dps_1759

CDS [Dpse\GA23217-cds]; CDS [Dpse\GA23217-cds]; exon [dpse_GLEANR_11789:3]; exon [dpse_GLEANR_11789:2]; intron [Dpse\GA23217-in]

Repeatable elements

Name	Class	Family	Strand
Gypsy9-I_Dpse-int	LTR	Gypsy	+

Name

Class

Family

Strand

Gypsy9-I_Dpse-int

LTR

Gypsy

Sense Strand Reads

##################################################------------------------------------------------------------################################################## TAAGCAAAGCAGCGAAGAAAGCGATCCGGTCTCCCGAGGGCACTGACGCGGTTCTACCAACGAAGGAAAAGGAACCCAGGACGCCCCTCTAGAAGACAACCCGGCCCCAGCAACAACGGCCGCCACGCAGCAGCCAGGCGCCCGACGTACCACCTCCGAC ************************************************...((.....((...............(((.....))).............)).....))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M040 female body
....................................................................AAGGAACCCAGGACGCCCCTCTAG....................................................................	24	0	1	1.00	1	1
..........................CGGTCTCCCGAGGGCACTGACG................................................................................................................	22	0	1	1.00	1	1
.............................................................GAAGGAAAAGGAACCCAGGACGCCCC.........................................................................	26	0	1	1.00	1	1
......................................................TACCAACGAAGGAAAAGGAACCCA..................................................................................	24	0	2	1.00	2	2
...............................TCCCGAGGGCACTGACGCGGTT...........................................................................................................	22	0	1	1.00	1	1
.........................................................................................TAGAAGACAACCCGGCCCCA...................................................	20	0	1	1.00	1	1
.........................................................................................TAGAAGACAACCCGGCCCCAGCAA...............................................	24	0	1	1.00	1	1
....................................................................AAGGAACCCAGGACGCCCCTCT......................................................................	22	0	1	1.00	1	1
....................................................TCTACCAACGAAGGAAAAGGAACCCA..................................................................................	26	0	2	0.50	1	1
......................................................TACCAACGAAGGAAAAGGAACCCAGGA...............................................................................	27	0	2	0.50	1	1
....................................AGGGCACTGACGCGGTTCTACCAACG..................................................................................................	26	0	2	0.50	1	1
.....................................................CTACCAACGAAGGAAAAGGAACCCA..................................................................................	25	0	2	0.50	1	1
.......................................................ACCCAAGAAGGAAAAGGAAC.....................................................................................	20	2	3	0.33	1	1
....................................................................AAGGAACCCAGGACGCCCCT........................................................................	20	0	20	0.10	2	2
..........................................................................................AGAAGACAACCCGGCCCCAGCA................................................	22	0	17	0.06	1	1
..................................................TTTCTACCAGCGAAGCAAAA..........................................................................................	20	3	17	0.06	1	1
..........................................................................................AGAAGACAACCCGGCCCCAGC.................................................	21	0	17	0.06	1	1
..........................................................................................................................CCACGCAGCAGCCAGGCGC...................	19	0	19	0.05	1	1
....................................................................AAGGAACCCAGGACGCCC..........................................................................	18	0	20	0.05	1	1

##################################################------------------------------------------------------------##################################################
TAAGCAAAGCAGCGAAGAAAGCGATCCGGTCTCCCGAGGGCACTGACGCGGTTCTACCAACGAAGGAAAAGGAACCCAGGACGCCCCTCTAGAAGACAACCCGGCCCCAGCAACAACGGCCGCCACGCAGCAGCCAGGCGCCCGACGTACCACCTCCGAC
**************************************************...((.....((...............(((.....))).............)).....))**************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

M040
female body

....................................................................AAGGAACCCAGGACGCCCCTCTAG....................................................................

1.00

..........................CGGTCTCCCGAGGGCACTGACG................................................................................................................

1.00

.............................................................GAAGGAAAAGGAACCCAGGACGCCCC.........................................................................

1.00

......................................................TACCAACGAAGGAAAAGGAACCCA..................................................................................

1.00

...............................TCCCGAGGGCACTGACGCGGTT...........................................................................................................

1.00

.........................................................................................TAGAAGACAACCCGGCCCCA...................................................

1.00

.........................................................................................TAGAAGACAACCCGGCCCCAGCAA...............................................

1.00

....................................................................AAGGAACCCAGGACGCCCCTCT......................................................................

1.00

....................................................TCTACCAACGAAGGAAAAGGAACCCA..................................................................................

0.50

......................................................TACCAACGAAGGAAAAGGAACCCAGGA...............................................................................

0.50

....................................AGGGCACTGACGCGGTTCTACCAACG..................................................................................................

0.50

.....................................................CTACCAACGAAGGAAAAGGAACCCA..................................................................................

0.50

.......................................................ACCCAAGAAGGAAAAGGAAC.....................................................................................

0.33

....................................................................AAGGAACCCAGGACGCCCCT........................................................................

0.10

..........................................................................................AGAAGACAACCCGGCCCCAGCA................................................

0.06

..................................................TTTCTACCAGCGAAGCAAAA..........................................................................................

0.06

..........................................................................................AGAAGACAACCCGGCCCCAGC.................................................

0.06

..........................................................................................................................CCACGCAGCAGCCAGGCGC...................

0.05

....................................................................AAGGAACCCAGGACGCCC..........................................................................

0.05

Anti-sense strand reads

ATTCGTTTCGTCGCTTCTTTCGCTAGGCCAGAGGGCTCCCGTGACTGCGCCAAGATGGTTGCTTCCTTTTCCTTGGGTCCTGCGGGGAGATCTTCTGTTGGGCCGGGGTCGTTGTTGCCGGCGGTGCGTCGTCGGTCCGCGGGCTGCATGGTGGAGGCTG ************************************************...((.....((...............(((.....))).............)).....))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M040 female body	SRR902010 ovaries	M059 embryo	V112 male body	GSM444067 head
......................................................ATGGTTGCTTCCTTTTCCTTGGGT..................................................................................	24	0	2	14.00	28	27	1	0	0	0
...........................................................................GGTCCTGCGGGGAGATCTTCTGTT.............................................................	24	0	1	11.00	11	11	0	0	0	0
............................................................................GTCCTGCGGGGAGATCTTCTGTT.............................................................	23	0	1	11.00	11	11	0	0	0	0
..........................................................................GGGTCCTGCGGGGAGATCTTCTGTT.............................................................	25	0	1	5.00	5	5	0	0	0	0
.....................................CCCGTGACTGCGCCAAGATGGTTGCTT................................................................................................	27	0	2	3.50	7	6	0	1	0	0
......................................CCGTGACTGCGCCAAGATGGTTGCTT................................................................................................	26	0	2	2.50	5	5	0	0	0	0
.......................................CGTGACTGCGCCAAGATGGTTGCTT................................................................................................	25	0	2	2.50	5	5	0	0	0	0
..............................................GCGCCAAGATGGTTGCTTCCTTTTCCT.......................................................................................	27	0	2	1.50	3	3	0	0	0	0
........................................GTGACTGCGCCAAGATGGTTGCTT................................................................................................	24	0	2	1.50	3	3	0	0	0	0
...............TCTTTCGCTAGGCCAGAGGGCTCCCGT......................................................................................................................	27	0	1	1.00	1	1	0	0	0	0
............................................................................GTCCTGCGGGGAGATCTTCTGT..............................................................	22	0	1	1.00	1	1	0	0	0	0
......................CTAGGCCAGAGGGCTCCCGTGACT..................................................................................................................	24	0	1	1.00	1	1	0	0	0	0
..................................................CAAGATGGTTGCTTCCTTTTCCTTGGGT..................................................................................	28	0	2	1.00	2	2	0	0	0	0
...........................................................................GGTCCTGCGGGGAGATCTTC.................................................................	20	0	1	1.00	1	1	0	0	0	0
....................................................AGATGGTTGCTTCCTTTTCCTTGGGT..................................................................................	26	0	2	1.00	2	2	0	0	0	0
..........................................GACTGCGCCAAGATGGTTGCTTCCT.............................................................................................	25	0	2	1.00	2	2	0	0	0	0
.....................AATAGGCCAGAGGGCTCCCGTGACT..................................................................................................................	25	2	1	1.00	1	1	0	0	0	0
.......................................................................................................................................TCCGCGGGCTGCATGGTGGAGGCT.	24	0	1	1.00	1	1	0	0	0	0
....GTTTCGTCGCTTCTTTCGCTAG......................................................................................................................................	22	0	1	1.00	1	1	0	0	0	0
..................................................................................CGGGGAGATCTTCTGTTGGGC.........................................................	21	0	1	1.00	1	1	0	0	0	0
...........CGCTTCTTTCGCTAGGCCAGAGGGCT...........................................................................................................................	26	0	1	1.00	1	1	0	0	0	0
.........GTCGCTTCTTTCGCTAGGCCAGAGGGC............................................................................................................................	27	0	1	1.00	1	1	0	0	0	0
.....................................CCCGTGACTGCGCCAAGATGGTTGCT.................................................................................................	26	0	2	1.00	2	2	0	0	0	0
...........................................................................GGTCCTGCGGGGAGATCTTCTG...............................................................	22	0	1	1.00	1	1	0	0	0	0
....................................TCCCGTGACTGCGCCAAGATGGTTGCTT................................................................................................	28	0	2	1.00	2	2	0	0	0	0
.........................................................................TGGGTCCTGCGGGGAGATCTTCTGTT.............................................................	26	0	1	1.00	1	1	0	0	0	0
.................................................CCAAGATGGTTGCTT................................................................................................	15	0	3	0.67	2	0	2	0	0	0
........................................................GGTTGCTTCCTTTTCCTTGGGT..................................................................................	22	0	2	0.50	1	1	0	0	0	0
.......................................................................................GGATCGTCTGTTGGGCAGGGG....................................................	21	3	2	0.50	1	1	0	0	0	0
.......................................CGTGACTGCGCCAAGATGGTTGCT.................................................................................................	24	0	2	0.50	1	0	0	0	1	0
..........................................GACTGCGCCAAGATGGTTGCTTCCTT............................................................................................	26	0	2	0.50	1	1	0	0	0	0
................................................GCCAAGATGGTTGCTTCCTTTTCCT.......................................................................................	25	0	2	0.50	1	1	0	0	0	0
.................................GGGTCCCGGGACTACGCCAA...........................................................................................................	20	3	5	0.20	1	0	0	0	0	1
.................................................................................................................GGTGCCGGCCGTGCGTCG.............................	18	2	10	0.10	1	1	0	0	0	0
......................................................ATGGTTGCTTCCCTTTCCTTGGGT..................................................................................	24	1	12	0.08	1	1	0	0	0	0

ATTCGTTTCGTCGCTTCTTTCGCTAGGCCAGAGGGCTCCCGTGACTGCGCCAAGATGGTTGCTTCCTTTTCCTTGGGTCCTGCGGGGAGATCTTCTGTTGGGCCGGGGTCGTTGTTGCCGGCGGTGCGTCGTCGGTCCGCGGGCTGCATGGTGGAGGCTG
**************************************************...((.....((...............(((.....))).............)).....))**************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

M040
female body

SRR902010
ovaries

M059
embryo

V112
male body

GSM444067
head

......................................................ATGGTTGCTTCCTTTTCCTTGGGT..................................................................................

14.00

...........................................................................GGTCCTGCGGGGAGATCTTCTGTT.............................................................

11.00

............................................................................GTCCTGCGGGGAGATCTTCTGTT.............................................................

11.00

..........................................................................GGGTCCTGCGGGGAGATCTTCTGTT.............................................................

5.00

.....................................CCCGTGACTGCGCCAAGATGGTTGCTT................................................................................................

3.50

......................................CCGTGACTGCGCCAAGATGGTTGCTT................................................................................................

2.50

.......................................CGTGACTGCGCCAAGATGGTTGCTT................................................................................................

2.50

..............................................GCGCCAAGATGGTTGCTTCCTTTTCCT.......................................................................................

1.50

........................................GTGACTGCGCCAAGATGGTTGCTT................................................................................................

1.50

...............TCTTTCGCTAGGCCAGAGGGCTCCCGT......................................................................................................................

1.00

............................................................................GTCCTGCGGGGAGATCTTCTGT..............................................................

1.00

......................CTAGGCCAGAGGGCTCCCGTGACT..................................................................................................................

1.00

..................................................CAAGATGGTTGCTTCCTTTTCCTTGGGT..................................................................................

1.00

...........................................................................GGTCCTGCGGGGAGATCTTC.................................................................

1.00

....................................................AGATGGTTGCTTCCTTTTCCTTGGGT..................................................................................

1.00

..........................................GACTGCGCCAAGATGGTTGCTTCCT.............................................................................................

1.00

.....................AATAGGCCAGAGGGCTCCCGTGACT..................................................................................................................

1.00

.......................................................................................................................................TCCGCGGGCTGCATGGTGGAGGCT.

1.00

....GTTTCGTCGCTTCTTTCGCTAG......................................................................................................................................

1.00

..................................................................................CGGGGAGATCTTCTGTTGGGC.........................................................

1.00

...........CGCTTCTTTCGCTAGGCCAGAGGGCT...........................................................................................................................

1.00

.........GTCGCTTCTTTCGCTAGGCCAGAGGGC............................................................................................................................

1.00

.....................................CCCGTGACTGCGCCAAGATGGTTGCT.................................................................................................

1.00

...........................................................................GGTCCTGCGGGGAGATCTTCTG...............................................................

1.00

....................................TCCCGTGACTGCGCCAAGATGGTTGCTT................................................................................................

1.00

.........................................................................TGGGTCCTGCGGGGAGATCTTCTGTT.............................................................

1.00

.................................................CCAAGATGGTTGCTT................................................................................................

0.67

........................................................GGTTGCTTCCTTTTCCTTGGGT..................................................................................

0.50

.......................................................................................GGATCGTCTGTTGGGCAGGGG....................................................

0.50

.......................................CGTGACTGCGCCAAGATGGTTGCT.................................................................................................

0.50

..........................................GACTGCGCCAAGATGGTTGCTTCCTT............................................................................................

0.50

................................................GCCAAGATGGTTGCTTCCTTTTCCT.......................................................................................

0.50

.................................GGGTCCCGGGACTACGCCAA...........................................................................................................

0.20

.................................................................................................................GGTGCCGGCCGTGCGTCG.............................

0.10

......................................................ATGGTTGCTTCCCTTTCCTTGGGT..................................................................................

0.08

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
dp5	Unknown_group_12:11272-11431 +	dps_1759	TAAGCAA--AGCAGCGAAGAA-------AGCGATCCGGTCTCCC-----------GAGGGCACTGACGCGGTTCTAC-----CAACGAA---GGAAAAGGAA--------------CCCAGGACGCCCCTCTAGAAGACAACCC--GGCCCCAGCAACAACGGCCGCCACGCAGCAGC-----------CAGGCGCCCGACGT-----ACCACCTC-----CGAC
droPer2	scaffold_55:34611-34770 +		TAAGCAA--AGCAGCGAAGAA-------AGCGATCCGGTCTCCC-----------GAGGGCACTGACGCGGTTCTAC-----CAACGAA---GGAAAAGGAA--------------CCCAGGACGCCCCTCTAGAAGACAACCC--GGCCCCAGCAACAACGGCCGCCACGCAGCAGC-----------CAGGCGCCCGACGT-----ACCACCTC-----CGAC
droKik1	scf7180000299893:23226-23366 +		CGCGTGG--ACCAGCGAAGGG-------AGCCATGCTCTAACCCACGGGACCAGCCCG--CAGAGCCACGCTCTGAC-----CAGCGAAAAACGACAAGGGA--------------GCCACGCTCCCCACCTGAAGAACAGCCA-------------------------TC------------------------CACGACAC-----ACCACTCAGAGCCAAGC
droFic1	scf7180000452674:140-294 -		CAAACCC--GGCAGCAGAGAACCCTCAAAGCCATCCC-----CAGCCGCAGCACCGAGAACAGAGACACAGTC--AC-----CAGAAGAACACGACCAGAA-----------------------GCCCA-GTCGAAGGATA-CC--AGCAACCGAGACCATGGCAGCGACGCAGAAGGAAGA-------CCGAAGACCAACG----------------------T
droEle1	scf7180000488233:21944-21969 +		AAAGCAC--AG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAACACCGAGGAAAGC
droRho1	scf7180000776997:11435-11616 +		GAGAAGCGGCGCA---CCGAA-------CGCGGTGTGCGCGGCA-------------------------GCTTCTCCTGATACAACGCA---GCTCCAGGAAAACCCCGTGGCAGCCCCACGACGTTTGGTGGGAAAACCCCATAGGGATACAGTCACTACAGCTCCCAAGCAACAGGAACGTGTACGACCGGCGCCTGCCGTGGATAACCACTTC-----CACC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

dp5

TAAGCAA--AGCAGCGAAGAA-------AGCGATCCGGTCTCCC-----------GAGGGCACTGACGCGGTTCTAC-----CAACGAA---GGAAAAGGAA--------------CCCAGGACGCCCCTCTAGAAGACAACCC--GGCCCCAGCAACAACGGCCGCCACGCAGCAGC-----------CAGGCGCCCGACGT-----ACCACCTC-----CGAC	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
................................................................................................AAGGAA--------------CCCAGGACGCCCCTCTAG...........................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...................................CGGTCTCCC-----------GAGGGCACTGACG.............................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
......................................................................................GAA---GGAAAAGGAA--------------CCCAGGACGCCCC................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..........................................................................TAC-----CAACGAA---GGAAAAGGAA--------------CCCA.........................................................................................................	24	2	1.00	2	0	2	0	0	0	0	0	0	0	0
........................................TCCC-----------GAGGGCACTGACGCGGTT........................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................TAGAAGACAACCC--GGCCCCA........................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................TAGAAGACAACCC--GGCCCCAGCAA....................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
................................................................................................AAGGAA--------------CCCAGGACGCCCCTCT.............................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........................................................................TCTAC-----CAACGAA---GGAAAAGGAA--------------CCCA.........................................................................................................	26	2	0.50	1	0	1	0	0	0	0	0	0	0	0
..........................................................................TAC-----CAACGAA---GGAAAAGGAA--------------CCCAGGA......................................................................................................	27	2	0.50	1	0	1	0	0	0	0	0	0	0	0
........................................................AGGGCACTGACGCGGTTCTAC-----CAACG..........................................................................................................................................	26	2	0.50	1	0	1	0	0	0	0	0	0	0	0
.........................................................................CTAC-----CAACGAA---GGAAAAGGAA--------------CCCA.........................................................................................................	25	2	0.50	1	0	1	0	0	0	0	0	0	0	0
................................................................................................AAGGAA--------------CCCAGGACGCCCCT...............................................................................................	20	20	0.10	2	0	2	0	0	0	0	0	0	0	0
....................................................................................................................................AGAAGACAACCC--GGCCCCAGCA.....................................................................	22	17	0.06	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................AGAAGACAACCC--GGCCCCAGC......................................................................	21	17	0.06	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................................................................................CCACGCAGCAGC-----------CAGGCGC.............................	19	19	0.05	1	0	1	0	0	0	0	0	0	0	0
................................................................................................AAGGAA--------------CCCAGGACGCCC.................................................................................................	18	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droPer2

TAAGCAA--AGCAGCGAAGAA-------AGCGATCCGGTCTCCC-----------GAGGGCACTGACGCGGTTCTAC-----CAACGAA---GGAAAAGGAA--------------CCCAGGACGCCCCTCTAGAAGACAACCC--GGCCCCAGCAACAACGGCCGCCACGCAGCAGC-----------CAGGCGCCCGACGT-----ACCACCTC-----CGAC	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
..................................................................................................................................CTAGAAGACAACCC--GGCCCCAGCA.....................................................................	24	2	0.50	1	0	1	0	0	0	0
..........................................................................TAC-----CAACGAA---GGAAAAGGAA--------------CCCAG........................................................................................................	25	2	0.50	1	0	1	0	0	0	0

droKik1

CGCGTGG--ACCAGCGAAGGG-------AGCCATGCTCTAACCCACGGGACCAGCCCG--CAGAGCCACGCTCTGAC-----CAGCGAAAAACGACAAGGGA--------------GCCACGCTCCCCACCTGAAGAACAGCCA-------------------------TC------------------------CACGACAC-----ACCACTCAGAGCCAAGC	Size	Hit Count	Total Norm	Total
No Reads

droFic1

CAAACCC--GGCAGCAGAGAACCCTCAAAGCCATCCC-----CAGCCGCAGCACCGAGAACAGAGACACAGTC--AC-----CAGAAGAACACGACCAGAA-----------------------GCCCA-GTCGAAGGATA-CC--AGCAACCGAGACCATGGCAGCGACGCAGAAGGAAGA-------CCGAAGACCAACG----------------------T	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AAAGCAC--AG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAACACCGAGGAAAGC	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GAGAAGCGGCGCA---CCGAA-------CGCGGTGTGCGCGGCA-------------------------GCTTCTCCTGATACAACGCA---GCTCCAGGAAAACCCCGTGGCAGCCCCACGACGTTTGGTGGGAAAACCCCATAGGGATACAGTCACTACAGCTCCCAAGCAACAGGAACGTGTACGACCGGCGCCTGCCGTGGATAACCACTTC-----CACC	Size	Hit Count	Total Norm	Total
No Reads

-5.7	-5.6	-4.9	-4.8

dps_1759

Unknown_group_12:11322-11381 +

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