dpe_312

Name	Class	Family	Strand
Gypsy12-I_Dpse-int	LTR	Gypsy	-

Name

Class

Family

Strand

Gypsy12-I_Dpse-int

LTR

Gypsy

TCCCCTTCAGGTGTCGCTTTTGATAATTACATAAAACTGTAGGTTACATCACTAACCATACATTATACAGTATACTGTATGGTTAGTGGTTACATGTATCCAATGTGTAGTTAGCGTATAGTTATCATATACCAAAGAAA *********************************......((.((((((((((((((((((.((((...)))).))))))))))))).....))))).))....*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V111 male body	V050 head	V057 head	M042 female body	V042 embryo
........................................................................TACTGTATGGTTAGTGGTTACA..............................................	22	0	2	8.50	17	8	3	2	2	2
........................................................................TACTGTATGGTTAGTGGTTAC...............................................	21	0	2	1.50	3	1	1	1	0	0
.......................................................................ATACTGTATGGTTAGTGGTTAC...............................................	22	0	2	1.50	3	0	1	0	1	1
......................................................................TATACTGTATGGTTAGTGG...................................................	19	0	20	1.45	29	29	0	0	0	0
........................................................................TACTGTATGGTTAGTGGTTACAT.............................................	23	0	2	1.00	2	2	0	0	0	0
........................................................................TACTGTATGGGTAGTGGGTACA..............................................	22	2	2	0.50	1	0	0	1	0	0
........................................................................TACTGGATGGTTAGTGGTTAC...............................................	21	1	2	0.50	1	0	0	1	0	0
......................................................................TATACTGTATGGTTAGTGGTT.................................................	21	0	20	0.20	4	4	0	0	0	0
.......................................................................ATACTGTATGGTTAGTGGTTA................................................	21	0	18	0.17	3	1	1	1	0	0
.......................................................................ATACTGTATGGTTAGTGGTT.................................................	20	0	20	0.10	2	0	2	0	0	0
......................................................................TATACTGTATGGTTAGTGGT..................................................	20	0	20	0.10	2	0	2	0	0	0
........................................................................TACTGTATGGTTAGTGGTTA................................................	20	0	18	0.06	1	0	0	1	0	0
......................................................................TATACTGTATGGTTATTGGT..................................................	20	1	20	0.05	1	0	0	1	0	0
.....................................................................GTATACTGTATGGTTAGTGGT..................................................	21	0	20	0.05	1	0	0	1	0	0

TCCCCTTCAGGTGTCGCTTTTGATAATTACATAAAACTGTAGGTTACATCACTAACCATACATTATACAGTATACTGTATGGTTAGTGGTTACATGTATCCAATGTGTAGTTAGCGTATAGTTATCATATACCAAAGAAA
***********************************......((.((((((((((((((((((.((((...)))).))))))))))))).....))))).))....***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

V111
male body

V050
head

V057
head

M042
female body

V042
embryo

........................................................................TACTGTATGGTTAGTGGTTACA..............................................

8.50

........................................................................TACTGTATGGTTAGTGGTTAC...............................................

1.50

.......................................................................ATACTGTATGGTTAGTGGTTAC...............................................

1.50

......................................................................TATACTGTATGGTTAGTGG...................................................

1.45

........................................................................TACTGTATGGTTAGTGGTTACAT.............................................

1.00

........................................................................TACTGTATGGGTAGTGGGTACA..............................................

0.50

........................................................................TACTGGATGGTTAGTGGTTAC...............................................

0.50

......................................................................TATACTGTATGGTTAGTGGTT.................................................

0.20

.......................................................................ATACTGTATGGTTAGTGGTTA................................................

0.17

.......................................................................ATACTGTATGGTTAGTGGTT.................................................

0.10

......................................................................TATACTGTATGGTTAGTGGT..................................................

0.10

........................................................................TACTGTATGGTTAGTGGTTA................................................

0.06

......................................................................TATACTGTATGGTTATTGGT..................................................

0.05

.....................................................................GTATACTGTATGGTTAGTGGT..................................................

0.05

Species	Coordinate	ID	Alignment
droPer2	scaffold_32:938149-938288 +	dpe_312	TCCCCTTCAGGTGTCGCTTTTGATAATTACATAAAACTGTAGGTTACATCACTAACCATACATTATACA-------GTATACTGTATGGTTAGTGGTTACATGTATCCAATGTGTAGTTAGCGTATAGTTATCATATACCAAAGAAA
dp5	XR_group8:544470-544616 -		TCCCCTTCAGGTGTCGCTTTTGATAATTACATAAAGCTGTAGGTTACATCAATAACCATACATTATACAGTATACAGTATACTGTATGGTTAGTGGTTACATGTATCCAATGTGTAGTTAGCGTATAGTTATCATGTACCAAAGAAA

Species

Coordinate

Alignment

droPer2

scaffold_32:938149-938288 +

dpe_312

TCCCCTTCAGGTGTCGCTTTTGATAATTACATAAAACTGTAGGTTACATCACTAACCATACATTATACA-------GTATACTGTATGGTTAGTGGTTACATGTATCCAATGTGTAGTTAGCGTATAGTTATCATATACCAAAGAAA

dp5

XR_group8:544470-544616 -

TCCCCTTCAGGTGTCGCTTTTGATAATTACATAAAGCTGTAGGTTACATCAATAACCATACATTATACAGTATACAGTATACTGTATGGTTAGTGGTTACATGTATCCAATGTGTAGTTAGCGTATAGTTATCATGTACCAAAGAAA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

TCCCCTTCAGGTGTCGCTTTTGATAATTACATAAAACTGTAGGTTACATCACTAACCATACATTATACA-------GTATACTGTATGGTTAGTGGTTACATGTATCCAATGTGTAGTTAGCGTATAGTTATCATATACCAAAGAAA	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
...............................................................................TACTGTATGGTTAGTGGTTACA..............................................	22	2	8.50	17	0	2	2	3	2	8
...............................................................................TACTGTATGGTTAGTGGTTAC...............................................	21	2	1.50	3	0	0	0	1	1	1
..............................................................................ATACTGTATGGTTAGTGGTTAC...............................................	22	2	1.50	3	0	1	1	1	0	0
.............................................................................TATACTGTATGGTTAGTGG...................................................	19	20	1.45	29	0	0	0	0	0	29
...............................................................................TACTGTATGGTTAGTGGTTACAT.............................................	23	2	1.00	2	0	0	0	0	0	2
.............................................................................TATACTGTATGGTTAGTGGTT.................................................	21	20	0.20	4	0	0	0	0	0	4
..............................................................................ATACTGTATGGTTAGTGGTTA................................................	21	18	0.17	3	0	0	0	1	1	1
..............................................................................ATACTGTATGGTTAGTGGTT.................................................	20	20	0.10	2	0	0	0	2	0	0
.............................................................................TATACTGTATGGTTAGTGGT..................................................	20	20	0.10	2	0	0	0	2	0	0
...............................................................................TACTGTATGGTTAGTGGTTA................................................	20	18	0.06	1	0	0	0	0	1	0
............................................................................GTATACTGTATGGTTAGTGGT..................................................	21	20	0.05	1	0	0	0	0	1	0

dp5

TCCCCTTCAGGTGTCGCTTTTGATAATTACATAAAGCTGTAGGTTACATCAATAACCATACATTATACAGTATACAGTATACTGTATGGTTAGTGGTTACATGTATCCAATGTGTAGTTAGCGTATAGTTATCATGTACCAAAGAAA	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
............................................................................GTATACTGTATGGTTAGTGG...................................................	20	20	30.55	611	0	605	6	0	0	0	0	0	0	0
........................................................................TACAGTATACTGTATGGTTAGTGG...................................................	24	20	0.45	9	0	2	0	0	0	0	2	3	2	0
......................................................................TATACAGTATACTGTATGGTTAGTGG...................................................	26	7	0.29	2	0	0	0	0	0	0	0	2	0	0
............................................................................GTATACTGTATGGTTAGTGGT..................................................	21	20	0.20	4	0	4	0	0	0	0	0	0	0	0
........................................................................TACAGTATACTGTATGGTTAGTG....................................................	23	20	0.10	2	0	2	0	0	0	0	0	0	0	0
...........................................................................AGTATACTGTATGGTTAGTGG...................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
..........................................................................CAGTATACTGTATGGTTAGTGGT..................................................	23	19	0.05	1	0	1	0	0	0	0	0	0	0	0
..........................................................................CAGTATACTGTATGGTTAGTGG...................................................	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0
............................................................................GTATACTGTATGGTTAGT.....................................................	18	20	0.05	1	0	0	0	0	1	0	0	0	0	0

dpe_312

scaffold_32:938199-938238 +

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

-24.5	-24.3	-23.8