dpe_196

Name	Class	Family	Strand
(TGGG)n	Simple_repeat	Simple_repeat	+

Name

Class

Family

Strand

(TGGG)n

Simple_repeat

AGGATGCGAAATGTAACGGAAGTGCGCGAAATTTTTGCACATTTCACCGAGCGTCTCCCTTGCGACCCGCAGCAGCAGCGTCTGTGTGGATGGTTGGGCGTGTGGGCGGGTGGGTGGTTGGTTGTGCGGGTGGTCCACTGAATAGTTGGGTGGATTGACAGTTCGGTACT *********************************((((((....(((((.((...(((...((.((((((((..((((((((....)))).)))).)).))))))))...))))).))))))))))).......*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V057 head	V111 male body	M042 female body	V050 head
.....................................................................................................GTGGGCGGGTGGGTGGTT...................................................	18	0	2	4.00	8	0	7	0	1
......................................................................................................TGGCCGGGGGGCTGGTTGGTTGTG............................................	24	3	1	2.00	2	2	0	0	0
.......................................................................................................AGGCGGGTGGGTGGTTGGTTTT.............................................	22	2	1	1.00	1	1	0	0	0
..............................................................................................AGGGCGTGTAGGCGGGTCGGT.......................................................	21	3	1	1.00	1	1	0	0	0
..........................................................................................................CGGGAGGGTGGTTGGCTGTG............................................	20	2	1	1.00	1	1	0	0	0
...........TGTAACGGAGGCGCGCGAT............................................................................................................................................	19	3	16	0.63	10	0	0	10	0
......................................................................................................TGGGAGGGTGGGTAGCTGGTTGTG............................................	24	3	2	0.50	1	1	0	0	0
......................................................................................................TGGCCGGGTGGGTGGTTGGTTCTG............................................	24	2	2	0.50	1	1	0	0	0
......................................................................................................TGGGCGGGTGGGTGGTTGG.................................................	19	0	2	0.50	1	0	0	1	0
..........................................................................................................CGGGTGGGTGGTTGGATGTG............................................	20	1	2	0.50	1	1	0	0	0
......................................................................................................TGGGAGGGTGGGTGGTTGGTTG..............................................	22	1	2	0.50	1	1	0	0	0
......................................................................................................AGGGAGGGTGGGTGGTTGGTTGTG............................................	24	2	2	0.50	1	1	0	0	0
......................................................................................................TGGCGGGGTGGGTAGTTGGTTGTG............................................	24	3	2	0.50	1	1	0	0	0
......................................................................................................TGGGAGGGTGGTTGGTTGGTTGTG............................................	24	2	2	0.50	1	1	0	0	0
......................................................................................................TGGGGGGGTGGGGGATTGGTTGTG............................................	24	3	3	0.33	1	1	0	0	0
......................................................................................................TGGCCGGGTGGCTAGTTGGTTGT.............................................	23	3	3	0.33	1	1	0	0	0
........AAGTGTAACGGAGGCGCGCG..............................................................................................................................................	20	3	6	0.33	2	0	0	2	0
......................................................................................................TGGGGGAGTGGGTTGTTGGTTGTG............................................	24	3	3	0.33	1	1	0	0	0
......................................................................................................TGGGCGGGTGGGTCGCTGGT................................................	20	2	4	0.25	1	1	0	0	0
......................................................................................................TGGCCGGGTGGGTAGCTGGTTGT.............................................	23	3	4	0.25	1	1	0	0	0
......................................................................................................TGGGCGCGTGGTTAGTTGGTTG..............................................	22	3	4	0.25	1	1	0	0	0
......................................................................................................TGGCAGGGTGGGTGGCTGGTTGTG............................................	24	3	8	0.25	2	2	0	0	0
.......................................................................................................GGCCGGGTGGGTTGTTGGTT...............................................	20	2	4	0.25	1	1	0	0	0
......................................................................................................TGGGCGGGGGGGTAGCTGGTTG..............................................	22	3	4	0.25	1	1	0	0	0
........AAGTGTAACGGAGGCGCGC...............................................................................................................................................	19	3	13	0.23	3	0	0	3	0
......................................................................................................TGGGAGAGTGGGTTGTTGGTTG..............................................	22	3	5	0.20	1	1	0	0	0
......................................................................................................AGGGCGGGTGGGTAGCTGGTT...............................................	21	3	5	0.20	1	1	0	0	0
......................................................................................................TGGGCGGGCGGGTGGTTGG.................................................	19	1	5	0.20	1	0	1	0	0
......................................................................................................TGGCCGGGGGGCTGGTTGGTT...............................................	21	3	20	0.20	4	4	0	0	0
......................................................................................................TGGGAGGGTGGGTGGTCGGTT...............................................	21	2	5	0.20	1	1	0	0	0
......................................................................................................TGGGAGGGAGGGTAGTTGGTTG..............................................	22	3	6	0.17	1	1	0	0	0
......................................................................................................TGGCCGGGTGGTTAGTTGGTT...............................................	21	3	20	0.15	3	3	0	0	0
.......................................................................................................GGGCGGGTGGGTTGTTGTTT...............................................	20	2	7	0.14	1	1	0	0	0
.....................................................................................................GTGGGCGGGTGGGCGGTT...................................................	18	1	7	0.14	1	0	1	0	0
......................................................................................................TGGGAGTGTGGGTGGTTGGTT...............................................	21	2	7	0.14	1	1	0	0	0
......................................................................................................TGGGCGTGTGGGTAGCTGGTT...............................................	21	3	8	0.13	1	1	0	0	0
.............................................................................................ATGGGCGTGTAGGCGGGT...........................................................	18	2	9	0.11	1	1	0	0	0
......................................................................................................TGGGAGGGTGGTTGGCTGGTTGTG............................................	24	3	9	0.11	1	1	0	0	0
.......................................................................................................GGGAGGGTGGTTTGTTGGTTGT.............................................	22	3	9	0.11	1	1	0	0	0
........................................................................................................GGCGGGTGGGGGGTTGGT................................................	18	1	9	0.11	1	0	0	1	0
......................................................................................................TGGCCGGGTGGTTGGCTGGTTGTG............................................	24	3	9	0.11	1	1	0	0	0
......................................................................................................TGGACGGGTGGCTGGTTGGTT...............................................	21	2	9	0.11	1	1	0	0	0
......................................................................................................TGGCCGGGTGGCTGGTTAGTTG..............................................	22	3	20	0.10	2	2	0	0	0
......................................................................................................TGGGGGGGTGGGTAGTTGGT................................................	20	2	10	0.10	1	1	0	0	0
......................................................................................................TGGGAGTGTGGGTAGTTGGTTG..............................................	22	3	10	0.10	1	1	0	0	0
......................................................................................................TGGGAGTGTGGGTTGTTGGTT...............................................	21	3	20	0.10	2	2	0	0	0
..................................................................................................................................TGGCCAACTGACTAGTTGGG....................	20	3	11	0.09	1	1	0	0	0
......................................................................................................TGGGGGGGTGGGTAGCTGGTTG..............................................	22	3	11	0.09	1	1	0	0	0
......................................................................................................TGGCAGGGTGGCTGGTTGGTTGTG............................................	24	3	11	0.09	1	1	0	0	0
......................................................................................................TTGGCGGGTGGGGCGTTGGTT...............................................	21	3	11	0.09	1	1	0	0	0
......................................................................................................TGGGGGAGTGGGTCGTTGGTT...............................................	21	3	12	0.08	1	1	0	0	0
......................................................................................................TGGCAGGGTGGGTGGTTGGT................................................	20	2	12	0.08	1	1	0	0	0
......................................................................................................TGGGAGGGTGGGTAGCTGGTTG..............................................	22	3	12	0.08	1	1	0	0	0
...............................................................................................GGGCGTGTGGGCGGTTTG.........................................................	18	2	13	0.08	1	0	0	1	0
......................................................................................................AGGGAGGGTGGGTGGTCGGTTG..............................................	22	3	13	0.08	1	1	0	0	0
...........................................................................................GGTGGGGCGTGTGGCCGGG............................................................	19	2	15	0.07	1	1	0	0	0
......................................................................................................TGGGCGGGTGGGTCGACGGT................................................	20	3	15	0.07	1	1	0	0	0
......................................................................................................TGGGAGGGAGGGTGGTTTGTT...............................................	21	3	16	0.06	1	1	0	0	0
......................................................................................................TGGACGGGTGGGTAGCTGGTT...............................................	21	3	16	0.06	1	0	0	0	1
......................................................................................................TGGCCGGGGGGCTGGTTGGTTG..............................................	22	3	17	0.06	1	1	0	0	0
......................................................................................................TGGGGGTGTGGGTGGCTGGTTG..............................................	22	3	20	0.05	1	1	0	0	0
...............................................................................................GGGCGTGTGGGTTGGTGGGTC......................................................	21	3	20	0.05	1	1	0	0	0
.............................................................................................TTGGGCGTGTGGCCGCGGG..........................................................	19	3	20	0.05	1	1	0	0	0
................................................................................................................GTTGGTTGGTTGTGGTGGTGGT....................................	22	3	20	0.05	1	0	1	0	0
.............................................................................................................GTGGGTGGCTGGTTGTGA...........................................	18	2	20	0.05	1	1	0	0	0
......................................................................................................TGGGAGGGGGGGTGGTAGGTT...............................................	21	3	20	0.05	1	1	0	0	0
......................................................................................................TGGCCGGGTGGTTGGTTGGTT...............................................	21	2	20	0.05	1	1	0	0	0
...........................................................................................................GGCAGGGTGGTTGTTTGTGC...........................................	20	3	20	0.05	1	1	0	0	0
......................................................................................................TGGACGGGGGGCTGGTTGGTTGTG............................................	24	3	20	0.05	1	1	0	0	0
........................................................................................................CGCGGGGGGGTGGGTGGTTGT.............................................	21	3	20	0.05	1	1	0	0	0
......................................................................................................TGGCCGGGTGGTTAGTTGGTTG..............................................	22	3	20	0.05	1	1	0	0	0

AGGATGCGAAATGTAACGGAAGTGCGCGAAATTTTTGCACATTTCACCGAGCGTCTCCCTTGCGACCCGCAGCAGCAGCGTCTGTGTGGATGGTTGGGCGTGTGGGCGGGTGGGTGGTTGGTTGTGCGGGTGGTCCACTGAATAGTTGGGTGGATTGACAGTTCGGTACT
***********************************((((((....(((((.((...(((...((.((((((((..((((((((....)))).)))).)).))))))))...))))).))))))))))).......***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

V057
head

V111
male body

M042
female body

V050
head

.....................................................................................................GTGGGCGGGTGGGTGGTT...................................................

4.00

......................................................................................................TGGCCGGGGGGCTGGTTGGTTGTG............................................

2.00

.......................................................................................................AGGCGGGTGGGTGGTTGGTTTT.............................................

1.00

..............................................................................................AGGGCGTGTAGGCGGGTCGGT.......................................................

1.00

..........................................................................................................CGGGAGGGTGGTTGGCTGTG............................................

1.00

...........TGTAACGGAGGCGCGCGAT............................................................................................................................................

0.63

......................................................................................................TGGGAGGGTGGGTAGCTGGTTGTG............................................

0.50

......................................................................................................TGGCCGGGTGGGTGGTTGGTTCTG............................................

0.50

......................................................................................................TGGGCGGGTGGGTGGTTGG.................................................

0.50

..........................................................................................................CGGGTGGGTGGTTGGATGTG............................................

0.50

......................................................................................................TGGGAGGGTGGGTGGTTGGTTG..............................................

0.50

......................................................................................................AGGGAGGGTGGGTGGTTGGTTGTG............................................

0.50

......................................................................................................TGGCGGGGTGGGTAGTTGGTTGTG............................................

0.50

......................................................................................................TGGGAGGGTGGTTGGTTGGTTGTG............................................

0.50

......................................................................................................TGGGGGGGTGGGGGATTGGTTGTG............................................

0.33

......................................................................................................TGGCCGGGTGGCTAGTTGGTTGT.............................................

0.33

........AAGTGTAACGGAGGCGCGCG..............................................................................................................................................

0.33

......................................................................................................TGGGGGAGTGGGTTGTTGGTTGTG............................................

0.33

......................................................................................................TGGGCGGGTGGGTCGCTGGT................................................

0.25

......................................................................................................TGGCCGGGTGGGTAGCTGGTTGT.............................................

0.25

......................................................................................................TGGGCGCGTGGTTAGTTGGTTG..............................................

0.25

......................................................................................................TGGCAGGGTGGGTGGCTGGTTGTG............................................

0.25

.......................................................................................................GGCCGGGTGGGTTGTTGGTT...............................................

0.25

......................................................................................................TGGGCGGGGGGGTAGCTGGTTG..............................................

0.25

........AAGTGTAACGGAGGCGCGC...............................................................................................................................................

0.23

......................................................................................................TGGGAGAGTGGGTTGTTGGTTG..............................................

0.20

......................................................................................................AGGGCGGGTGGGTAGCTGGTT...............................................

0.20

......................................................................................................TGGGCGGGCGGGTGGTTGG.................................................

0.20

......................................................................................................TGGCCGGGGGGCTGGTTGGTT...............................................

0.20

......................................................................................................TGGGAGGGTGGGTGGTCGGTT...............................................

0.20

......................................................................................................TGGGAGGGAGGGTAGTTGGTTG..............................................

0.17

......................................................................................................TGGCCGGGTGGTTAGTTGGTT...............................................

0.15

.......................................................................................................GGGCGGGTGGGTTGTTGTTT...............................................

0.14

.....................................................................................................GTGGGCGGGTGGGCGGTT...................................................

0.14

......................................................................................................TGGGAGTGTGGGTGGTTGGTT...............................................

0.14

......................................................................................................TGGGCGTGTGGGTAGCTGGTT...............................................

0.13

.............................................................................................ATGGGCGTGTAGGCGGGT...........................................................

0.11

......................................................................................................TGGGAGGGTGGTTGGCTGGTTGTG............................................

0.11

.......................................................................................................GGGAGGGTGGTTTGTTGGTTGT.............................................

0.11

........................................................................................................GGCGGGTGGGGGGTTGGT................................................

0.11

......................................................................................................TGGCCGGGTGGTTGGCTGGTTGTG............................................

0.11

......................................................................................................TGGACGGGTGGCTGGTTGGTT...............................................

0.11

......................................................................................................TGGCCGGGTGGCTGGTTAGTTG..............................................

0.10

......................................................................................................TGGGGGGGTGGGTAGTTGGT................................................

0.10

......................................................................................................TGGGAGTGTGGGTAGTTGGTTG..............................................

0.10

......................................................................................................TGGGAGTGTGGGTTGTTGGTT...............................................

0.10

..................................................................................................................................TGGCCAACTGACTAGTTGGG....................

0.09

......................................................................................................TGGGGGGGTGGGTAGCTGGTTG..............................................

0.09

......................................................................................................TGGCAGGGTGGCTGGTTGGTTGTG............................................

0.09

......................................................................................................TTGGCGGGTGGGGCGTTGGTT...............................................

0.09

......................................................................................................TGGGGGAGTGGGTCGTTGGTT...............................................

0.08

......................................................................................................TGGCAGGGTGGGTGGTTGGT................................................

0.08

......................................................................................................TGGGAGGGTGGGTAGCTGGTTG..............................................

0.08

...............................................................................................GGGCGTGTGGGCGGTTTG.........................................................

0.08

......................................................................................................AGGGAGGGTGGGTGGTCGGTTG..............................................

0.08

...........................................................................................GGTGGGGCGTGTGGCCGGG............................................................

0.07

......................................................................................................TGGGCGGGTGGGTCGACGGT................................................

0.07

......................................................................................................TGGGAGGGAGGGTGGTTTGTT...............................................

0.06

......................................................................................................TGGACGGGTGGGTAGCTGGTT...............................................

0.06

......................................................................................................TGGCCGGGGGGCTGGTTGGTTG..............................................

0.06

......................................................................................................TGGGGGTGTGGGTGGCTGGTTG..............................................

0.05

...............................................................................................GGGCGTGTGGGTTGGTGGGTC......................................................

0.05

.............................................................................................TTGGGCGTGTGGCCGCGGG..........................................................

0.05

................................................................................................................GTTGGTTGGTTGTGGTGGTGGT....................................

0.05

.............................................................................................................GTGGGTGGCTGGTTGTGA...........................................

0.05

......................................................................................................TGGGAGGGGGGGTGGTAGGTT...............................................

0.05

......................................................................................................TGGCCGGGTGGTTGGTTGGTT...............................................

0.05

...........................................................................................................GGCAGGGTGGTTGTTTGTGC...........................................

0.05

......................................................................................................TGGACGGGGGGCTGGTTGGTTGTG............................................

0.05

........................................................................................................CGCGGGGGGGTGGGTGGTTGT.............................................

0.05

......................................................................................................TGGCCGGGTGGTTAGTTGGTTG..............................................

0.05

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droPer2	scaffold_44:46523-46692 +	dpe_196	AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTCA----C--CGAGCGTCTCC--------------------CTTGC----GACCCGCAGCAGCAG---CGTCTG---------T---GT-----------------------------------------------------------GGATGGTTGGGCGT-----GTGGGCGGGTGG--------GTGGTTGGTTGTGCGGG------------------------------TGGTCC-ACTGAATAGTTGGGTGGATTGACAGTTCGGTAC------T
dp5	3:11836182-11836356 +		AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTCA----C--CGAGCGTCTCC--------------------CTTGC----GACTCGCAGCAGCAG---CGTCTG---------T---GT-----------------------------------------------------------GGATGGTTGGGCGT-----GTGGGCGGGTGGGTGGTTGT------------GCGGGT----------------------GGTCCACTGAGTTGGGTGAATAGTTGGGTGGATTGACAGTTCGGTAC------T
droWil2	scf2_1100000004513:2214901-2215035 +		AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGTACATTTTA----C--CAAG-TAGTAG--------------------TCGCT----------------------CGTTCG---------T---TC-----------------------------------------------------------GGTCGGTTGGACGC-----TTA----------------------------------TAGTACATAATAGTTGAGAGGGAGTAA---------------GGG---------------GACTGGAGGTTTTTTTT
droVir3	scaffold_12823:1010134-1010269 +		AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTTG---A--GAAGTGTCTCCATCTACTTACTGCAGCAGCA-----ACAGCAGTTGTTGTTGATG---ATGTTG---------T---------------------------------------GGGCA-----------AGTCTGTGCGGGTGGCTTAGCG--------------------------------------------------------------------------------------------------------------GGG------C
droMoj3	scaffold_6496:2922211-2922359 -		AGGATGCGCAATGTTAAAAGGAAGTGCGCGAAATTTTTGCACATTTTTGGGGC--CAA-CTACT---------TAC------------TGC----C-ATCGC---CAT-----------TGCCATCTCCCTCC-CCATCGCCGCCGTCGCCGTCGTCGTCGTTGCTGTCGCTGTTGTTGTCCGTTGCCTGTGC-------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15245:8696818-8696969 -		AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTT----G--AAAGCGTCTAC--------------------TTTCA----CAGTTGTTGTTGTTG---C--------TACAT----------TTGCTGCTGGTTCTGTTTTAGTTGTTGCTTTCGGTA-----------TGTCTGTGCG--------------------------------------------------------------------------------------------------------GGCGGCTAGTGGGCCGCCTGT------C
droAna3	scaffold_12943:2074004-2074169 +		AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTA----C--CAA-CGTCTCC--------------------TACCC----------------------CGCCCTGTCCAGCTAT---TA-----------------------------------------------------------ATGCTGCTGTACAT-----TTG-GCGGAAGAGTTGGTGG------------AGGGGA----------------------GGAACGGCGGGTT-GCTGAATGGTTGGGTGAATTGACAGTTCGGGGC------T
droBip1	scf7180000396710:267641-267809 -		AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTA----C--CAA-CGACTCT--------------------CCTGC----C-CCCGC---CTT-----------GTCCAGCTAT---TA-----------------------------------------------------------AGCCAGCTGCACAT-----TTG-ACGGAGGAGCGGTTGG------------AAGGCA----------------------AGAGCGACGGGTT-GCTGAATGGTTGGGTGAATTGACAGTTTGGGGG------T
droKik1	scf7180000302435:32007-32132 +		AGGATGCGCAATGT--AACGGAAGTGCGCGAAATTTGTGAACATTTTA----C--CAAGCAGCCCC-------------------TCCTCA----CAATTGTGGCAGAGA---ACTCTG---------G------------------------------------------------------------------------------------------------------------------------------------------------------AGGAAA-GCTGGGTGGACTGGTGAATTGACAGTTTAAGGA------T
droFic1	scf7180000454108:109676-109805 +		AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTC----T--ACGG-------------------------CT-----ACTG---------------CAAT---------------------------------------------------------------------------------------------GACTAGTGGGGGAATGG--------GTGGCTTGCTGC-----------------------------------TGAATT-GCTGAATGGTCGGGTGAATTGACAGTTCGAGGC------T
droEle1	scf7180000491325:97-225 +		AGGATGCGAAAAGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTT----A------CGTT----------------------T-----TCTG---------------CACT---------------------------------------------------------------------------------------------GCCTGGTGGGTGGATGC--------GTGGCTTGATGT-----------------------------------TAAAAT-GCTGAATGGTAGGGCGAATTGATAACTGGAGGT------T
droRho1	scf7180000763312:9727-9858 +		AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTCTGCACATTTTC----TACTGAAAATG---------------------CT-----CCAG---------------CGAT---------------------------------------------------------------------------------------------GACTAGTGGG----TGG--------GTGGCTTGATGT-----------------------------------TGGAAT-GCTGAATGGTCGGGCGAATTGACAGCCGGAGGC------T

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTCA----C--CGAGCGTCTCC--------------------CTTGC----GACCCGCAGCAGCAG---CGTCTG---------T---GT-----------------------------------------------------------GGATGGTTGGGCGT-----GTGGGCGGGTGG--------GTGGTTGGTTGTGCGGG------------------------------TGGTCC-ACTGAATAGTTGGGTGGATTGACAGTTCGGTAC------T	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
....................................................................................................................................................................................................................GTGGGCGGGTGG--------GTGGTT........................................................................................	18	2	4.00	8	0	0	0	1	0	7
.....................................................................................................................................................................................................................TGGGCGGGTGG--------GTGGTTGG......................................................................................	19	2	0.50	1	0	1	0	0	0	0

dp5

AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTCA----C--CGAGCGTCTCC--------------------CTTGC----GACTCGCAGCAGCAG---CGTCTG---------T---GT-----------------------------------------------------------GGATGGTTGGGCGT-----GTGGGCGGGTGGGTGGTTGT------------GCGGGT----------------------GGTCCACTGAGTTGGGTGAATAGTTGGGTGGATTGACAGTTCGGTAC------T	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
....................................................................................................................................................................................................................GTGGGCGGGTGGGTGGTT................................................................................................	18	2	3.00	6	0	2	0	0	0	1	3	0	0	0
.....................................................................................................................................................................................................................TGGGCGGGTGGGTGGTTG...............................................................................................	18	3	1.67	5	0	2	0	0	0	2	1	0	0	0
....................................................................................................................................................................................................................GTGGGCGGGTGGGTGGTTG...............................................................................................	19	2	1.50	3	0	3	0	0	0	0	0	0	0	0

droWil2

AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGTACATTTTA----C--CAAG-TAGTAG--------------------TCGCT----------------------CGTTCG---------T---TC-----------------------------------------------------------GGTCGGTTGGACGC-----TTA----------------------------------TAGTACATAATAGTTGAGAGGGAGTAA---------------GGG---------------GACTGGAGGTTTTTTTT	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
No Reads

droVir3

AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTTG---A--GAAGTGTCTCCATCTACTTACTGCAGCAGCA-----ACAGCAGTTGTTGTTGATG---ATGTTG---------T---------------------------------------GGGCA-----------AGTCTGTGCGGGTGGCTTAGCG--------------------------------------------------------------------------------------------------------------GGG------C	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
............................................................GTCTCCATCTACTTACTGCAG.....................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................CAGCAGTTGTTGTTGATG---ATG..................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droMoj3

AGGATGCGCAATGTTAAAAGGAAGTGCGCGAAATTTTTGCACATTTTTGGGGC--CAA-CTACT---------TAC------------TGC----C-ATCGC---CAT-----------TGCCATCTCCCTCC-CCATCGCCGCCGTCGCCGTCGTCGTCGTTGCTGTCGCTGTTGTTGTCCGTTGCCTGTGC-------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droGri2

AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTT----G--AAAGCGTCTAC--------------------TTTCA----CAGTTGTTGTTGTTG---C--------TACAT----------TTGCTGCTGGTTCTGTTTTAGTTGTTGCTTTCGGTA-----------TGTCTGTGCG--------------------------------------------------------------------------------------------------------GGCGGCTAGTGGGCCGCCTGT------C	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droAna3

AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTA----C--CAA-CGTCTCC--------------------TACCC----------------------CGCCCTGTCCAGCTAT---TA-----------------------------------------------------------ATGCTGCTGTACAT-----TTG-GCGGAAGAGTTGGTGG------------AGGGGA----------------------GGAACGGCGGGTT-GCTGAATGGTTGGGTGAATTGACAGTTCGGGGC------T	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droBip1

AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTA----C--CAA-CGACTCT--------------------CCTGC----C-CCCGC---CTT-----------GTCCAGCTAT---TA-----------------------------------------------------------AGCCAGCTGCACAT-----TTG-ACGGAGGAGCGGTTGG------------AAGGCA----------------------AGAGCGACGGGTT-GCTGAATGGTTGGGTGAATTGACAGTTTGGGGG------T	Size	Hit Count	Total Norm	Total
No Reads

droKik1

AGGATGCGCAATGT--AACGGAAGTGCGCGAAATTTGTGAACATTTTA----C--CAAGCAGCCCC-------------------TCCTCA----CAATTGTGGCAGAGA---ACTCTG---------G------------------------------------------------------------------------------------------------------------------------------------------------------AGGAAA-GCTGGGTGGACTGGTGAATTGACAGTTTAAGGA------T	Size	Hit Count	Total Norm	Total
No Reads

droFic1

AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTC----T--ACGG-------------------------CT-----ACTG---------------CAAT---------------------------------------------------------------------------------------------GACTAGTGGGGGAATGG--------GTGGCTTGCTGC-----------------------------------TGAATT-GCTGAATGGTCGGGTGAATTGACAGTTCGAGGC------T	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AGGATGCGAAAAGT--AACGGAAGTGCGCGAAATTTTTGCACATTTTT----A------CGTT----------------------T-----TCTG---------------CACT---------------------------------------------------------------------------------------------GCCTGGTGGGTGGATGC--------GTGGCTTGATGT-----------------------------------TAAAAT-GCTGAATGGTAGGGCGAATTGATAACTGGAGGT------T	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AGGATGCGAAATGT--AACGGAAGTGCGCGAAATTTCTGCACATTTTC----TACTGAAAATG---------------------CT-----CCAG---------------CGAT---------------------------------------------------------------------------------------------GACTAGTGGG----TGG--------GTGGCTTGATGT-----------------------------------TGGAAT-GCTGAATGGTCGGGCGAATTGACAGCCGGAGGC------T	Size	Hit Count	Total Norm	Total
No Reads

dpe_196

scaffold_44:46573-46642 +

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

-38.9	-38.4	-38.4