dpe_925

Name	Class	Family	Strand
BEL-1_DPer-LTR	LTR	Pao	-
Gypsy-3_DPer-LTR	LTR	Gypsy	+

------------------------------------------########--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GGAAGGCGTCACTAACTCTAAGTCTTATGCTCTAAGCTTACGATGCTGCGGTGAGCGCAGTGCGGATCGTGTAGTGTCGATCGTGGATCTTCCGAGCGCCCTTCCGAGCGTGCGAGAGCGAGTTGGGACCGGCGTTAGTACAGTGCGCAGCAATTATCTGCGGCTGTCCTGAACAGATAGTACAGATCCTGACTATTAATAGGTGGCCCTGAAGGATGATGGTAAAGTGGGCGTTCTCAACAATGGGCGAT ******************************************************************************......((.......(((((..(((.(((.(((....))).))).)))..)))))..))**************************************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	V057 head	M021 embryo	V111 male body	V042 embryo	V050 head
................................................................................TCGTGGATCTTCCGAGCGCC.......................................................................................................................................................	20	0	3	0.67	2	0	0	2	0	0	0
......................................................................................................................CGAGTTGGGACCGGCGTTAGT................................................................................................................	21	0	2	0.50	1	1	0	0	0	0	0
......................................................................................................................................................................................................................GATGATGGTAAAGTGGGCG..................	19	0	2	0.50	1	0	1	0	0	0	0
................................................................GATCGTGTAGTGTCGATCGTGGATC..................................................................................................................................................................	25	0	2	0.50	1	1	0	0	0	0	0
......................................................................................................................................................................................................ATAGGTGGCCCTGAAGGATGATGGTAAA.........................	28	0	2	0.50	1	0	0	0	1	0	0
....................................................................................................................................................AGCAATTATCTGCGGCTGTCCC.................................................................................	22	1	2	0.50	1	0	0	1	0	0	0
...........................................................................................................................TGGGAAGGGCGTTAGTACGGT...........................................................................................................	21	3	2	0.50	1	0	1	0	0	0	0
..................................................................................................................................................................................................................GAAGGATGATGATCAAGTG......................	19	2	3	0.33	1	0	0	0	0	1	0
..............................................................................GATCGTGGATCTTCCGAGCGC........................................................................................................................................................	21	0	3	0.33	1	1	0	0	0	0	0
......................................................................................................................................TTAGTACAGTGCGCAGAAATTATCT............................................................................................	25	1	4	0.25	1	1	0	0	0	0	0
......................................................................................................TCCGAGCGTGCGAGAGCGAGTCG..............................................................................................................................	23	1	5	0.20	1	1	0	0	0	0	0
......................................................................................................TCCGAGCGTGCGAGTGCGAGA................................................................................................................................	21	2	5	0.20	1	1	0	0	0	0	0
....................................................GAGCGCAGTGCGGTTCTT.....................................................................................................................................................................................	18	2	6	0.17	1	0	1	0	0	0	0
......................................................................................................TCAGAGCGTGCGACAGCGACTT...............................................................................................................................	22	3	7	0.14	1	0	1	0	0	0	0
.............................................................GCGGATCGCGTAGTGACGG...........................................................................................................................................................................	19	3	9	0.11	1	0	1	0	0	0	0
......................................................................................................TCCGTGCGTGCGTGAGCGAGCT...............................................................................................................................	22	3	9	0.11	1	0	1	0	0	0	0
.........................................................................................................................................................................................................GGTGAACCTGAGGGATGATG..............................	20	3	10	0.10	1	0	0	0	0	1	0
...................................................TGAGCGCAGTACGGATCCG.....................................................................................................................................................................................	19	3	12	0.08	1	0	1	0	0	0	0
......................................................................................................TCAGCGCGTGCGAGAGCGACT................................................................................................................................	21	3	15	0.07	1	0	0	0	0	0	1
...........................................AGCTGCGGTGAGCGCGGTG.............................................................................................................................................................................................	19	2	20	0.05	1	0	1	0	0	0	0
..........................................................................................................................................................................................................ATGGGCCTGAAGGATGATC..............................	19	3	20	0.05	1	1	0	0	0	0	0
................................................................................................................CGAGAGCGGGTTGGGACCGG.......................................................................................................................	20	1	20	0.05	1	1	0	0	0	0	0

CCTTCCGCAGTGATTGAGATTCAGAATACGAGATTCGAATGCTACGACGCCACTCGCGTCACGCCTAGCACATCACAGCTAGCACCTAGAAGGCTCGCGGGAAGGCTCGCACGCTCTCGCTCAACCCTGGCCGCAATCATGTCACGCGTCGTTAATAGACGCCGACAGGACTTGTCTATCATGTCTAGGACTGATAATTATCCACCGGGACTTCCTACTACCATTTCACCCGCAAGAGTTGTTACCCGCTA **************************************************************************************************************......((.......(((((..(((.(((.(((....))).))).)))..)))))..))******************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V057 head	M042 female body
.................................................................................................................................TCCGCAATCAGGCCACGCGTC.....................................................................................................	21	3	4	0.25	1	1	0
...........................................................................................................CGTATGCTCTCGCTCAACCCT...........................................................................................................................	21	2	6	0.17	1	0	1
....................................................................................CCTAGAAGGCTAGCGGACA....................................................................................................................................................	19	3	20	0.05	1	1	0

Species	Coordinate	ID	Alignment
droPer2	scaffold_183:59873-60123 +	dpe_925	GGAAGGCGTCACTAACTCTAAGTCTTATGCTCTAAGCTTACGATGCTGCGGTGAGCGCAGTGCGGATCGTGTAGTGTCGATCGTGGATCTTCCGAGCGCCCTTCCGAGCGTGCGAGAGCGAGTTGGGACCGGCGTTAGTACAGTGCGCAGCAATTATCTGCGGCTGTCCTGAACAGATAGTACAGATCCTGACTATTAATAGGTGGCCCTGAAGGATGATGGTAAAGTGGGCGTTCTCAACAATGGGCGAT
dp5	Unknown_group_679:3079-3251 +		TGAAAGCGTAACTAACTCTAAGTCTTGTGCTCTAAGCTT--GATGCTGCGGTGAGCGCCGTGTGGATCGTGTAGTGTCGATCGTAGATTTTCCGAGTGCCCCTCCGAGCGCGCGAGAGCGAGCTGGGACCGGAGTTAGTACAGTGCGCAGCAATTATCTGCGGCTGCACTGAACA----------------------------------------------------------------------------
droWil2	scf2_1100000014064:1217-1291 -		ACATGTTGGAGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCCTCA--ATTCAGACGTGGCC-TG-AGGATCATGGTAGGGTGGGCGTTCACAAGATAGGCCTAT
droBip1	scf7180000394073:3538-3538 +		T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droFic1	scf7180000451564:2433-2433 -		T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEle1	scf7180000489435:577-580 +		CGAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

GGAAGGCGTCACTAACTCTAAGTCTTATGCTCTAAGCTTACGATGCTGCGGTGAGCGCAGTGCGGATCGTGTAGTGTCGATCGTGGATCTTCCGAGCGCCCTTCCGAGCGTGCGAGAGCGAGTTGGGACCGGCGTTAGTACAGTGCGCAGCAATTATCTGCGGCTGTCCTGAACAGATAGTACAGATCCTGACTATTAATAGGTGGCCCTGAAGGATGATGGTAAAGTGGGCGTTCTCAACAATGGGCGAT	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
................................................................................TCGTGGATCTTCCGAGCGCC.......................................................................................................................................................	20	3	0.67	2	2	0	0	0	0	0
......................................................................................................................CGAGTTGGGACCGGCGTTAGT................................................................................................................	21	2	0.50	1	0	1	0	0	0	0
......................................................................................................................................................................................................................GATGATGGTAAAGTGGGCG..................	19	2	0.50	1	0	0	0	0	1	0
................................................................GATCGTGTAGTGTCGATCGTGGATC..................................................................................................................................................................	25	2	0.50	1	0	1	0	0	0	0
......................................................................................................................................................................................................ATAGGTGGCCCTGAAGGATGATGGTAAA.........................	28	2	0.50	1	0	0	0	0	0	1
....................................................................................................................................................AGCAATTATCTGCGGCTGTCCC.................................................................................	22	2	0.50	1	1	0	0	0	0	0
..............................................................................GATCGTGGATCTTCCGAGCGC........................................................................................................................................................	21	3	0.33	1	0	1	0	0	0	0

dp5

TGAAAGCGTAACTAACTCTAAGTCTTGTGCTCTAAGCTT--GATGCTGCGGTGAGCGCCGTGTGGATCGTGTAGTGTCGATCGTAGATTTTCCGAGTGCCCCTCCGAGCGCGCGAGAGCGAGCTGGGACCGGAGTTAGTACAGTGCGCAGCAATTATCTGCGGCTGCACTGAACA----------------------------------------------------------------------------	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
.....GCGTAACTAACTCTAAGTCTTGTGCTC...........................................................................................................................................................................................................................	27	3	1.00	3	0	3	0	0	0	0	0	0	0	0
..............................................................TGGATCGTGTAGTGTCGATCGTAGATTT.................................................................................................................................................................	28	4	0.50	2	0	0	0	0	0	0	0	2	0	0
..............................................................TGGATCGTGTAGTGTCGATCGTAGA....................................................................................................................................................................	25	4	0.50	2	0	0	0	0	0	0	0	1	1	0
..........................................................................TGTCGATCGTAGATTTTCCGAGTGC........................................................................................................................................................	25	4	0.50	2	0	1	0	0	0	0	1	0	0	0
..............................................................TGGATCGTGTAGTGTCGATCGTAGATT..................................................................................................................................................................	27	4	0.50	2	0	0	0	0	0	0	0	2	0	0
.........................TGTGCTCTAAGCTT--GATGCTGCGG........................................................................................................................................................................................................	24	4	0.50	2	0	2	0	0	0	0	0	0	0	0
..............................................TGCGGTGAGCGCCGTGTGGATCG......................................................................................................................................................................................	23	20	0.35	7	0	7	0	0	0	0	0	0	0	0
.....GCGTAACTAACTCTAAGTCTTGTGC.............................................................................................................................................................................................................................	25	3	0.33	1	0	1	0	0	0	0	0	0	0	0
............TAACTCTAAGTCTTGTGCTC...........................................................................................................................................................................................................................	20	3	0.33	1	0	1	0	0	0	0	0	0	0	0
.....GCGTAACTAACTCTAAGTCTTGTGCT............................................................................................................................................................................................................................	26	3	0.33	1	0	1	0	0	0	0	0	0	0	0
....AGCGTAACTAACTCTAAGTCTTG................................................................................................................................................................................................................................	23	3	0.33	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................TCCGAGTGCCCCTCCGAGCGCGCGA........................................................................................................................................	25	4	0.25	1	0	1	0	0	0	0	0	0	0	0
.............................................................GTGGATCGTGTAGTGTCGATCGTAGATT..................................................................................................................................................................	28	4	0.25	1	0	1	0	0	0	0	0	0	0	0
...................................................TGAGCGCCGTGTGGATCGTGTAGTGT..............................................................................................................................................................................	26	4	0.25	1	0	1	0	0	0	0	0	0	0	0
............................................................TGTGGATCGTGTAGTGTCGAT..........................................................................................................................................................................	21	4	0.25	1	0	1	0	0	0	0	0	0	0	0
...........................................................................GTCGATCGTAGATTTTCCGAGTGCCC......................................................................................................................................................	26	4	0.25	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................AATTATCTGCGGCTGCACT.................................................................................	19	4	0.25	1	0	1	0	0	0	0	0	0	0	0
....................................................GAGCGCCGTGTGGATCGTGTAGTGT..............................................................................................................................................................................	25	4	0.25	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................CGCGCGAGAGCGAGCTGGGACCG........................................................................................................................	23	5	0.20	1	0	1	0	0	0	0	0	0	0	0
...................................................TGAGCGCCGTGTGGATCGTG....................................................................................................................................................................................	20	20	0.20	4	0	2	0	0	0	0	0	2	0	0
..............................................TGCGGTGAGCGCCGTGTGGATCGTG....................................................................................................................................................................................	25	20	0.15	3	0	2	0	0	0	0	0	1	0	0
......................................................................................................TCCGAGCGCGCGAGAGCGAG.................................................................................................................................	20	20	0.15	3	0	3	0	0	0	0	0	0	0	0
..............................................TGCGGTGAGCGCCGTGTGGATCGT.....................................................................................................................................................................................	24	20	0.10	2	0	2	0	0	0	0	0	0	0	0
..............................................TGCGGTGAGCGCCGTGTGGATC.......................................................................................................................................................................................	22	20	0.10	2	0	1	0	0	1	0	0	0	0	0
...............................................GCGGTGAGCGCCGTGTGGATCG......................................................................................................................................................................................	22	20	0.10	2	0	2	0	0	0	0	0	0	0	0
...................................................TGAGCGCCGTGTGGATCGT.....................................................................................................................................................................................	19	20	0.10	2	0	2	0	0	0	0	0	0	0	0
......................................................................................................TCCGAGCGCGCGAGAGCGAGC................................................................................................................................	21	19	0.05	1	0	0	1	0	0	0	0	0	0	0
...........................................TGCTGCGGTGAGCGCCGTGTGG..........................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0
................................................CGGTGAGCGCCGTGTGGATC.......................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0
...........................................TGCTGCGGTGAGCGCCGTGTGGAA........................................................................................................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	0	1	0
...........................................TGCTGCGGTGAGCGCCGTG.............................................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0
...........................................TGCTGCGGTGAGCGCCGTGTGGATA.......................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0
....................................................GAGCGCCGTGTGGATCGTG....................................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.............................................CTGCGGTGAGCGCCGTGTGG..........................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.....................................................................................................CTCCGAGCGCGCGAGAGCGAG.................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	1	0	0	0
.............................................CTGCGGTGAGCGCCGTGTGGATC.......................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0
..............................................TGCGGTGAGCGCCGTGTGGAT........................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droWil2

ACATGTTGGAGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCCTCA--ATTCAGACGTGGCC-TG-AGGATCATGGTAGGGTGGGCGTTCACAAGATAGGCCTAT	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...TGTTGGAGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCCTCA--ATTCAGACG................................................	26	11	0.09	1	0	1	0	0	0
......TGGAGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCCTCA--ATTCAGACGTGGCC-..........................................	28	18	0.06	1	0	1	0	0	0
......TGGAGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCCTCA--ATTCAGACGTGG.............................................	26	18	0.06	1	0	1	0	0	0
.........................................................................................................................................................................................ATCCTCA--ATTCAGACGTGGCC-..........................................	21	20	0.05	1	0	1	0	0	0

droBip1

T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droFic1

T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

CGAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

-23.6	-23.3	-23.2	-22.9

dpe_925

scaffold_183:59923-60073 +

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