dmo_286

Name	Class	Family	Strand
Gypsy6-I_Dmoj-int	LTR	Gypsy	+

Name

Class

Family

Strand

Gypsy6-I_Dmoj-int

LTR

Gypsy

TACCAAGTGGATGTCAGCTATTTGCCGAGAGCGATGCCAGAGTTATTGACTGAGCGGGCCGAGGATTGGCTGAGGGAAAGCGGACTCCAAGGCGCGACATGGGAAACTTTTAAAAGCGAATTTCTGCAATTCTTTCTCCCGCCGCGGTATTTCA *********************************...((((((.((.......((.(((..(((((.(((.......))).)).)))..))).))......))))))))........**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body	M060 embryo	V056 head	V041 embryo
................................................................................CGGACTCCAAGGCGCGACATGGG...................................................	23	0	5	4.20	21	21	0	0	0
................................................................................CGGACTCCAAGGCGCGACATGG....................................................	22	0	5	2.40	12	11	1	0	0
................................................................................CGGACTCCAAGGCGCGACATGGGA..................................................	24	0	5	1.00	5	5	0	0	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGCGGT......	23	0	9	0.78	7	4	3	0	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGCGG.......	22	0	9	0.44	4	3	1	0	0
................................................................................CGGACTCCAAGGCGCGACATGGGAA.................................................	25	0	5	0.40	2	2	0	0	0
.................................................................................GGACTCCAAGGCGCGACATGGG...................................................	22	0	5	0.40	2	2	0	0	0
................................................................................CGGACTCCAAGGCGCGACATGGGAAAC...............................................	27	0	5	0.40	2	2	0	0	0
................................................................ATTGGCAGTGGGACAGCGGAC.....................................................................	21	3	4	0.25	1	0	0	1	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGCGGTA.....	24	0	9	0.22	2	2	0	0	0
................................................................................CGCACTCCAAGGCGCGACATGG....................................................	22	1	5	0.20	1	0	1	0	0
................................................................................CTGACTCCAAGGCGCGACATGG....................................................	22	1	5	0.20	1	0	1	0	0
................................................................................CTGACTCCAAGGCGCGACA.......................................................	19	1	5	0.20	1	0	1	0	0
................................................................................CGGACTCCAAGGCGCGACATGGC...................................................	23	1	5	0.20	1	1	0	0	0
................................................................................CTGACTCCAAGGCGCGACATGGG...................................................	23	1	5	0.20	1	0	1	0	0
................................................................................CGGACTCCAAGGCGCGACATG.....................................................	21	0	5	0.20	1	1	0	0	0
................................................................................CGGACTCCAAGGCGCGACATGGGAAACT..............................................	28	0	5	0.20	1	1	0	0	0
................................................................................GGGACTCCAAGGCGCGACATGGGAAAC...............................................	27	1	5	0.20	1	1	0	0	0
..................................................TGAGCGGGCCGAGGATTGGC....................................................................................	20	0	8	0.13	1	1	0	0	0
......GTGGATGTCAGCTATTTGCC................................................................................................................................	20	0	9	0.11	1	0	1	0	0
.............................................................................................................................GGAATTCTTTCTCCCGCCGCGGTAT....	25	1	9	0.11	1	0	1	0	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGC.........	20	0	9	0.11	1	0	1	0	0
..............................................................................................................................CAATTCTTTCTCCCGCCGCGGTAT....	24	0	9	0.11	1	1	0	0	0
.........................................................................................................................AACCGCAATTCTTTCTCCCGCCGCGGTA.....	28	3	9	0.11	1	1	0	0	0
TACCAAGTGGATGTCAGCTATTTGCC................................................................................................................................	26	0	9	0.11	1	1	0	0	0
..............................................................................................................................CAATTCTTTCTCCCGCCGCGGTATT...	25	0	9	0.11	1	1	0	0	0
..............................................................................................................................CAATTCTTTCTCCCGCCGCGGTA.....	23	0	9	0.11	1	1	0	0	0
............................................................................................................................TGCAATTATTTCTCCCGCCGCGGTAT....	26	1	9	0.11	1	1	0	0	0
..CCAAGTGGATGTCAGCTATTTGCC................................................................................................................................	24	0	9	0.11	1	1	0	0	0
.............................................................................................................................GCAATACTTTCTACCCCCGCGG.......	22	3	9	0.11	1	0	0	0	1
............................................................................................................................TGCAATTCTTTCTCCCGCCGCGGTAT....	26	0	9	0.11	1	1	0	0	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGCGGTAT....	25	0	9	0.11	1	1	0	0	0

TACCAAGTGGATGTCAGCTATTTGCCGAGAGCGATGCCAGAGTTATTGACTGAGCGGGCCGAGGATTGGCTGAGGGAAAGCGGACTCCAAGGCGCGACATGGGAAACTTTTAAAAGCGAATTTCTGCAATTCTTTCTCCCGCCGCGGTATTTCA
***********************************...((((((.((.......((.(((..(((((.(((.......))).)).)))..))).))......))))))))........************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

M046
female body

M060
embryo

V056
head

V041
embryo

................................................................................CGGACTCCAAGGCGCGACATGGG...................................................

4.20

................................................................................CGGACTCCAAGGCGCGACATGG....................................................

2.40

................................................................................CGGACTCCAAGGCGCGACATGGGA..................................................

1.00

.............................................................................................................................GCAATTCTTTCTCCCGCCGCGGT......

0.78

.............................................................................................................................GCAATTCTTTCTCCCGCCGCGG.......

0.44

................................................................................CGGACTCCAAGGCGCGACATGGGAA.................................................

0.40

.................................................................................GGACTCCAAGGCGCGACATGGG...................................................

0.40

................................................................................CGGACTCCAAGGCGCGACATGGGAAAC...............................................

0.40

................................................................ATTGGCAGTGGGACAGCGGAC.....................................................................

0.25

.............................................................................................................................GCAATTCTTTCTCCCGCCGCGGTA.....

0.22

................................................................................CGCACTCCAAGGCGCGACATGG....................................................

0.20

................................................................................CTGACTCCAAGGCGCGACATGG....................................................

0.20

................................................................................CTGACTCCAAGGCGCGACA.......................................................

0.20

................................................................................CGGACTCCAAGGCGCGACATGGC...................................................

0.20

................................................................................CTGACTCCAAGGCGCGACATGGG...................................................

0.20

................................................................................CGGACTCCAAGGCGCGACATG.....................................................

0.20

................................................................................CGGACTCCAAGGCGCGACATGGGAAACT..............................................

0.20

................................................................................GGGACTCCAAGGCGCGACATGGGAAAC...............................................

0.20

..................................................TGAGCGGGCCGAGGATTGGC....................................................................................

0.13

......GTGGATGTCAGCTATTTGCC................................................................................................................................

0.11

.............................................................................................................................GGAATTCTTTCTCCCGCCGCGGTAT....

0.11

.............................................................................................................................GCAATTCTTTCTCCCGCCGC.........

0.11

..............................................................................................................................CAATTCTTTCTCCCGCCGCGGTAT....

0.11

.........................................................................................................................AACCGCAATTCTTTCTCCCGCCGCGGTA.....

0.11

TACCAAGTGGATGTCAGCTATTTGCC................................................................................................................................

0.11

..............................................................................................................................CAATTCTTTCTCCCGCCGCGGTATT...

0.11

..............................................................................................................................CAATTCTTTCTCCCGCCGCGGTA.....

0.11

............................................................................................................................TGCAATTATTTCTCCCGCCGCGGTAT....

0.11

..CCAAGTGGATGTCAGCTATTTGCC................................................................................................................................

0.11

.............................................................................................................................GCAATACTTTCTACCCCCGCGG.......

0.11

............................................................................................................................TGCAATTCTTTCTCCCGCCGCGGTAT....

0.11

.............................................................................................................................GCAATTCTTTCTCCCGCCGCGGTAT....

0.11

ATGGTTCACCTACAGTCGATAAACGGCTCTCGCTACGGTCTCAATAACTGACTCGCCCGGCTCCTAACCGACTCCCTTTCGCCTGAGGTTCCGCGCTGTACCCTTTGAAAATTTTCGCTTAAAGACGTTAAGAAAGAGGGCGGCGCCATAAAGT **********************************...((((((.((.......((.(((..(((((.(((.......))).)).)))..))).))......))))))))........*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body	M060 embryo	V110 male body	V041 embryo
......................................................................................GGTTCCGCGCTGTACCCTTTGAAA............................................	24	0	5	8.80	44	32	9	1	2
...............................................................................CGCCTGAGGTTCCGCGCTGTACCCTTT................................................	27	0	5	2.60	13	7	6	0	0
.......................CGGCTCTCGCTACGGTCTCAAT.............................................................................................................	22	0	3	2.00	6	3	3	0	0
...............................................................................CGCCTGAGGTTCCGCGCTGTACCCTT.................................................	26	0	5	2.00	10	3	7	0	0
......................ACGGCTCTCGCTACGGTCTCAAT.............................................................................................................	23	0	3	1.67	5	5	0	0	0
...............................................................................CGCCTGAGGTTCCGCGCTGTACCCT..................................................	25	0	5	1.00	5	4	1	0	0
.....................AACGGCTCTCGCTACGGTCTCA...............................................................................................................	22	0	1	1.00	1	0	1	0	0
...................TAAACGGCTCTCGCTACGGTCTCAAT.............................................................................................................	26	0	1	1.00	1	0	1	0	0
.......................................................................................GTTCCGCGCTGTACCCTTTGAAA............................................	23	0	5	1.00	5	3	0	2	0
...............................................................................CGCCTGAGGTTCCGCGCTGTACCC...................................................	24	0	5	0.80	4	2	1	0	1
.....................................................................................AGGTTCCGCGCTGTACCCTTTGAAA............................................	25	0	5	0.80	4	4	0	0	0
....................................................................................GAGGTTCCGCGCTGTACCCTTTGAAA............................................	26	0	5	0.80	4	4	0	0	0
.................................................................................CCTGAGGTTCCGCGCTGTACCCTTT................................................	25	0	5	0.80	4	1	3	0	0
........................GGCTCTCGCTACGGTCTCAAT.............................................................................................................	21	0	3	0.67	2	2	0	0	0
..........................................................................................CCGCGCTGTACCCTTTGAAA............................................	20	0	8	0.63	5	3	2	0	0
....................................................................................GAGGTTCCGCGCTGTACCCTTTGAA.............................................	25	0	5	0.60	3	3	0	0	0
................................................................................GCCTGAGGTTCCGCGCTGTACCCTT.................................................	25	0	5	0.60	3	0	0	3	0
.............................TCGCTACGGTCTCAATAACTGACT.....................................................................................................	24	0	4	0.50	2	1	1	0	0
.................................................................................CCTGAGGTTCCGCGCTGTACCCTT.................................................	24	0	5	0.40	2	0	1	0	1
......................................................................................GGTTCCGCGCTGTACCCTTTGAAAA...........................................	25	0	5	0.40	2	2	0	0	0
.................................................................................CCTGAGGTTCCGCGCTGTACCC...................................................	22	0	5	0.40	2	1	1	0	0
..............................................................................TCGCCTGAGGTTCCGCGCTGTACCCTT.................................................	27	0	5	0.40	2	0	2	0	0
..................................................................................CTGAGGTTCCGCGCTGTACCCTTT................................................	24	0	5	0.40	2	1	1	0	0
................................................................................GCCTGAGGTTCCGCGCTGTACCC...................................................	23	0	5	0.40	2	2	0	0	0
.......................................................................................GTTCCGCGCTGTACCCTTTGAAAA...........................................	24	0	5	0.40	2	2	0	0	0
.....................................................................................AGGTTCCGCGCTGTACCCTTTGAA.............................................	24	0	5	0.40	2	1	0	1	0
....................AGACGGCTCTCGCTACGGTCTCAAT.............................................................................................................	25	1	3	0.33	1	0	1	0	0
.......................CGGCTCTCGCTACGATCTCAAT.............................................................................................................	22	1	3	0.33	1	0	0	0	1
............................CTCGCTACGGTCTCAATAACTGACT.....................................................................................................	25	0	4	0.25	1	0	1	0	0
.............................TCGCTACGGTCTCAATAACTGACTGG...................................................................................................	26	1	4	0.25	1	0	1	0	0
......................................................................................GGTTCCGCGCTGTACCCTTTGAA.............................................	23	0	5	0.20	1	1	0	0	0
................................................................................GCCTGAGGTTCCGCGCTGTATCCTT.................................................	25	1	5	0.20	1	0	1	0	0
..................................................................................CTGGGGTTCCGCGCTGTACCCTT.................................................	23	1	5	0.20	1	1	0	0	0
...............................................CTGACTCGCCCGGCTCCTAACCGACTCCC..............................................................................	29	0	5	0.20	1	0	1	0	0
..............................................................................TCGCCTGAGGTTCCGCGCTGTACCCTTT................................................	28	0	5	0.20	1	0	1	0	0
................................................................................GCCTGAGGTTCCGCGCTGTACCCT..................................................	24	0	5	0.20	1	1	0	0	0
..................................................................................CTGAGGTTCCGCGCTGTACCCTT.................................................	23	0	5	0.20	1	1	0	0	0
..............................................................................CCGCCTGAGGTTCCGCGCTGTACCCT..................................................	26	1	5	0.20	1	1	0	0	0
....................................................................................GAGGTTCCGCGCTGTACCCTTTG...............................................	23	0	5	0.20	1	1	0	0	0
...............................................................................CGCCTGAGGTTCCGCGCTGTACCCTGT................................................	27	1	5	0.20	1	0	1	0	0
......................................................................................GGCTCCGCGCTGTACCCTTTGAAA............................................	24	1	5	0.20	1	0	0	0	1
..............................................................................CCGCCTGAGGTTCCGCGCTGTACCCGT.................................................	27	2	5	0.20	1	0	1	0	0
......................................................................................AGTTCCGCGCTGTACCCTTTGAAA............................................	24	1	5	0.20	1	0	1	0	0
..................................................................................CTGAGGTTCCGCGCTGTACCATT.................................................	23	1	5	0.20	1	0	1	0	0
....................................................................................TTGGTTCCGCGCTGTACCCTTTGAAA............................................	26	2	5	0.20	1	1	0	0	0
..............................................................................TCGCCTGAGGTTCCGCGCTGTACCC...................................................	25	0	5	0.20	1	1	0	0	0
...............................................................................CGCCTGAGGTTCCGCGCTG........................................................	19	0	5	0.20	1	1	0	0	0
...................................................................................CGAGGTTCCGCGCTGTACCCTTT................................................	23	1	5	0.20	1	0	1	0	0
......................................................................................GGTTCCTCGCTGTACCCTTTGAAA............................................	24	1	5	0.20	1	0	1	0	0
...............................................................................CGCCTGAGGTTCCGCGCTGTACCCGT.................................................	26	1	5	0.20	1	0	1	0	0
...................................................................................TGAGGTTCCGCGCTGTACCCTT.................................................	22	0	5	0.20	1	1	0	0	0
.....................................................................................CGGTTCCGCGCTGTACCCTTTGAAA............................................	25	1	5	0.20	1	0	1	0	0
................................................................................GCCTGAGGTTCCGCGCTGTACCCTTT................................................	26	0	5	0.20	1	1	0	0	0
...............................................................................CGCCTGAGGTTCCGCGCTGTTCCC...................................................	24	1	5	0.20	1	0	1	0	0
...................................................................................TGAGGTTCCGCGCTGTACCCTCTG...............................................	24	1	5	0.20	1	0	1	0	0
...................................................................................CGAGGTTCCGCGCTGTACCCTTTGAAAG...........................................	28	2	5	0.20	1	1	0	0	0
.................................................................................CCTGAGGTTCCGCGCTGTACCCT..................................................	23	0	5	0.20	1	1	0	0	0
...............................................................................CGCCTGAGGTTCCGCGCTGTACCCCTT................................................	27	1	5	0.20	1	0	1	0	0
...................................................................................TGAGGTTCCGCGCTGTACCCTTT................................................	23	0	5	0.20	1	0	1	0	0
...............................................................................CGCCTGAGGTTCCGCGCTGTACCCTTTC...............................................	28	1	6	0.17	1	0	1	0	0
.......................................................................................................TTTGAAAATTTTCGCTTAAAGACGT..........................	25	0	7	0.14	1	1	0	0	0
........................................................................................................TTGAAAATTTTCGCTTAAAGACGTT.........................	25	0	7	0.14	1	1	0	0	0
..............................................................................................................ATTTTCGCTTAAAGACGTTAAGAAA...................	25	0	8	0.13	1	1	0	0	0
........................................................................................TTCCGCGCTGTACCCTTTGAAA............................................	22	0	8	0.13	1	1	0	0	0
..........................................................................................CCGCGCTGTACCCTTTGAAAA...........................................	21	0	8	0.13	1	0	1	0	0
.........................................................................................TCCGCGCTGTACCCTTTGAAA............................................	21	0	8	0.13	1	0	0	0	1
............................................................................................................AAATTTTCGCTTAAAGACGTTAAGAAA...................	27	0	8	0.13	1	0	1	0	0
.........................................................................................ACCGCGCTGTACCCTTTGAAAATT.........................................	24	1	8	0.13	1	1	0	0	0
.........................................................................................CCCGCGCTGTACCCTTTGAAAATTT........................................	25	1	8	0.13	1	0	1	0	0
.........................................................................................TCCGCGCTGTACCCTTTGAAAATT.........................................	24	0	8	0.13	1	1	0	0	0
..........................................................................................CCGCGCTGTACCCTTTGAAAAT..........................................	22	0	8	0.13	1	0	1	0	0
.........................................................................................CCCGCGCTGTACCCTTTGAAA............................................	21	1	8	0.13	1	0	1	0	0
...........................................................................................................AAAATTTTCGCTTAAAGACGTTAAGAAA...................	28	0	8	0.13	1	1	0	0	0
.............................................................................................................AATTTTCGCTTAAAGACGTTAAGAAA...................	26	0	8	0.13	1	1	0	0	0
.....................................................CGCCCGGCTCCTAACCGACGC................................................................................	21	1	8	0.13	1	0	1	0	0
..........................................................................................CCGCGCTGTACCCTTTGAAAATT.........................................	23	0	8	0.13	1	0	1	0	0
........................................................................................TTCCGCGCTGTACCTTTTGAAAATT.........................................	25	1	8	0.13	1	0	1	0	0
..................................................................................................................TCGCTTAAAGACGTTAAGAAAGAGG...............	25	0	8	0.13	1	1	0	0	0
................................................................................................................................TAAGAAAGAGGGCGGCGCCATAAAG.	25	0	9	0.11	1	1	0	0	0
..................................................................................................................................AGAAAGAGGGCGGCGCCATA....	20	0	9	0.11	1	1	0	0	0
.TGGTTCACCTACAGTCGATAA....................................................................................................................................	21	0	9	0.11	1	0	1	0	0
.......................................................................................................................................GAGGGCGGCGCCATAAAGT	19	0	9	0.11	1	0	0	1	0
.......................................................................................................TGTAAAAATTTTCGCTTAA................................	19	2	20	0.10	2	1	0	1	0
..................................................................................................................TCGCTTAAAGACGTTAAGAAA...................	21	0	10	0.10	1	0	1	0	0
.TGGTTCACCTACAGTCGAT......................................................................................................................................	19	0	11	0.09	1	1	0	0	0
..GGTTCACCTACAGTCGAT......................................................................................................................................	18	0	11	0.09	1	1	0	0	0
.......................................................CCCGCCTGCTAACTGACTCC...............................................................................	20	3	17	0.06	1	0	0	1	0
AGGGTCCGCCTACAGTCGAT......................................................................................................................................	20	3	20	0.05	1	0	0	0	1

ATGGTTCACCTACAGTCGATAAACGGCTCTCGCTACGGTCTCAATAACTGACTCGCCCGGCTCCTAACCGACTCCCTTTCGCCTGAGGTTCCGCGCTGTACCCTTTGAAAATTTTCGCTTAAAGACGTTAAGAAAGAGGGCGGCGCCATAAAGT
************************************...((((((.((.......((.(((..(((((.(((.......))).)).)))..))).))......))))))))........***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

M046
female body

M060
embryo

V110
male body

V041
embryo

......................................................................................GGTTCCGCGCTGTACCCTTTGAAA............................................

8.80

...............................................................................CGCCTGAGGTTCCGCGCTGTACCCTTT................................................

2.60

.......................CGGCTCTCGCTACGGTCTCAAT.............................................................................................................

2.00

...............................................................................CGCCTGAGGTTCCGCGCTGTACCCTT.................................................

2.00

......................ACGGCTCTCGCTACGGTCTCAAT.............................................................................................................

1.67

...............................................................................CGCCTGAGGTTCCGCGCTGTACCCT..................................................

1.00

.....................AACGGCTCTCGCTACGGTCTCA...............................................................................................................

1.00

...................TAAACGGCTCTCGCTACGGTCTCAAT.............................................................................................................

1.00

.......................................................................................GTTCCGCGCTGTACCCTTTGAAA............................................

1.00

...............................................................................CGCCTGAGGTTCCGCGCTGTACCC...................................................

0.80

.....................................................................................AGGTTCCGCGCTGTACCCTTTGAAA............................................

0.80

....................................................................................GAGGTTCCGCGCTGTACCCTTTGAAA............................................

0.80

.................................................................................CCTGAGGTTCCGCGCTGTACCCTTT................................................

0.80

........................GGCTCTCGCTACGGTCTCAAT.............................................................................................................

0.67

..........................................................................................CCGCGCTGTACCCTTTGAAA............................................

0.63

....................................................................................GAGGTTCCGCGCTGTACCCTTTGAA.............................................

0.60

................................................................................GCCTGAGGTTCCGCGCTGTACCCTT.................................................

0.60

.............................TCGCTACGGTCTCAATAACTGACT.....................................................................................................

0.50

.................................................................................CCTGAGGTTCCGCGCTGTACCCTT.................................................

0.40

......................................................................................GGTTCCGCGCTGTACCCTTTGAAAA...........................................

0.40

.................................................................................CCTGAGGTTCCGCGCTGTACCC...................................................

0.40

..............................................................................TCGCCTGAGGTTCCGCGCTGTACCCTT.................................................

0.40

..................................................................................CTGAGGTTCCGCGCTGTACCCTTT................................................

0.40

................................................................................GCCTGAGGTTCCGCGCTGTACCC...................................................

0.40

.......................................................................................GTTCCGCGCTGTACCCTTTGAAAA...........................................

0.40

.....................................................................................AGGTTCCGCGCTGTACCCTTTGAA.............................................

0.40

....................AGACGGCTCTCGCTACGGTCTCAAT.............................................................................................................

0.33

.......................CGGCTCTCGCTACGATCTCAAT.............................................................................................................

0.33

............................CTCGCTACGGTCTCAATAACTGACT.....................................................................................................

0.25

.............................TCGCTACGGTCTCAATAACTGACTGG...................................................................................................

0.25

......................................................................................GGTTCCGCGCTGTACCCTTTGAA.............................................

0.20

................................................................................GCCTGAGGTTCCGCGCTGTATCCTT.................................................

0.20

..................................................................................CTGGGGTTCCGCGCTGTACCCTT.................................................

0.20

...............................................CTGACTCGCCCGGCTCCTAACCGACTCCC..............................................................................

0.20

..............................................................................TCGCCTGAGGTTCCGCGCTGTACCCTTT................................................

0.20

................................................................................GCCTGAGGTTCCGCGCTGTACCCT..................................................

0.20

..................................................................................CTGAGGTTCCGCGCTGTACCCTT.................................................

0.20

..............................................................................CCGCCTGAGGTTCCGCGCTGTACCCT..................................................

0.20

....................................................................................GAGGTTCCGCGCTGTACCCTTTG...............................................

0.20

...............................................................................CGCCTGAGGTTCCGCGCTGTACCCTGT................................................

0.20

......................................................................................GGCTCCGCGCTGTACCCTTTGAAA............................................

0.20

..............................................................................CCGCCTGAGGTTCCGCGCTGTACCCGT.................................................

0.20

......................................................................................AGTTCCGCGCTGTACCCTTTGAAA............................................

0.20

..................................................................................CTGAGGTTCCGCGCTGTACCATT.................................................

0.20

....................................................................................TTGGTTCCGCGCTGTACCCTTTGAAA............................................

0.20

..............................................................................TCGCCTGAGGTTCCGCGCTGTACCC...................................................

0.20

...............................................................................CGCCTGAGGTTCCGCGCTG........................................................

0.20

...................................................................................CGAGGTTCCGCGCTGTACCCTTT................................................

0.20

......................................................................................GGTTCCTCGCTGTACCCTTTGAAA............................................

0.20

...............................................................................CGCCTGAGGTTCCGCGCTGTACCCGT.................................................

0.20

...................................................................................TGAGGTTCCGCGCTGTACCCTT.................................................

0.20

.....................................................................................CGGTTCCGCGCTGTACCCTTTGAAA............................................

0.20

................................................................................GCCTGAGGTTCCGCGCTGTACCCTTT................................................

0.20

...............................................................................CGCCTGAGGTTCCGCGCTGTTCCC...................................................

0.20

...................................................................................TGAGGTTCCGCGCTGTACCCTCTG...............................................

0.20

...................................................................................CGAGGTTCCGCGCTGTACCCTTTGAAAG...........................................

0.20

.................................................................................CCTGAGGTTCCGCGCTGTACCCT..................................................

0.20

...............................................................................CGCCTGAGGTTCCGCGCTGTACCCCTT................................................

0.20

...................................................................................TGAGGTTCCGCGCTGTACCCTTT................................................

0.20

...............................................................................CGCCTGAGGTTCCGCGCTGTACCCTTTC...............................................

0.17

.......................................................................................................TTTGAAAATTTTCGCTTAAAGACGT..........................

0.14

........................................................................................................TTGAAAATTTTCGCTTAAAGACGTT.........................

0.14

..............................................................................................................ATTTTCGCTTAAAGACGTTAAGAAA...................

0.13

........................................................................................TTCCGCGCTGTACCCTTTGAAA............................................

0.13

..........................................................................................CCGCGCTGTACCCTTTGAAAA...........................................

0.13

.........................................................................................TCCGCGCTGTACCCTTTGAAA............................................

0.13

............................................................................................................AAATTTTCGCTTAAAGACGTTAAGAAA...................

0.13

.........................................................................................ACCGCGCTGTACCCTTTGAAAATT.........................................

0.13

.........................................................................................CCCGCGCTGTACCCTTTGAAAATTT........................................

0.13

.........................................................................................TCCGCGCTGTACCCTTTGAAAATT.........................................

0.13

..........................................................................................CCGCGCTGTACCCTTTGAAAAT..........................................

0.13

.........................................................................................CCCGCGCTGTACCCTTTGAAA............................................

0.13

...........................................................................................................AAAATTTTCGCTTAAAGACGTTAAGAAA...................

0.13

.............................................................................................................AATTTTCGCTTAAAGACGTTAAGAAA...................

0.13

.....................................................CGCCCGGCTCCTAACCGACGC................................................................................

0.13

..........................................................................................CCGCGCTGTACCCTTTGAAAATT.........................................

0.13

........................................................................................TTCCGCGCTGTACCTTTTGAAAATT.........................................

0.13

..................................................................................................................TCGCTTAAAGACGTTAAGAAAGAGG...............

0.13

................................................................................................................................TAAGAAAGAGGGCGGCGCCATAAAG.

0.11

..................................................................................................................................AGAAAGAGGGCGGCGCCATA....

0.11

.TGGTTCACCTACAGTCGATAA....................................................................................................................................

0.11

.......................................................................................................................................GAGGGCGGCGCCATAAAGT

0.11

.......................................................................................................TGTAAAAATTTTCGCTTAA................................

0.10

..................................................................................................................TCGCTTAAAGACGTTAAGAAA...................

0.10

.TGGTTCACCTACAGTCGAT......................................................................................................................................

0.09

..GGTTCACCTACAGTCGAT......................................................................................................................................

0.09

.......................................................CCCGCCTGCTAACTGACTCC...............................................................................

0.06

AGGGTCCGCCTACAGTCGAT......................................................................................................................................

0.05

Species	Coordinate	ID	Alignment
droMoj3	scaffold_1990:5358-5511 +	dmo_286	TACCAAGTGGATGTCAGCTATTTGCCGAGAGCGATGCCAGAGTTATTGACTGAGCGGGCCGAGGATTGGCTGAGGGAAAGCGGACTCCAAGGCGCGACATGGGAAACTTTTAAAAGCGAATTTCTGCAATTCTTTCTCCCGCCGCGGTATTTCA-
droVir3	scaffold_12736:45160-45306 -		AAGTGTA----TATCCG---CATGCCTAGGGGAATGTTCGAGGTATTCTGCGACCGGGCTGCATGTTGGTTCTTGAGTAGTGGGCTGAGGAATGTGCCATGGGCAGTGTTTAGGAGGTGTTTCTTGGAGTTTTTTCTGCCAACGCGTTTTTTTG-
droWil2	scf2_1100000004929:20665-20817 -		TACCGTTTGAGTTTGGAGACTCTGCCTCCGATGATAGCCAT-CGATAGACCGGACGGGCCGAAAGTTGGTGGCAACCCAGCGGTTATCCAGAGATGACATGGGTCGATTTCAAGTCCGAATTTCTAGAGTTCTTTCTACCCCCACGGTATTTTG-
dp5	Unknown_group_36:2881-3034 +		TACGTGGTAGATATGAACTACCTGCCGCGAGCCATGGCGGAGCTCCTCACCGACCGAGCCAACCGTTGGTTCCGCACCAGCCGACTCCAGAGCGCCTCATGGGCCGATTTCCGCCAGGAATTCCTAGCCTTTTTCCTGCCTCCCCGGTACTTCG-
droPer2	scaffold_16:224221-224374 +		TACGGGGTAGACATGAACTACGTGCCGCGAGCCATGGAAGAGCTCCTCACCGACCGAGCCAACCGTTGGTTCCGCAACAGCCGACTCCAGAGCGCCTCATGGGCCGATTTCCGCCAGGAATTTCTAGCCTTTTTCCTGCCTCCCCGGTACTTCG-
droBip1	scf7180000394830:6045-6198 -		TATGGTTTGGACATAAACATGATCCCTAGGTCTATGCCAGAACTACTGCAGGGCAGGGCTCAAAGATGGTTCATCAAGAACGACGAAGAATGGCCAACATGGGCAAGATTTAAGGCAAGCTTCGAAAACTTTTTCCTACCGAAAGGATATTTCG-
droKik1	scf7180000298699:97-249 -		TATCAGGTCGATCTAAG-GCCCTACCCCAGGCAATGCCAGTGCTCCTAACCGGAAGGGCAGAGAGCTGGTTCCGAACGAGCAGACTGCAGGGCACGACATGGAAAACTTTTAAGAAGGAGTTTCTGGAATTTTTCTTACCACCACGGTACTTCC-
droFic1	scf7180000454119:4854-5007 +		TACGGCATCGAGTTACAAACACTTCCACGGGCTATGGCAGAGCTTTTGACTGACCGGGCGGATAAATGGTTTCAGACCAGCCGGCTTCAAGGCGCGAAGTGGATAACCTTCCGCAAGGAATTTTTAGAATTCTTTTTACCTCCACGGTACCTCC-
droEle1	scf7180000486807:4429-4581 +		TACGGCATCGATTTGCAGACACTTGCTTGAGCAATGGCTGAGCTTTTGATCGACCGGGCGGATAAATGGTTTCAGACCAGCCGACTTCCAGGGGCGGACTGGATGACCTTCCGAAAGGAATTTTTAGAAT-CTTTTTACCTCCACGGTATCTCC-
droRho1	scf7180000778019:9565-9718 +		TATCAAGTCGATCTTCGGACGCTACCCCGAGCGATGCCGGTGCTACTAGCCGGAAGGGCGGAGAGCTGGTTTCGTACGAGCAGACTGCAGGGTACAACATGGGAAACTTTTAAGAAGGAGTTCCTTGAGTTTTTCTTACCGCCGCGCTACTTCC-
droBia1	scf7180000302494:3914-4067 -		TACGAAGTTGATGTGGAGAAGATGCCGCAGGCCATCCCTGGTCTTTTGACGGATACAGCTGAGCACTGGTTTCGGACAAGCCAGCTGCTAGGAGAATCTTGGACGAACTTCAACAAGGCGTTTCTTGACTTCTTTCTGCCACCGAGGTACTTTC-
droTak1	scf7180000412396:14755-14908 +		TATCAAGTCGATCTACGGGCGCTACCCCAATCGATGCCGGTACTACTAGCAGGAAGGGCGGAAAGCTGGTTTCGTACGAGCAGACTGCAGGGCACGACATGGGAAACTTTTAAGAAGGAGTTCCTTGAGTTTTTCTTACCGCCACGGTACTTCC-
droEug1	scf7180000407681:6047-6200 -		TACTAAGTTGACGTGGAGAAGATGCCGCAGGCCATCCCTGGTCTTTTGACGGACACAGCTGAGCACTGGTTTCGGACAAGGCAGCTGCTAGGAGAATCTTGGATGAACTTCAACAAGGCGTTTCTTGACTTCTTTCTGCCGCCCAGGTACTTTC-
droSim2	node_13580:2889-3042 -		TATGAAGCCAACGCGGATAGGACGACGCAAGCTATACCTGGACTGTTGACAGACACGGCGGAACATTGGTTTAGGAACAGCCAACTATTAGGGGAGTCATGGGCAAATTTCAAGAAGAAGTTTCTTGATTTCTTTTTGCCGCCGAGGTATTTTC-
droSec2	scaffold_354:5808-5961 +		TATGAAGCCAACGCGGATAGGACGACGCAAGCTATACCTGGACTGTTGACAGACACGGCGGAACATTGGTTTAGGAACAGCCAACTATTAGGGGTGTCATGGGCAAATTTCAAGCAGAAGTTTCTTGATTTCTTTTTGCCGCCGAGTTATTTTC-
droYak3	v2_chrUn_964:12-166 -		TATCAGGTCGATGTACGATCTCTACCCCAAGCGATGCTGGTCCTACTTGTCGAAAAAGCCGAAAGTTGGTTCCGAATGAGTAGACTCCAGGGTGCGACATGGAAGACATTTAGGAAGGAGTTCCTATAATTTTTCTTGCCACCCCCATACTTCCA
droEre2	scaffold_4784:24345727-24345880 +		TATCAAGTCGATCTACGGGCCCTACGCCAAGCGATGCCGGTGCTACTAGTCGGAAGGGCGGAGAGCTGGTTCCGAACAAGCAGACTCCGGGACGCGACATGGAAGACCGTTAGGCAGGAGTTTCTCGAGTTTTTCCCACCGCCCCGATACTTCC-

Species

Coordinate

Alignment

droMoj3

scaffold_1990:5358-5511 +

dmo_286

TACCAAGTGGATGTCAGCTATTTGCCGAGAGCGATGCCAGAGTTATTGACTGAGCGGGCCGAGGATTGGCTGAGGGAAAGCGGACTCCAAGGCGCGACATGGGAAACTTTTAAAAGCGAATTTCTGCAATTCTTTCTCCCGCCGCGGTATTTCA-

droVir3

scaffold_12736:45160-45306 -

AAGTGTA----TATCCG---CATGCCTAGGGGAATGTTCGAGGTATTCTGCGACCGGGCTGCATGTTGGTTCTTGAGTAGTGGGCTGAGGAATGTGCCATGGGCAGTGTTTAGGAGGTGTTTCTTGGAGTTTTTTCTGCCAACGCGTTTTTTTG-

droWil2

scf2_1100000004929:20665-20817 -

TACCGTTTGAGTTTGGAGACTCTGCCTCCGATGATAGCCAT-CGATAGACCGGACGGGCCGAAAGTTGGTGGCAACCCAGCGGTTATCCAGAGATGACATGGGTCGATTTCAAGTCCGAATTTCTAGAGTTCTTTCTACCCCCACGGTATTTTG-

dp5

Unknown_group_36:2881-3034 +

TACGTGGTAGATATGAACTACCTGCCGCGAGCCATGGCGGAGCTCCTCACCGACCGAGCCAACCGTTGGTTCCGCACCAGCCGACTCCAGAGCGCCTCATGGGCCGATTTCCGCCAGGAATTCCTAGCCTTTTTCCTGCCTCCCCGGTACTTCG-

droPer2

scaffold_16:224221-224374 +

TACGGGGTAGACATGAACTACGTGCCGCGAGCCATGGAAGAGCTCCTCACCGACCGAGCCAACCGTTGGTTCCGCAACAGCCGACTCCAGAGCGCCTCATGGGCCGATTTCCGCCAGGAATTTCTAGCCTTTTTCCTGCCTCCCCGGTACTTCG-

droBip1

scf7180000394830:6045-6198 -

TATGGTTTGGACATAAACATGATCCCTAGGTCTATGCCAGAACTACTGCAGGGCAGGGCTCAAAGATGGTTCATCAAGAACGACGAAGAATGGCCAACATGGGCAAGATTTAAGGCAAGCTTCGAAAACTTTTTCCTACCGAAAGGATATTTCG-

droKik1

scf7180000298699:97-249 -

TATCAGGTCGATCTAAG-GCCCTACCCCAGGCAATGCCAGTGCTCCTAACCGGAAGGGCAGAGAGCTGGTTCCGAACGAGCAGACTGCAGGGCACGACATGGAAAACTTTTAAGAAGGAGTTTCTGGAATTTTTCTTACCACCACGGTACTTCC-

droFic1

scf7180000454119:4854-5007 +

TACGGCATCGAGTTACAAACACTTCCACGGGCTATGGCAGAGCTTTTGACTGACCGGGCGGATAAATGGTTTCAGACCAGCCGGCTTCAAGGCGCGAAGTGGATAACCTTCCGCAAGGAATTTTTAGAATTCTTTTTACCTCCACGGTACCTCC-

droEle1

scf7180000486807:4429-4581 +

TACGGCATCGATTTGCAGACACTTGCTTGAGCAATGGCTGAGCTTTTGATCGACCGGGCGGATAAATGGTTTCAGACCAGCCGACTTCCAGGGGCGGACTGGATGACCTTCCGAAAGGAATTTTTAGAAT-CTTTTTACCTCCACGGTATCTCC-

droRho1

scf7180000778019:9565-9718 +

TATCAAGTCGATCTTCGGACGCTACCCCGAGCGATGCCGGTGCTACTAGCCGGAAGGGCGGAGAGCTGGTTTCGTACGAGCAGACTGCAGGGTACAACATGGGAAACTTTTAAGAAGGAGTTCCTTGAGTTTTTCTTACCGCCGCGCTACTTCC-

droBia1

scf7180000302494:3914-4067 -

TACGAAGTTGATGTGGAGAAGATGCCGCAGGCCATCCCTGGTCTTTTGACGGATACAGCTGAGCACTGGTTTCGGACAAGCCAGCTGCTAGGAGAATCTTGGACGAACTTCAACAAGGCGTTTCTTGACTTCTTTCTGCCACCGAGGTACTTTC-

droTak1

scf7180000412396:14755-14908 +

TATCAAGTCGATCTACGGGCGCTACCCCAATCGATGCCGGTACTACTAGCAGGAAGGGCGGAAAGCTGGTTTCGTACGAGCAGACTGCAGGGCACGACATGGGAAACTTTTAAGAAGGAGTTCCTTGAGTTTTTCTTACCGCCACGGTACTTCC-

droEug1

scf7180000407681:6047-6200 -

TACTAAGTTGACGTGGAGAAGATGCCGCAGGCCATCCCTGGTCTTTTGACGGACACAGCTGAGCACTGGTTTCGGACAAGGCAGCTGCTAGGAGAATCTTGGATGAACTTCAACAAGGCGTTTCTTGACTTCTTTCTGCCGCCCAGGTACTTTC-

droSim2

node_13580:2889-3042 -

TATGAAGCCAACGCGGATAGGACGACGCAAGCTATACCTGGACTGTTGACAGACACGGCGGAACATTGGTTTAGGAACAGCCAACTATTAGGGGAGTCATGGGCAAATTTCAAGAAGAAGTTTCTTGATTTCTTTTTGCCGCCGAGGTATTTTC-

droSec2

scaffold_354:5808-5961 +

TATGAAGCCAACGCGGATAGGACGACGCAAGCTATACCTGGACTGTTGACAGACACGGCGGAACATTGGTTTAGGAACAGCCAACTATTAGGGGTGTCATGGGCAAATTTCAAGCAGAAGTTTCTTGATTTCTTTTTGCCGCCGAGTTATTTTC-

droYak3

v2_chrUn_964:12-166 -

TATCAGGTCGATGTACGATCTCTACCCCAAGCGATGCTGGTCCTACTTGTCGAAAAAGCCGAAAGTTGGTTCCGAATGAGTAGACTCCAGGGTGCGACATGGAAGACATTTAGGAAGGAGTTCCTATAATTTTTCTTGCCACCCCCATACTTCCA

droEre2

scaffold_4784:24345727-24345880 +

TATCAAGTCGATCTACGGGCCCTACGCCAAGCGATGCCGGTGCTACTAGTCGGAAGGGCGGAGAGCTGGTTCCGAACAAGCAGACTCCGGGACGCGACATGGAAGACCGTTAGGCAGGAGTTTCTCGAGTTTTTCCCACCGCCCCGATACTTCC-

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

TACCAAGTGGATGTCAGCTATTTGCCGAGAGCGATGCCAGAGTTATTGACTGAGCGGGCCGAGGATTGGCTGAGGGAAAGCGGACTCCAAGGCGCGACATGGGAAACTTTTAAAAGCGAATTTCTGCAATTCTTTCTCCCGCCGCGGTATTTCA-	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
................................................................................CGGACTCCAAGGCGCGACATGGG....................................................	23	5	4.20	21	21	0	0	0	0	0
................................................................................CGGACTCCAAGGCGCGACATGG.....................................................	22	5	2.40	12	11	0	0	0	1	0
................................................................................CGGACTCCAAGGCGCGACATGGGA...................................................	24	5	1.00	5	5	0	0	0	0	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGCGGT.......	23	9	0.78	7	4	0	0	0	3	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGCGG........	22	9	0.44	4	3	0	0	0	1	0
................................................................................CGGACTCCAAGGCGCGACATGGGAA..................................................	25	5	0.40	2	2	0	0	0	0	0
.................................................................................GGACTCCAAGGCGCGACATGGG....................................................	22	5	0.40	2	2	0	0	0	0	0
................................................................................CGGACTCCAAGGCGCGACATGGGAAAC................................................	27	5	0.40	2	2	0	0	0	0	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGCGGTA......	24	9	0.22	2	2	0	0	0	0	0
................................................................................CGGACTCCAAGGCGCGACATGGC....................................................	23	5	0.20	1	1	0	0	0	0	0
................................................................................CGGACTCCAAGGCGCGACATG......................................................	21	5	0.20	1	1	0	0	0	0	0
................................................................................CGGACTCCAAGGCGCGACATGGGAAACT...............................................	28	5	0.20	1	1	0	0	0	0	0
..................................................TGAGCGGGCCGAGGATTGGC.....................................................................................	20	8	0.13	1	1	0	0	0	0	0
......GTGGATGTCAGCTATTTGCC.................................................................................................................................	20	9	0.11	1	0	0	0	0	1	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGC..........	20	9	0.11	1	0	0	0	0	1	0
..............................................................................................................................CAATTCTTTCTCCCGCCGCGGTAT.....	24	9	0.11	1	1	0	0	0	0	0
TACCAAGTGGATGTCAGCTATTTGCC.................................................................................................................................	26	9	0.11	1	1	0	0	0	0	0
..............................................................................................................................CAATTCTTTCTCCCGCCGCGGTATT....	25	9	0.11	1	1	0	0	0	0	0
..............................................................................................................................CAATTCTTTCTCCCGCCGCGGTA......	23	9	0.11	1	1	0	0	0	0	0
..CCAAGTGGATGTCAGCTATTTGCC.................................................................................................................................	24	9	0.11	1	1	0	0	0	0	0
............................................................................................................................TGCAATTCTTTCTCCCGCCGCGGTAT.....	26	9	0.11	1	1	0	0	0	0	0
.............................................................................................................................GCAATTCTTTCTCCCGCCGCGGTAT.....	25	9	0.11	1	1	0	0	0	0	0

droVir3

AAGTGTA----TATCCG---CATGCCTAGGGGAATGTTCGAGGTATTCTGCGACCGGGCTGCATGTTGGTTCTTGAGTAGTGGGCTGAGGAATGTGCCATGGGCAGTGTTTAGGAGGTGTTTCTTGGAGTTTTTTCTGCCAACGCGTTTTTTTG-	Size	Hit Count	Total Norm	Total	M027 Male-body	M028 Head	M047 Female-body	M061 Embryo	SRR060654 Ovary	SRR060655 Testis	SRR060656 Ovary	SRR060657 Testis	SRR060658 Ovary	SRR060659 Testis	SRR060660 Ovary	SRR060661 Embryo	SRR060662 Embryo	SRR060663 Embryo	SRR060664 Male-body	SRR060665 Female-body	SRR060666 Male-body	SRR060667 Female-body	SRR060668 Male-body	SRR060669 Female-body	SRR060670 Testis	SRR060671 Male-body	SRR060672 Female-body	SRR060673 Ovary	SRR060674 Ovary	SRR060675 Ovary	SRR060676 Ovary	SRR060677 Ovary	SRR060678 Testis	SRR060679 Testis	SRR060680 Testis	SRR060681 Testis	SRR060682 Embryo	SRR060683 Testis	SRR060684 Embryo	SRR060685 Embryo	SRR060686 Embryo	SRR060687 Embryo	SRR060688 Ovary	SRR060689 Testis	SRR1106712 embryo_0-2h	SRR1106713 embryo_0-2h	SRR1106714 embryo_2-4h	SRR1106715 embryo_4-6h	SRR1106716 embryo_4-6h	SRR1106717 embryo_6-8h	SRR1106718 embryo_6-8h	SRR1106719 embryo_8-10h	SRR1106720 embryo_8-10h	SRR1106721 embryo_10-12h	SRR1106722 embryo_10-12h	SRR1106723 embryo_12-14h	SRR1106724 embryo_12-14h	SRR1106725 embryo_14-16h	SRR1106726 embryo_14-16h	SRR1106727 larvae	SRR1106728 larvae	SRR1106729 mixed whole adult body	SRR1106730 embryo_16-30h	V047 Embryo	V053 Head	V116 Male-body	GSM1528803 follicle cells
..............................................................................................................TAGGAGGTGTTTCTTGGAGTTTTTTC...................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0

droWil2

TACCGTTTGAGTTTGGAGACTCTGCCTCCGATGATAGCCAT-CGATAGACCGGACGGGCCGAAAGTTGGTGGCAACCCAGCGGTTATCCAGAGATGACATGGGTCGATTTCAAGTCCGAATTTCTAGAGTTCTTTCTACCCCCACGGTATTTTG-	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.......TGAGTTTGGAGACTCTGCCTCCGA............................................................................................................................	24	11	1.55	17	0	15	0	2	0
.......TGAGTTTGGAGACTCTGCCTCCG.............................................................................................................................	23	11	0.36	4	0	4	0	0	0
.......TGAGTTTGGAGACTCTGCCTC...............................................................................................................................	21	11	0.18	2	0	2	0	0	0
........GAGTTTGGAGACTCTGCCTCCGA............................................................................................................................	23	11	0.18	2	0	2	0	0	0
TACCGTTTGAGTTTGGAGACTCTGCC.................................................................................................................................	26	11	0.09	1	0	1	0	0	0
TACCGTTTGAGTTTGGAGACTCTG...................................................................................................................................	24	11	0.09	1	0	0	0	1	0
.......TGAGTTTGGAGACTCTGCCTCC..............................................................................................................................	22	11	0.09	1	0	1	0	0	0

dp5

TACGTGGTAGATATGAACTACCTGCCGCGAGCCATGGCGGAGCTCCTCACCGACCGAGCCAACCGTTGGTTCCGCACCAGCCGACTCCAGAGCGCCTCATGGGCCGATTTCCGCCAGGAATTCCTAGCCTTTTTCCTGCCTCCCCGGTACTTCG-	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
..........ATATGAACTACCTGCCGCGAGCC..........................................................................................................................	23	1	3.00	3	0	2	0	0	0	0	0	1	0	0
.................................................................................CGACTCCAGAGCGCCTCATGG.....................................................	21	12	2.25	27	0	27	0	0	0	0	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGG....................................................	22	12	2.17	26	0	25	0	0	0	1	0	0	0	0
..........ATATGAACTACCTGCCGCGAGC...........................................................................................................................	22	1	2.00	2	0	2	0	0	0	0	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGC...................................................	23	12	2.00	24	0	22	0	0	0	0	2	0	0	0
..........ATATGAACTACCTGCCGCGAGCCA.........................................................................................................................	24	1	2.00	2	0	2	0	0	0	0	0	0	0	0
...........TATGAACTACCTGCCGCGAGCC..........................................................................................................................	22	1	2.00	2	0	2	0	0	0	0	0	0	0	0
...........TATGAACTACCTGCCGCGAGCCATGG......................................................................................................................	26	1	2.00	2	0	2	0	0	0	0	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGCCGA................................................	26	12	1.83	22	0	21	0	0	0	0	1	0	0	0
.......TAGATATGAACTACCTGCCGCGAGCC..........................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGCC..................................................	24	12	1.00	12	0	12	0	0	0	0	0	0	0	0
..........ATATGAACTACCTGCCGCGAG............................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.......TAGATATGAACTACCTGCCGCGAGC...........................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...........TATGAACTACCTGCCGCGAGCCATG.......................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGCCGAT...............................................	27	12	0.58	7	0	7	0	0	0	0	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGCCGATT..............................................	28	12	0.50	6	0	6	0	0	0	0	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGCCG.................................................	25	12	0.50	6	0	5	0	0	0	0	1	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATG......................................................	20	13	0.38	5	0	4	0	0	0	0	1	0	0	0
..................................TGGCGGAGCTCCTCACCGACCGA..................................................................................................	23	3	0.33	1	0	1	0	0	0	0	0	0	0	0
..................................................................................GACTCCAGAGCGCCTCATGGG....................................................	21	12	0.33	4	0	4	0	0	0	0	0	0	0	0
...........................................TCCTCACCGACCGAGCCAACCGTTG.......................................................................................	25	16	0.25	4	0	4	0	0	0	0	0	0	0	0
............ATGAACTACCTGCCGCGAGA...........................................................................................................................	20	8	0.25	2	0	2	0	0	0	0	0	0	0	0
..........................................................................CACCAGCCGACTCCAGAGCGCC...........................................................	22	17	0.24	4	0	4	0	0	0	0	0	0	0	0
...........................................TCCTCACCGACCGAGCCAACCGTTGG......................................................................................	26	16	0.19	3	0	2	0	0	0	0	1	0	0	0
..................................................................................GACTCCAGAGCGCCTCATGGGCC..................................................	23	12	0.17	2	0	2	0	0	0	0	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGCCGT................................................	26	12	0.17	2	0	2	0	0	0	0	0	0	0	0
..............GAACTACCTGCCGCGAGCCATGGCG....................................................................................................................	25	7	0.14	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................TCCGCCAGGAATTCCTAGCCTTTTTCC...................	27	15	0.13	2	0	2	0	0	0	0	0	0	0	0
............ATGAACTACCTGCCGCGAGCC..........................................................................................................................	21	8	0.13	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................CCTAGCCTTTTTCCTGCCTCCCCGGTA......	27	17	0.12	2	0	2	0	0	0	0	0	0	0	0
..........................................................................CACCAGCCGACTCCAGAGCGCCT..........................................................	23	17	0.12	2	0	2	0	0	0	0	0	0	0	0
..........................................CTCCTCACCGACCGAGCCAACCG..........................................................................................	23	18	0.11	2	0	2	0	0	0	0	0	0	0	0
.............TGAACTACCTGCCGCGAGCC..........................................................................................................................	20	10	0.10	1	0	0	0	0	0	1	0	0	0	0
..................................................................................GACTCCAGAGCGCCTCATGGGCCC.................................................	24	12	0.08	1	0	1	0	0	0	0	0	0	0	0
..................................................................................GACTCCAGAGCGCCTCATGG.....................................................	20	12	0.08	1	0	1	0	0	0	0	0	0	0	0
...............................................................................GCCGACTCCAGAGCGCCTCATGGG....................................................	24	12	0.08	1	0	1	0	0	0	0	0	0	0	0
..................................................................................GACTCCAGAGCGCCTCATGGGC...................................................	22	12	0.08	1	0	1	0	0	0	0	0	0	0	0
..................................................................................GACTCCAGAGCGCCTCATGGGCCGA................................................	25	12	0.08	1	0	1	0	0	0	0	0	0	0	0
..................................................................................GACTCCAGAGCGCCTCATGGGCCGATT..............................................	27	12	0.08	1	0	1	0	0	0	0	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGT....................................................	22	12	0.08	1	0	1	0	0	0	0	0	0	0	0
..................................................................................GACTCCAGAGCGCCTCATGGGCCG.................................................	24	12	0.08	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................TTCCGCCAGGAATTCCTAGCCTTTT......................	25	13	0.08	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................TCCGCCAGGAATTCCTAGCCTTTTTC....................	26	15	0.07	1	0	1	0	0	0	0	0	0	0	0
............................................CCTCACCGACCGAGCCAACCGTTGG......................................................................................	25	16	0.06	1	0	1	0	0	0	0	0	0	0	0
..........................................................................CACCAGCCGACTCCAGAGCGCCTC.........................................................	24	16	0.06	1	0	1	0	0	0	0	0	0	0	0
................................................ACCGACCGAGCCAACCGTTGGTTCCG.................................................................................	26	16	0.06	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................TTCCGCCAGGAATTCCTAGCCTT........................	23	16	0.06	1	0	1	0	0	0	0	0	0	0	0
............................................CCTCACCGACCGAGCCAACCGTTG.......................................................................................	24	16	0.06	1	0	1	0	0	0	0	0	0	0	0
......................................................................................CCAGAGCGCCTCATGGGCCGATT..............................................	23	16	0.06	1	0	1	0	0	0	0	0	0	0	0
...........................................TCCTCACCGACCGAGCCAACCGTTGGTA....................................................................................	28	16	0.06	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................CCTAGCCTTTTTCCTGCCTCCCC..........	23	17	0.06	1	0	1	0	0	0	0	0	0	0	0
..................................................................TGGTTCCGCACCAGCCGACTCCAGAG...............................................................	26	17	0.06	1	0	1	0	0	0	0	0	0	0	0
.................................................CCGACCGAGCCAACCGTTGG......................................................................................	20	17	0.06	1	0	1	0	0	0	0	0	0	0	0
..........................................................................CACCAGCCGACTCCAGAGCGC............................................................	21	17	0.06	1	0	1	0	0	0	0	0	0	0	0
...........................................TCCTCACCGACCGAGCCAACCGTT........................................................................................	24	18	0.06	1	0	1	0	0	0	0	0	0	0	0
...........................................TCCTCACCGACCGAGCCAACCG..........................................................................................	22	18	0.06	1	0	1	0	0	0	0	0	0	0	0
...........................................TCCTCACCGACCGAGCCAACCGT.........................................................................................	23	18	0.06	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................TCCTAGCCTTTTTCCTGCCTCC............	22	18	0.06	1	0	1	0	0	0	0	0	0	0	0
............................................CCTCACCGACCGAGCCAACCG..........................................................................................	21	18	0.06	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................CAGGAATTCCTAGCCTTTTTCCTGCCT..............	27	19	0.05	1	0	0	0	0	0	0	0	1	0	0
..........................................................................................................................CCTAGCCTTTTTCCTGCCTC.............	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droPer2

TACGGGGTAGACATGAACTACGTGCCGCGAGCCATGGAAGAGCTCCTCACCGACCGAGCCAACCGTTGGTTCCGCAACAGCCGACTCCAGAGCGCCTCATGGGCCGATTTCCGCCAGGAATTTCTAGCCTTTTTCCTGCCTCCCCGGTACTTCG-	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
...............AACTACGTGCCGCGAGCCATGG......................................................................................................................	22	20	0.45	9	0	9	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGG....................................................	22	20	0.25	5	0	5	0	0	0	0
...............AACTACGTGCCGCGAGCCATG.......................................................................................................................	21	20	0.20	4	0	4	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGCC..................................................	24	20	0.15	3	0	3	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGCCG.................................................	25	20	0.10	2	0	0	0	0	0	2
...........CATGAACTACGTGCCGCGAGC...........................................................................................................................	21	20	0.10	2	0	2	0	0	0	0
.................................................................................CGACTCCAGAGCGCCTCATGGGC...................................................	23	20	0.10	2	0	2	0	0	0	0
..................TACGTGCCGCGAGCCATGG......................................................................................................................	19	20	0.05	1	0	0	0	1	0	0
TACGGGGTAGACATGAACTACGTGC..................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0
..........ACATGAACTACGTGCCGCGAG............................................................................................................................	21	20	0.05	1	0	0	0	0	0	1
..........ACATGAACTACGTGCCGCGAGCCA.........................................................................................................................	24	20	0.05	1	0	1	0	0	0	0
........AGACATGAACTACGTGCCGC...............................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
..................................................................................GACTCCAGAGCGCCTCATGG.....................................................	20	20	0.05	1	0	0	0	0	0	1
..................................................................................GACTCCAGAGCGCCTCATGGGC...................................................	22	20	0.05	1	0	0	0	0	0	1

droBip1

TATGGTTTGGACATAAACATGATCCCTAGGTCTATGCCAGAACTACTGCAGGGCAGGGCTCAAAGATGGTTCATCAAGAACGACGAAGAATGGCCAACATGGGCAAGATTTAAGGCAAGCTTCGAAAACTTTTTCCTACCGAAAGGATATTTCG-	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TATCAGGTCGATCTAAG-GCCCTACCCCAGGCAATGCCAGTGCTCCTAACCGGAAGGGCAGAGAGCTGGTTCCGAACGAGCAGACTGCAGGGCACGACATGGAAAACTTTTAAGAAGGAGTTTCTGGAATTTTTCTTACCACCACGGTACTTCC-	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TACGGCATCGAGTTACAAACACTTCCACGGGCTATGGCAGAGCTTTTGACTGACCGGGCGGATAAATGGTTTCAGACCAGCCGGCTTCAAGGCGCGAAGTGGATAACCTTCCGCAAGGAATTTTTAGAATTCTTTTTACCTCCACGGTACCTCC-	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TACGGCATCGATTTGCAGACACTTGCTTGAGCAATGGCTGAGCTTTTGATCGACCGGGCGGATAAATGGTTTCAGACCAGCCGACTTCCAGGGGCGGACTGGATGACCTTCCGAAAGGAATTTTTAGAAT-CTTTTTACCTCCACGGTATCTCC-	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TATCAAGTCGATCTTCGGACGCTACCCCGAGCGATGCCGGTGCTACTAGCCGGAAGGGCGGAGAGCTGGTTTCGTACGAGCAGACTGCAGGGTACAACATGGGAAACTTTTAAGAAGGAGTTCCTTGAGTTTTTCTTACCGCCGCGCTACTTCC-	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TACGAAGTTGATGTGGAGAAGATGCCGCAGGCCATCCCTGGTCTTTTGACGGATACAGCTGAGCACTGGTTTCGGACAAGCCAGCTGCTAGGAGAATCTTGGACGAACTTCAACAAGGCGTTTCTTGACTTCTTTCTGCCACCGAGGTACTTTC-	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TATCAAGTCGATCTACGGGCGCTACCCCAATCGATGCCGGTACTACTAGCAGGAAGGGCGGAAAGCTGGTTTCGTACGAGCAGACTGCAGGGCACGACATGGGAAACTTTTAAGAAGGAGTTCCTTGAGTTTTTCTTACCGCCACGGTACTTCC-	Size	Hit Count	Total Norm	Total
No Reads

droEug1

TACTAAGTTGACGTGGAGAAGATGCCGCAGGCCATCCCTGGTCTTTTGACGGACACAGCTGAGCACTGGTTTCGGACAAGGCAGCTGCTAGGAGAATCTTGGATGAACTTCAACAAGGCGTTTCTTGACTTCTTTCTGCCGCCCAGGTACTTTC-	Size	Hit Count	Total Norm	Total
No Reads

droSim2

TATGAAGCCAACGCGGATAGGACGACGCAAGCTATACCTGGACTGTTGACAGACACGGCGGAACATTGGTTTAGGAACAGCCAACTATTAGGGGAGTCATGGGCAAATTTCAAGAAGAAGTTTCTTGATTTCTTTTTGCCGCCGAGGTATTTTC-	Size	Hit Count	Total Norm	Total	M023 Head	M024 Male-body	M025 Embryo	M053 Female-body	O001 Testis	O002 Head	SRR553485 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553488 Ovary	SRR618934 Ovary	V044 Embryo	SRR902008 Ovary	SRR902009 Testis	SRR1275487 Male larvae	SRR1275485 Male prepupae	SRR1275483 Male prepupae
..TGAAGCCAACGCGGATAGGACGACGCA..............................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
.....................................................................TTTAGGAACAGCCAACTATTAGGGGA............................................................	26	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
............................AAGCTATACCTGGACTGTTGACAGACAC...................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
..................................TACCTGGACTGTTGACAGACACG..................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

TATGAAGCCAACGCGGATAGGACGACGCAAGCTATACCTGGACTGTTGACAGACACGGCGGAACATTGGTTTAGGAACAGCCAACTATTAGGGGTGTCATGGGCAAATTTCAAGCAGAAGTTTCTTGATTTCTTTTTGCCGCCGAGTTATTTTC-	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
No Reads

droYak3

TATCAGGTCGATGTACGATCTCTACCCCAAGCGATGCTGGTCCTACTTGTCGAAAAAGCCGAAAGTTGGTTCCGAATGAGTAGACTCCAGGGTGCGACATGGAAGACATTTAGGAAGGAGTTCCTATAATTTTTCTTGCCACCCCCATACTTCCA

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

droEre2

TATCAAGTCGATCTACGGGCCCTACGCCAAGCGATGCCGGTGCTACTAGTCGGAAGGGCGGAGAGCTGGTTCCGAACAAGCAGACTCCGGGACGCGACATGGAAGACCGTTAGGCAGGAGTTTCTCGAGTTTTTCCCACCGCCCCGATACTTCC-	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
No Reads

dmo_286

scaffold_1990:5408-5461 +

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

-21.0	-20.9	-20.9