dpe_595

Name	Class	Family	Strand
DNAREP1_DYak	RC	Helitron	+
ISFUN1	RC	Helitron	+

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ACGGACACGGACATGGCTCTCGGCGGCAGTTTGCGCCTGGAAATGATGTGGTTAGCTGTGGCTCCTGCGGTGTGCTGTACTGATGCTTCAGTTGTTATTACAGTTGTAGTTGTTGCTCTGTGGTGTTCCCGATGACGACTGACTGACTGTCCGTCTGTCTGTCTGTCCGTCCGTCCGACTGGGGGGAAATCTTTTTTCGGTCCCGGGCGAATGAACGGTAACTGAAAACGCTTGAAACGATGCCCGCCAGG ************************************************..((((((.(((((.(((((....)))))..)).))).)))))).((((((((..(((.....))).))))))))...((((.((((((.(((.(((.....))).))).))).)))..(((.(((....))).))).........)))).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	V042 embryo
.................................................................................................................................................................................................TGTTCGGTCCCGGGCGGA........................................	18	2	6	0.17	1	1	0
......................................GGAGTTGATGTGTTTAGCTG.................................................................................................................................................................................................	20	3	10	0.10	1	0	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droPer2	scaffold_1:9118693-9118943 +	dpe_595	ACGGACACGGACATGG-------------CT-------C-TCGGCGGCAGTTTGCGCCT----------------GGAAATGATGTGG-------TTAGCTGTGGCTCCTGCGGTGTGCTG-TACTG----ATGCT------TCAGTTGTTATTACAGT---TG--------------TAGTTGTTGCTCTGTG------GTGTTCCCGATGACGAC----T-----GACTGACTGTCCGTCTGTCTGTCTGTCCGTCCGTCCGACTGGGGGGAAATCTT---------------T-T--TTCGGTCC-CGGGCGAAT--GAACGGTAA----------CTGAAAACGCTTGAAACGATGCCCGCCAGG
dp5	4_group3:7672740-7672980 +		ACGGACATGGCTC---------------------------TCGGCGGCAGTTTGCGCCT----------------GGAAATGATGTGG-------TTAGCTGTGGCTCCTGCGGTGTGCTG-TACTG----ATGCT------TCAGTTGTTATTACAGT---TG--------------TAGTTGTTGCTCTGTG------GTGTTCCCGATGACGAC----T-----GACTGACTGTCCGTCTGTCTGTCTGTCCGTCC----GACTGGGGGAAAAACTT---------------T-T--TTCGGTCC-AGGGCGAAT--GAACGGTAA----------CTGAAAACGCTTGAAACGCCGCCCGCCAGG
droWil2	scf2_1100000004521:2059109-2059193 -		GTAAAAGTGGATATG---------GAGAACT-------------GGGCAGTTTGCGCCT----------------GGAAATGATGTGG-------TTAGTTGTGGCTTGTGCGGTC--CTGATACTG----ATGCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12963:13455770-13455846 +		ACATGCA----CA--------TGGTTGAATGTGCCGCGC-CTCGCGGCAGTTTGCGCCT----------------GGAAATGATGTGGCATGTGGTTAGTTGTGGC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6680:7603465-7603620 +		ACGGACAGGGACAGGGACACGGGCGAGG--------------------ACTCTGTGCCGGACTTGGACTACGGCCAAATGCAATGAGC----------------------------------------------CA------AAAGTTGTT----------------T-----------A--------------ATGTATG---------CAACGCCTGTCT-----GTCTGACCGTCCGCCTGTCCGTCTGTCCGCCCG--------------------T-----TCGCCTCTCT-T--CTCGATCC-CGG---------------------------------------------------------
droAna3	scaffold_12916:7145249-7145475 -		GCAGATG--GATA------CCT------ACT-------CATTGCCGTCAGTTTGTGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGTGGTCG-----GTC--CTTGTGTTG----GGGCAACCAGCCCAGTGGTTAGTGTAGC---TGCTGA---------------------------TGG-AG---------TGACGAC----T-----GGA------------------------------------TGTTGGACTAC-TTTCAGTTTTTTTTT--TTT--TTTGGGTAACAG-TCAGTTGTAACGGTTACTGACTGTTACTGGAACTGGTTAAAGTTAGATCTACCGGC
droBip1	scf7180000396566:317192-317301 -		GCAGATG--GATA------CCT------ACT-------CATTGCCGTCAGTTTGTGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGTGGTCG-----GTC--CTTGTGTTG----GGGCAACCGACCCAGTGGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGGTAG----------CTG---------------------------
droKik1	scf7180000302408:827221-827414 +		ACAAATG------------ACCGTGGAAACT-------CACTGCCGGCAGTTTGCGACT----------------GGAAATGATGTGGT---TGGTTAGTTGTGGTCCATGCGGTGT---------------GG----C----CATTTGA----------------AATGACGAT-GGGA--------------GTGGAAATGGGCATGACGACGGC----TGGCCCGGC------------------------------------TGATGGGAAAAACT---------------TTT--TCCG---------------------GCAA----CTGTAACTACC-ACAGCTAAAGTTAGGCCCTCCGGT
droFic1	scf7180000453842:141240-141435 -		ACGAATA------------CTCGGGAAAACT-------CACTGCCGGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGTGGTCCATGTGGTG-----------GTTG----TTGT-----------------TGCTTCTCCTGA-----------A--------------ATGGAAA---------TGACGAC----T-----GGC------------------------------------TGACTGAGAAC-TT--------------TT-T--TTTGGGCT-CAGCCAACTTGTAACCGTAA----ATGTAACTACA-TCATTTAAAGTTAGGCCCGCCGGC
droEle1	scf7180000491186:631831-632026 -		TCCGACAGGAATA----------------------------TGGCGGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGCGGTCCTTGTGGC-----------CGTTG----TTGC-----------------TGCTTTTACTGATGACGTC-GGGC--------------ATGGAAA---------TAACGAC----T-----GAC------------------------------------TGACGGCAAAGCTT---------------TTT--TTCGGGC--CGGCCATGTAACAACCGTAA----ATGTAAC-ACA-GCAGTTAAAGTTAGGCCCGTTGGC
droRho1	scf7180000777920:52175-52344 -		TCCGACATGGAAA----------------------------TGGTGGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGC------------------------------------------------------------CCTGATGACGTT-GGGC--------------ATGGAAA---------TGACGAC----T-----GGC------------------------------------TGACGGAAAAACTT---------------TTT--TTCGGGCC-CGGCCAAGTTGTAACCGTAA----ATGTAACTACA-GCAGTTAAAGTTTGGCCCGTCGGC
droBia1	scf7180000302422:7454318-7454525 +		ATGGAAATGGATA------CTCTGGGAAATT-------CACTGCCGGTAGTTTGCGCCT----------------GGAAATGATGTGGT---CGGTTAGTTGCGGTCCGTGTGGT-----------TGTTGGATCAGGC-----------------CGCTTCTCTTGATGACGTT-GGGC--------------ATGGAAA---------TGACGAC----C-----GCC------------------------------------TGACGGCAAAACTT---------------TTTTTTGCGGACC-C-----------AACCGTAA----ATGTAACTACA-GCAGATAGAACTAGGCCCTCCGGC
droTak1	scf7180000415104:163880-164093 +		ACGAATA------------CTCGGGAAAACT-------CACTGCCGGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGCGGTCCATGTGGTGGC--------CGTTGGTCCTTGC-----------------TGCTACTCCTGATGACGCT-GGTC--------------ATGGAAA---------TGACGAC----T-----GCC------------------------------------TGACGGAAAAACTTT---TTTTCCTCTTTT-T--TTCGGACC-C-----------AACCGTAA----ATGTAACTACA-GCAGTTAAAGTTAGGCCCTCCGGC
droEug1	scf7180000409767:659798-660014 +		ATGTATA------------CTTGGGAAAGCT-------CACTGCCAGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGCGGTCCATGTGCT-----------G----GTTCTTCC-----------------TGCTCCTCCTGATGACGTTCGGGC--------------ATGGAAA---------TGACGAC----T-----GGC------------------------------------TGACTGCAAAACTTT-----TTCCCTTTTT-T--TTCGGCCT-CGACCAAGTTGTAACCGTAA----ATGTAACTACG-GCAGTTAAAGTTGGGTCCGTCGGC
droSec2	scaffold_4:2195500-2195543 +		ACGGACACGGACATTG------CTTGA-------CCAGC-AAGGCGGCATTTCGCGCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droYak3	X:16964544-16964567 +		ACGGACACGGACAAG------------GATC-------TG--G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AC
droEre2	scaffold_4845:3819856-3820062 +		ATGGAAATGGACTTGAGTACTCGGGAAAACT-------CACTGCCATCAGTTTGTGTC-----------------GGAAATGATGTGGT---TGGTTACTTGCGGTCCATGTGCT-----------G----CAG----C-----------------TGCT-CTCCTGATGACGTT-GGAC--------------ATGGATA---------TGACGAC----T-----GGC------------------------------------TGCCGGAAAAC-TTA--------------CTC--CT-------TGACCAAGTTTTAACCGTAA----ATGTAACTACC-GCAGTTAAACTTAGGCCCGCTGGC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

ACGGACACGGACATGG-------------CT-------C-TCGGCGGCAGTTTGCGCCT----------------GGAAATGATGTGG-------TTAGCTGTGGCTCCTGCGGTGTGCTG-TACTG----ATGCT------TCAGTTGTTATTACAGT---TG--------------TAGTTGTTGCTCTGTG------GTGTTCCCGATGACGAC----T-----GACTGACTGTCCGTCTGTCTGTCTGTCCGTCCGTCCGACTGGGGGGAAATCTT---------------T-T--TTCGGTCC-CGGGCGAAT--GAACGGTAA----------CTGAAAACGCTTGAAACGATGCCCGCCAGG	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

dp5

ACGGACATGGCTC---------------------------TCGGCGGCAGTTTGCGCCT----------------GGAAATGATGTGG-------TTAGCTGTGGCTCCTGCGGTGTGCTG-TACTG----ATGCT------TCAGTTGTTATTACAGT---TG--------------TAGTTGTTGCTCTGTG------GTGTTCCCGATGACGAC----T-----GACTGACTGTCCGTCTGTCTGTCTGTCCGTCC----GACTGGGGGAAAAACTT---------------T-T--TTCGGTCC-AGGGCGAAT--GAACGGTAA----------CTGAAAACGCTTGAAACGCCGCCCGCCAGG	Size	Hit Count	Total Norm	Total	M022 Male-body	M040 Female-body	M059 Embryo	M062 Head	V043 Embryo	V051 Head	V112 Male-body	SRR902010 Ovary	SRR902011 Testis	SRR902012 CNS imaginal disc
................................................................................................................................................................................................................................................TCTGTCTGTCTGTCCGTCC----..........................................................................................................	19	20	0.10	2	0	2	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................TGTCCGTCTGTCTGTCTGTCC..................................................................................................................	21	14	0.07	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................GTCCGTCTGTCTGTCTGTCC..................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droWil2

GTAAAAGTGGATATG---------GAGAACT-------------GGGCAGTTTGCGCCT----------------GGAAATGATGTGG-------TTAGTTGTGGCTTGTGCGGTC--CTGATACTG----ATGCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
No Reads

droVir3

ACATGCA----CA--------TGGTTGAATGTGCCGCGC-CTCGCGGCAGTTTGCGCCT----------------GGAAATGATGTGGCATGTGGTTAGTTGTGGC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	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
....................................................TGCGCCT----------------GGAAATGATGTGT.........................................................................................................................................................................................................................................................................................	20	1	2.00	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	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

droMoj3

ACGGACAGGGACAGGGACACGGGCGAGG--------------------ACTCTGTGCCGGACTTGGACTACGGCCAAATGCAATGAGC----------------------------------------------CA------AAAGTTGTT----------------T-----------A--------------ATGTATG---------CAACGCCTGTCT-----GTCTGACCGTCCGCCTGTCCGTCTGTCCGCCCG--------------------T-----TCGCCTCTCT-T--CTCGATCC-CGG---------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droAna3

GCAGATG--GATA------CCT------ACT-------CATTGCCGTCAGTTTGTGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGTGGTCG-----GTC--CTTGTGTTG----GGGCAACCAGCCCAGTGGTTAGTGTAGC---TGCTGA---------------------------TGG-AG---------TGACGAC----T-----GGA------------------------------------TGTTGGACTAC-TTTCAGTTTTTTTTT--TTT--TTTGGGTAACAG-TCAGTTGTAACGGTTACTGACTGTTACTGGAACTGGTTAAAGTTAGATCTACCGGC	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droBip1

GCAGATG--GATA------CCT------ACT-------CATTGCCGTCAGTTTGTGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGTGGTCG-----GTC--CTTGTGTTG----GGGCAACCGACCCAGTGGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGGTAG----------CTG---------------------------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

ACAAATG------------ACCGTGGAAACT-------CACTGCCGGCAGTTTGCGACT----------------GGAAATGATGTGGT---TGGTTAGTTGTGGTCCATGCGGTGT---------------GG----C----CATTTGA----------------AATGACGAT-GGGA--------------GTGGAAATGGGCATGACGACGGC----TGGCCCGGC------------------------------------TGATGGGAAAAACT---------------TTT--TCCG---------------------GCAA----CTGTAACTACC-ACAGCTAAAGTTAGGCCCTCCGGT	Size	Hit Count	Total Norm	Total
No Reads

droFic1

ACGAATA------------CTCGGGAAAACT-------CACTGCCGGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGTGGTCCATGTGGTG-----------GTTG----TTGT-----------------TGCTTCTCCTGA-----------A--------------ATGGAAA---------TGACGAC----T-----GGC------------------------------------TGACTGAGAAC-TT--------------TT-T--TTTGGGCT-CAGCCAACTTGTAACCGTAA----ATGTAACTACA-TCATTTAAAGTTAGGCCCGCCGGC	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TCCGACAGGAATA----------------------------TGGCGGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGCGGTCCTTGTGGC-----------CGTTG----TTGC-----------------TGCTTTTACTGATGACGTC-GGGC--------------ATGGAAA---------TAACGAC----T-----GAC------------------------------------TGACGGCAAAGCTT---------------TTT--TTCGGGC--CGGCCATGTAACAACCGTAA----ATGTAAC-ACA-GCAGTTAAAGTTAGGCCCGTTGGC	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TCCGACATGGAAA----------------------------TGGTGGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGC------------------------------------------------------------CCTGATGACGTT-GGGC--------------ATGGAAA---------TGACGAC----T-----GGC------------------------------------TGACGGAAAAACTT---------------TTT--TTCGGGCC-CGGCCAAGTTGTAACCGTAA----ATGTAACTACA-GCAGTTAAAGTTTGGCCCGTCGGC	Size	Hit Count	Total Norm	Total
No Reads

droBia1

ATGGAAATGGATA------CTCTGGGAAATT-------CACTGCCGGTAGTTTGCGCCT----------------GGAAATGATGTGGT---CGGTTAGTTGCGGTCCGTGTGGT-----------TGTTGGATCAGGC-----------------CGCTTCTCTTGATGACGTT-GGGC--------------ATGGAAA---------TGACGAC----C-----GCC------------------------------------TGACGGCAAAACTT---------------TTTTTTGCGGACC-C-----------AACCGTAA----ATGTAACTACA-GCAGATAGAACTAGGCCCTCCGGC	Size	Hit Count	Total Norm	Total
No Reads

droTak1

ACGAATA------------CTCGGGAAAACT-------CACTGCCGGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGCGGTCCATGTGGTGGC--------CGTTGGTCCTTGC-----------------TGCTACTCCTGATGACGCT-GGTC--------------ATGGAAA---------TGACGAC----T-----GCC------------------------------------TGACGGAAAAACTTT---TTTTCCTCTTTT-T--TTCGGACC-C-----------AACCGTAA----ATGTAACTACA-GCAGTTAAAGTTAGGCCCTCCGGC	Size	Hit Count	Total Norm	Total
No Reads

droEug1

ATGTATA------------CTTGGGAAAGCT-------CACTGCCAGCAGTTTGCGCCT----------------GGAAATGATGTGGT---TGGTTAGTTGCGGTCCATGTGCT-----------G----GTTCTTCC-----------------TGCTCCTCCTGATGACGTTCGGGC--------------ATGGAAA---------TGACGAC----T-----GGC------------------------------------TGACTGCAAAACTTT-----TTCCCTTTTT-T--TTCGGCCT-CGACCAAGTTGTAACCGTAA----ATGTAACTACG-GCAGTTAAAGTTGGGTCCGTCGGC	Size	Hit Count	Total Norm	Total
No Reads

droSec2

ACGGACACGGACATTG------CTTGA-------CCAGC-AAGGCGGCATTTCGCGCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
No Reads

droYak3

ACGGACACGGACAAG------------GATC-------TG--G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AC

Size

Hit Count

Total Norm

Total

M026
Head

M043
Female-body

M056
Embryo

V046
Embryo

V052
Head

V058
Head

V120
Male-body

SRR1275488
Male larvae

SRR1275486
Male prepupae

SRR1275484
Male prepupae

GSM1528802
follicle cells

No Reads

droEre2

ATGGAAATGGACTTGAGTACTCGGGAAAACT-------CACTGCCATCAGTTTGTGTC-----------------GGAAATGATGTGGT---TGGTTACTTGCGGTCCATGTGCT-----------G----CAG----C-----------------TGCT-CTCCTGATGACGTT-GGAC--------------ATGGATA---------TGACGAC----T-----GGC------------------------------------TGCCGGAAAAC-TTA--------------CTC--CT-------TGACCAAGTTTTAACCGTAA----ATGTAACTACC-GCAGTTAAACTTAGGCCCGCTGGC	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

dpe_595

scaffold_1:9118743-9118893 +

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