dpe_278

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

CATAAGAAATGAAAACCGCTGTGTTTCGTGGTATATATATAATTATGTGTGTGTATTTGGTTGGGGGGTCGCGTGGTAGATCGGCCGTCTGAAGCGGGGGTGAAATCGTAACTAACTAACTCTATGCCTTATGATGCTTTTGATGCCGTGAGCGCCGTGTGGATCGTGTGGATCGTGGAT ********************************************......((((..((((((..(((.(((......(((..((((.....)))).))).....))).)))..))))))..)))).................**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M021 embryo	M042 female body	V057 head	V111 male body	V042 embryo
.........................................................................................................TCGTAACTAACTAACTCTATGCCT...................................................	24	0	3	8.33	25	23	2	0	0	0
.........................................................................TGGTAGACCGGCCGTCAGAAG......................................................................................	21	2	1	1.00	1	0	0	1	0	0
.........................................................................TGGTAGACCGGCCGTCTGAAGA.....................................................................................	22	2	1	1.00	1	0	0	1	0	0
.........................................................................................................TCGTAACTAACTAACTCTATGCCC...................................................	24	1	3	1.00	3	3	0	0	0	0
.............................................................TGGGGGGTCGCGTGGTAGATCGGCCG.............................................................................................	26	0	1	1.00	1	0	1	0	0	0
.........................................................................................................TCGTAACTAACTAACTCTATGCCTT..................................................	25	0	3	1.00	3	0	3	0	0	0
..............................................................................................CTGGGGTGAAGTCGTAACAA..................................................................	20	3	20	0.75	15	0	2	2	11	0
..............................................................................................CTGGGGTGAAGTCGTAAC....................................................................	18	2	16	0.69	11	5	5	0	1	0
..............................................................................................CTGGGGTGAAGTCGTAACA...................................................................	19	3	20	0.65	13	0	4	0	9	0
....................................................................................................................................GATGCTTTTGATGCCGTGAGCGCCG.......................	25	0	2	0.50	1	0	1	0	0	0
.........................................................................................................TCGTAACTAACTAACTCTATGCCTTA.................................................	26	0	3	0.33	1	0	1	0	0	0
.........................................................................................................TCGTAACTAACTAACTCTATGCCTTATGA..............................................	29	0	3	0.33	1	0	1	0	0	0
.........................................................................................................TCGTAACTAACTAACTCTATGCCG...................................................	24	1	3	0.33	1	1	0	0	0	0
.........................................................................................................TCGTAACTAACTAACTCTATGCC....................................................	23	0	3	0.33	1	0	1	0	0	0
....................................................................................................................................................TGAGCGCCGTGTGGATCGTGT...........	21	0	4	0.25	1	0	1	0	0	0
.............................................................................................................................GCCTAATGATGCGTTTGAT....................................	19	2	5	0.20	1	0	0	0	0	1
..........................................................................................................CGTAACTAACTAACTCTATGCCT...................................................	23	0	13	0.15	2	0	2	0	0	0
..................................................GTGTATTTGGTTGGGGGGTC..............................................................................................................	20	0	7	0.14	1	0	1	0	0	0
.......................................TAATTATGTGTGTGTATTTGGTTG.....................................................................................................................	24	0	8	0.13	1	0	1	0	0	0
........................................AATTATGTGTGTGTATTTGGT.......................................................................................................................	21	0	8	0.13	1	0	1	0	0	0
...................................................................GTCGCGTGCTAGATCGGG...............................................................................................	18	2	9	0.11	1	0	1	0	0	0
....................................................................................................................................................TGAGCGCCGTGTGGATCGTG............	20	0	20	0.10	2	0	2	0	0	0
..............................................................................................CTGGGGTGAAGTCGTAACG...................................................................	19	3	20	0.10	2	0	0	0	2	0
..............................................GTGGGTGTATGTGGTTGGGG..................................................................................................................	20	2	12	0.08	1	0	0	0	1	0
...............................................TGACTGCATTTGGTTGGGGGG................................................................................................................	21	3	12	0.08	1	0	0	0	0	1
..........................................................................................................CGTAACTAACTAACTCTATGCCTTATGA..............................................	28	0	13	0.08	1	0	1	0	0	0
..........................................................................................GAAGCGGGGGTGAAATCGTA......................................................................	20	0	15	0.07	1	0	0	0	1	0
...................................................................................................................................TTATGCTTATGATGCCGT...............................	18	2	18	0.06	1	0	0	1	0	0
..............................................................................................CTGGGGAGAAGTCGTAAC....................................................................	18	3	20	0.05	1	0	0	1	0	0
...............................................TGTGTATATTTGGTGGGG...................................................................................................................	18	2	20	0.05	1	0	0	0	0	1

GTATTCTTTACTTTTGGCGACACAAAGCACCATATATATATTAATACACACACATAAACCAACCCCCCAGCGCACCATCTAGCCGGCAGACTTCGCCCCCACTTTAGCATTGATTGATTGAGATACGGAATACTACGAAAACTACGGCACTCGCGGCACACCTAGCACACCTAGCACCTA **********************************......((((..((((((..(((.(((......(((..((((.....)))).))).....))).)))..))))))..)))).................********************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	V111 male body	V057 head
...........................................................................................TTCGCCCCCACTTTAGCATTGATT.................................................................	24	0	13	1.23	16	16	0	0
............................................................................................TCGCCCCCACTTTAGCATTGATT.................................................................	23	0	13	0.54	7	7	0	0
..............TGGCGACACAAAGCACCATATATATATT..........................................................................................................................................	28	0	2	0.50	1	1	0	0
...............GGCGACACAAAGCACCATATATATATT..........................................................................................................................................	27	0	2	0.50	1	1	0	0
.......................................................................................AGACTTCGCCCCCACTTTAGCATTGATT.................................................................	28	0	6	0.33	2	2	0	0
..........................................................................................................................................................GGCACACCTAGCACACCTAGCAC...	23	0	4	0.25	1	1	0	0
..............................................................................................GCCCCCACTTTAGCATTGATT.................................................................	21	0	13	0.23	3	3	0	0
............................................................................................TCGCCCCCACTTTAGCATTGAT..................................................................	22	0	14	0.21	3	3	0	0
...........................................................................................TTCGCCCCCACTTTAGCATTGAT..................................................................	23	0	14	0.21	3	3	0	0
........................................................................................GACTTCGCCCCCACTTTAGCATTGATT.................................................................	27	0	6	0.17	1	1	0	0
..........................................................................................CTTCGCCCCCACTTTAGCATTGATT.................................................................	25	0	13	0.15	2	2	0	0
.................................................................................................................................................GGCACTCGCGGCACACCTAGCAC............	23	0	20	0.15	3	3	0	0
..................................................................................CCGGCAGACTTCGCCCCCATTTTAGCAT......................................................................	28	1	7	0.14	1	1	0	0
.............................................................................................CGCCCCCACTTTAGCATTGATT.................................................................	22	0	13	0.08	1	1	0	0
..........................................................................................ATTCGCCCCCACTTTAGCATTGATT.................................................................	25	1	13	0.08	1	1	0	0
...........................................................................................TTCGCCCCCACTTTATCATTGATT.................................................................	24	1	13	0.08	1	1	0	0
...............................................................................................................GATTGATTGAGATACGGAATA................................................	21	0	15	0.07	1	0	1	0
............................................................................................CCGCCCCCACTTTAGCATTGAT..................................................................	22	1	16	0.06	1	1	0	0
...................................................................GAGCGTACCATCAAGCCG...............................................................................................	18	3	20	0.05	1	0	0	1

Species	Coordinate	ID	Alignment
droPer2	scaffold_502:9594-9773 -	dpe_278	CATAAGAAATGAAAACCGCTGTGTTTCGTGGTATATATATA--ATTATGTGTGTGTATTTGGTTGGG-GGGTCGCGTGGTAGATCGGCCGTCTGAAGCGGGGGTGAAATCGTAACTAACTAACTCTATGCCTTATGATGCTTTTGATGCCGTGAGCGCCGTGTGGATCGTGTGGATCGTGGAT
dp5	Unknown_singleton_3136:2586-2759 +		CATAAGAAATGAAAACCGCTGTGTTTCGTGGTATATATATAGAATTATGTGTGTGTATTTGGTTGGGGGGGTCGCGCGGTAGATCGGCCGTCTGAAGCGGGGGTGAAATCGTAACTAACTAACTCTATGCCTTATGATGCTTTTGATGCCGTGAGCGCCG---------TGTGGATCGTGGAT
droMoj3	scaffold_6170:1827-1863 -		TGT-------------------ATTTTTTAGTATATATATA--AGTATTTATATATAT-----------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000395330:5945-5987 +		TATA-------------------------------TATATA--TATATGAGTGTATATTGGATTGTG-GATTTACGT----------------------------------------------------------------------------------------------------------
droRho1	scf7180000764004:11227-11233 +		CGAGGAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droYak3	v2_chrUh_007:70109-70130 -		GCG-----------------------------------------------------------------------------------------------------------------------------------------------------------------GAGTTTGGAGATCGCGAGC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

CATAAGAAATGAAAACCGCTGTGTTTCGTGGTATATATATA--ATTATGTGTGTGTATTTGGTTGGG-GGGTCGCGTGGTAGATCGGCCGTCTGAAGCGGGGGTGAAATCGTAACTAACTAACTCTATGCCTTATGATGCTTTTGATGCCGTGAGCGCCGTGTGGATCGTGTGGATCGTGGAT	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
............................................................................................................TCGTAACTAACTAACTCTATGCCT...................................................	24	3	8.33	25	23	2	0	0	0	0
............................................................................................................TCGTAACTAACTAACTCTATGCCC...................................................	24	3	1.00	3	3	0	0	0	0	0
...............................................................TGGG-GGGTCGCGTGGTAGATCGGCCG.............................................................................................	26	1	1.00	1	0	1	0	0	0	0
............................................................................................................TCGTAACTAACTAACTCTATGCCTT..................................................	25	3	1.00	3	0	3	0	0	0	0
.......................................................................................................................................GATGCTTTTGATGCCGTGAGCGCCG.......................	25	2	0.50	1	0	1	0	0	0	0
............................................................................................................TCGTAACTAACTAACTCTATGCCTTA.................................................	26	3	0.33	1	0	1	0	0	0	0
............................................................................................................TCGTAACTAACTAACTCTATGCCTTATGA..............................................	29	3	0.33	1	0	1	0	0	0	0
............................................................................................................TCGTAACTAACTAACTCTATGCCG...................................................	24	3	0.33	1	1	0	0	0	0	0
............................................................................................................TCGTAACTAACTAACTCTATGCC....................................................	23	3	0.33	1	0	1	0	0	0	0
.......................................................................................................................................................TGAGCGCCGTGTGGATCGTGT...........	21	4	0.25	1	0	1	0	0	0	0
.............................................................................................................CGTAACTAACTAACTCTATGCCT...................................................	23	13	0.15	2	0	2	0	0	0	0
....................................................GTGTATTTGGTTGGG-GGGTC..............................................................................................................	20	7	0.14	1	0	1	0	0	0	0
.......................................TA--ATTATGTGTGTGTATTTGGTTG......................................................................................................................	24	8	0.13	1	0	1	0	0	0	0
........................................A--ATTATGTGTGTGTATTTGGT........................................................................................................................	21	8	0.13	1	0	1	0	0	0	0
.......................................................................................................................................................TGAGCGCCGTGTGGATCGTG............	20	20	0.10	2	0	2	0	0	0	0
.............................................................................................................CGTAACTAACTAACTCTATGCCTTATGA..............................................	28	13	0.08	1	0	1	0	0	0	0
.............................................................................................GAAGCGGGGGTGAAATCGTA......................................................................	20	15	0.07	1	0	0	0	0	0	1

dp5

CATAAGAAATGAAAACCGCTGTGTTTCGTGGTATATATATAGAATTATGTGTGTGTATTTGGTTGGGGGGGTCGCGCGGTAGATCGGCCGTCTGAAGCGGGGGTGAAATCGTAACTAACTAACTCTATGCCTTATGATGCTTTTGATGCCGTGAGCGCCG---------TGTGGATCGTGGAT	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
............................................................................................................TCGTAACTAACTAACTCTATGCCT...................................................	24	2	5.50	11	0	9	0	0	0	0	0	2	0	0
............................................................................................................TCGTAACTAACTAACTCTATGCCTTA.................................................	26	2	2.50	5	0	3	0	0	0	0	0	2	0	0
.........................................................................................................................................TGCTTTTGATGCCGTGAGCGCCG---------TG............	25	1	2.00	2	0	2	0	0	0	0	0	0	0	0
............................................................................................................TCGTAACTAACTAACTCTATGCC....................................................	23	2	1.00	2	0	0	0	0	0	0	0	2	0	0
.........TGAAAACCGCTGTGTTTCGTGGT.......................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................TGCTTTTGATGCCGTGAGCGCCG---------T.............	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................TGCTTTTGATGCCGTGAGCGCCG---------TGT...........	26	1	1.00	1	0	0	0	0	0	0	1	0	0	0
.............................................................................GGTAGATCGGCCGTCTGAAGCGGGG.................................................................................	25	3	0.67	2	0	0	0	0	0	0	0	2	0	0
.......................................................................................................................................................TGAGCGCCG---------TGTGGATCGTGG..	21	20	0.65	13	0	13	0	0	0	0	0	0	0	0
............................................................................................................TCGTAACTAACTAACTCTATGCCTT..................................................	25	2	0.50	1	0	1	0	0	0	0	0	0	0	0
...............................................................................TAGATCGGCCGTCTGAAGCGGGG.................................................................................	23	3	0.33	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................TGAGCGCCG---------TGTGGATCGTGGA.	22	20	0.30	6	0	2	1	0	0	0	0	2	1	0
.................................................................................................CGGGGGTGAAATCGTAAC....................................................................	18	4	0.25	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................................................TGATGCTTTTGATGCCGTGAGCGCCG---------A.............	27	4	0.25	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................TGAGCGCCG---------TGTGGATCGTG...	20	20	0.20	4	0	2	0	0	0	0	0	2	0	0
...............................................................................TAGATCGGCCGTCTGAAGCGG...................................................................................	21	5	0.20	1	0	1	0	0	0	0	0	0	0	0
...............................................................................TAGATCGGCCGTCTGAAGCG....................................................................................	20	5	0.20	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................CGTAACTAACTAACTCTATGCCT...................................................	23	10	0.20	2	0	2	0	0	0	0	0	0	0	0
..................................................................................................................CTAACTAACTCTATGCCTTATGATGCTTT........................................	29	8	0.13	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................TAACTAACTCTATGCCTTATGATGCTTT........................................	28	8	0.13	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................TAACTAACTAACTCTATGCCTTATG...............................................	25	10	0.10	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................TGAGCGCCG---------TGTGGATCGTGGAT	23	20	0.10	2	0	0	0	0	0	0	0	2	0	0
..................................................................................................................................................TGCCGTGAGCGCCG---------TGTGGATCGTG...	25	20	0.10	2	0	2	0	0	0	0	0	0	0	0
................................................................................................................AACTAACTAACTCTATGCCTTATGA..............................................	25	10	0.10	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................GTAACTAACTAACTCTATGCCTTATG...............................................	26	10	0.10	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................TGCCGTGAGCGCCG---------TGTGGATC......	22	20	0.10	2	0	2	0	0	0	0	0	0	0	0
.............................................................................................................CGTAACTAACTAACTCTATGCC....................................................	22	10	0.10	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................TAACTAACTAACTCTATGCCTTATGA..............................................	26	10	0.10	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................GTAACTAACTAACTCTATGCCT...................................................	22	10	0.10	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................GCCGTGAGCGCCG---------TGTGGATCGTGG..	25	20	0.10	2	0	2	0	0	0	0	0	0	0	0
..................................................................................................................................................TGCCGTGAGCGCCG---------TGTG..........	18	20	0.05	1	0	1	0	0	0	0	0	0	0	0
...................................................................GGGGTCGCGCGGTAGAT...................................................................................................	17	20	0.05	1	0	0	0	0	0	0	0	1	0	0
...................................................................................................................................................GCCGTGAGCGCCG---------TGTGGATCGTG...	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................TGAGCGCCG---------TGTGGATCG.....	18	20	0.05	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................TGCCGTGAGCGCCG---------TGTGGATCGTGG..	26	20	0.05	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................TGCCGTGAGCGCCG---------TGTGGA........	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................GAGCGCCG---------TGTGGATCGTG...	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................................................GCGCCG---------TGTGGATCGTGGAT	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................GAGCGCCG---------TGTGGATCGTGGAT	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droMoj3

TGT-------------------ATTTTTTAGTATATATATA--AGTATTTATATATAT-----------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droBip1

TATA-------------------------------TATATA--TATATGAGTGTATATTGGATTGTG-GATTTACGT----------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

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

droYak3

GCG-----------------------------------------------------------------------------------------------------------------------------------------------------------------GAGTTTGGAGATCGCGAGC

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

dpe_278

scaffold_502:9644-9723 -

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