---GA	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
...............................................................................................................................................................................................................................................................CTCAAATCTTGACGATGACCAAG...........................................	23	1	1.00	1	0	0	1	0
...................................................................................................................................................................................................................................................................AATCTTGACGATGACCAA............................................	18	1	1.00	1	0	0	1	0
............................................................................................................................................................................................................................................................AATCTCAAATCTTGACGATGACC..............................................	23	1	1.00	1	0	0	1	0
...................................................................................................................................................................................................................................................................AATCTTGACGATGACCAAG...........................................	19	1	1.00	1	0	0	1	0

-18.5	-18.1	-18.0	-17.7

dmo_773

scaffold_6473:13575465-13575615 +

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