dan_152

CCGAAGGTTATTTTGTCAATGCGGCAGCGGGCATCTTCGATCAGTCCATCTTTGGATTCTCTGACAAGGACTTATGACCCTTACTGGAGTCCTTGTCAGAGAATCCAAAGATGGTCAGATCCCCAAGGAACGCTGGGCGGTACAGAAGCCTCGCTTGGAGAG *********************************...((((...((((((((((((((((((((((((((((.............))))))))))))))))))))))))))))...)))).....**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V106 head	M044 female body	V105 male body	M058 embryo	V055 head
..................................................TTTGGATTCTCTGACAAGGACT..........................................................................................	22	0	2	5.50	11	8	2	0	1	0
..................................................TTTGGATTCTCTGACAAGGA............................................................................................	20	0	2	1.50	3	2	1	0	0	0
....................................................TGGATTCTCTGACAAGGACTT.........................................................................................	21	0	1	1.00	1	1	0	0	0	0
...................................................TTGGATTCTCTGACAAGGACTT.........................................................................................	22	0	1	1.00	1	0	1	0	0	0
...................................................TTGGATTCTCTGACAAGGA............................................................................................	19	0	2	0.50	1	1	0	0	0	0
.................................................CTTTGGATTCTCTGACAAGGACT..........................................................................................	23	0	2	0.50	1	0	0	1	0	0
................................................................................................................GGTCAGATCCCGAAGGAAGC..............................	20	3	4	0.50	2	1	0	1	0	0
.................................................CTTTGGATTCTCTGACAAGGA............................................................................................	21	0	2	0.50	1	0	1	0	0	0
..................................................TCTGGATTCTCTGACAAGGACT..........................................................................................	22	1	2	0.50	1	0	1	0	0	0
..................................................TTTGGATTCTCTGACAAGG.............................................................................................	19	0	2	0.50	1	0	1	0	0	0
..................................................TTTGGATTCTCTGACAGGGACT..........................................................................................	22	1	2	0.50	1	1	0	0	0	0
..................................................TTTGGATTATCTGACAAGGA............................................................................................	20	1	2	0.50	1	0	1	0	0	0
................................................TCTTTGGATTCTCTGACAAGG.............................................................................................	21	0	2	0.50	1	0	1	0	0	0
...........................................................................................CTTGTCAGAGAATCCAAAGA...................................................	20	0	2	0.50	1	0	0	0	1	0
..................................................TTTGGATTCTCGGACAAGGACT..........................................................................................	22	1	2	0.50	1	0	0	1	0	0
................................................TCTTTGGATTCTCTGACAAGGA............................................................................................	22	0	2	0.50	1	0	1	0	0	0
....................................................TGGATTCTCTGACAAGGACT..........................................................................................	20	0	2	0.50	1	1	0	0	0	0
.CGTTGGTGATTTTGTCAATGC............................................................................................................................................	21	3	3	0.33	1	0	1	0	0	0
CCGTTGGTAATTTTGTCAATG.............................................................................................................................................	21	3	4	0.25	1	0	1	0	0	0
................................................................................................................GGTCAGATCCGGAAGGAA................................	18	2	5	0.20	1	1	0	0	0	0
.........................................................................................................CGAAGATGATCAGATACCCA.....................................	20	3	6	0.17	1	0	0	0	0	1
................................................................................................................GGTCAGATCCGCAAGGAAGC..............................	20	3	7	0.14	1	0	0	1	0	0

CCGAAGGTTATTTTGTCAATGCGGCAGCGGGCATCTTCGATCAGTCCATCTTTGGATTCTCTGACAAGGACTTATGACCCTTACTGGAGTCCTTGTCAGAGAATCCAAAGATGGTCAGATCCCCAAGGAACGCTGGGCGGTACAGAAGCCTCGCTTGGAGAG
***********************************...((((...((((((((((((((((((((((((((((.............))))))))))))))))))))))))))))...)))).....************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

V106
head

M044
female body

V105
male body

M058
embryo

V055
head

..................................................TTTGGATTCTCTGACAAGGACT..........................................................................................

5.50

..................................................TTTGGATTCTCTGACAAGGA............................................................................................

1.50

....................................................TGGATTCTCTGACAAGGACTT.........................................................................................

1.00

...................................................TTGGATTCTCTGACAAGGACTT.........................................................................................

1.00

...................................................TTGGATTCTCTGACAAGGA............................................................................................

0.50

.................................................CTTTGGATTCTCTGACAAGGACT..........................................................................................

0.50

................................................................................................................GGTCAGATCCCGAAGGAAGC..............................

0.50

.................................................CTTTGGATTCTCTGACAAGGA............................................................................................

0.50

..................................................TCTGGATTCTCTGACAAGGACT..........................................................................................

0.50

..................................................TTTGGATTCTCTGACAAGG.............................................................................................

0.50

..................................................TTTGGATTCTCTGACAGGGACT..........................................................................................

0.50

..................................................TTTGGATTATCTGACAAGGA............................................................................................

0.50

................................................TCTTTGGATTCTCTGACAAGG.............................................................................................

0.50

...........................................................................................CTTGTCAGAGAATCCAAAGA...................................................

0.50

..................................................TTTGGATTCTCGGACAAGGACT..........................................................................................

0.50

................................................TCTTTGGATTCTCTGACAAGGA............................................................................................

0.50

....................................................TGGATTCTCTGACAAGGACT..........................................................................................

0.50

.CGTTGGTGATTTTGTCAATGC............................................................................................................................................

0.33

CCGTTGGTAATTTTGTCAATG.............................................................................................................................................

0.25

................................................................................................................GGTCAGATCCGGAAGGAA................................

0.20

.........................................................................................................CGAAGATGATCAGATACCCA.....................................

0.17

................................................................................................................GGTCAGATCCGCAAGGAAGC..............................

0.14

GGCTTCCAATAAAACAGTTACGCCGTCGCCCGTAGAAGCTAGTCAGGTAGAAACCTAAGAGACTGTTCCTGAATACTGGGAATGACCTCAGGAACAGTCTCTTAGGTTTCTACCAGTCTAGGGGTTCCTTGCGACCCGCCATGTCTTCGGAGCGAACCTCTC **********************************...((((...((((((((((((((((((((((((((((.............))))))))))))))))))))))))))))...)))).....*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V106 head	M044 female body	M058 embryo	V105 male body	V055 head
.......................................................................................TCAGGAACAGTCTCTTAGGTTT.....................................................	22	0	2	5.50	11	8	2	1	0	0
......................................................................................CTCAGGAACAGTCTCTTAGGTT......................................................	22	0	1	3.00	3	0	1	2	0	0
.........................................................................................AGGAACAGTCTCTTAGGTTT.....................................................	20	0	2	1.50	3	2	1	0	0	0
.......................................................................................TCAGGGACAGTCTCTTAGGTTT.....................................................	22	1	2	0.50	1	1	0	0	0	0
.........................................................................................AGGAACAGTCTATTAGGTTT.....................................................	20	1	2	0.50	1	0	1	0	0	0
.........................................................................................AGGAACAGTCTCTTAGGTT......................................................	19	0	2	0.50	1	1	0	0	0	0
.........................................................................................AGGAACAGTCTCTTAGGTTTCT...................................................	22	0	2	0.50	1	0	1	0	0	0
.......................................................................................TCAGGAACAGTCTCTTAGGTTTC....................................................	23	0	2	0.50	1	0	0	0	1	0
..........................................................................................GGAACAGTCTCTTAGGTTT.....................................................	19	0	2	0.50	1	0	1	0	0	0
.......................................................................................TCAGGAACAGTCTCTTAGGT.......................................................	20	0	2	0.50	1	1	0	0	0	0
................................................AGAAACCTAAGAGACTGTTC..............................................................................................	20	0	2	0.50	1	0	0	1	0	0
.......................................................................................TCAGGAACAGTCTCTTAGGTCT.....................................................	22	1	2	0.50	1	0	1	0	0	0
..........................................................................................GGAACAGTCTCTTAGGTTTCT...................................................	21	0	2	0.50	1	0	1	0	0	0
.........................................................................................AGGAACAGTCTCTTAGGTTTC....................................................	21	0	2	0.50	1	0	1	0	0	0
.......................................................................................TCAGGAACAGGCTCTTAGGTTT.....................................................	22	1	2	0.50	1	0	0	0	1	0
.................................................................TTCCTGAATAGTGGGCATCAC............................................................................	21	3	3	0.33	1	0	0	0	0	1
...........................................................................................................TTCTACCAGGCTAGGGAT.....................................	18	2	5	0.20	1	0	0	0	0	1
........................................................................................................................................CAACATGTCTTCGAAGCGA.......	19	3	13	0.08	1	0	1	0	0	0

GGCTTCCAATAAAACAGTTACGCCGTCGCCCGTAGAAGCTAGTCAGGTAGAAACCTAAGAGACTGTTCCTGAATACTGGGAATGACCTCAGGAACAGTCTCTTAGGTTTCTACCAGTCTAGGGGTTCCTTGCGACCCGCCATGTCTTCGGAGCGAACCTCTC
************************************...((((...((((((((((((((((((((((((((((.............))))))))))))))))))))))))))))...)))).....***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

V106
head

M044
female body

M058
embryo

V105
male body

V055
head

.......................................................................................TCAGGAACAGTCTCTTAGGTTT.....................................................

5.50

......................................................................................CTCAGGAACAGTCTCTTAGGTT......................................................

3.00

.........................................................................................AGGAACAGTCTCTTAGGTTT.....................................................

1.50

.......................................................................................TCAGGGACAGTCTCTTAGGTTT.....................................................

0.50

.........................................................................................AGGAACAGTCTATTAGGTTT.....................................................

0.50

.........................................................................................AGGAACAGTCTCTTAGGTT......................................................

0.50

.........................................................................................AGGAACAGTCTCTTAGGTTTCT...................................................

0.50

.......................................................................................TCAGGAACAGTCTCTTAGGTTTC....................................................

0.50

..........................................................................................GGAACAGTCTCTTAGGTTT.....................................................

0.50

.......................................................................................TCAGGAACAGTCTCTTAGGT.......................................................

0.50

................................................AGAAACCTAAGAGACTGTTC..............................................................................................

0.50

.......................................................................................TCAGGAACAGTCTCTTAGGTCT.....................................................

0.50

..........................................................................................GGAACAGTCTCTTAGGTTTCT...................................................

0.50

.........................................................................................AGGAACAGTCTCTTAGGTTTC....................................................

0.50

.......................................................................................TCAGGAACAGGCTCTTAGGTTT.....................................................

0.50

.................................................................TTCCTGAATAGTGGGCATCAC............................................................................

0.33

...........................................................................................................TTCTACCAGGCTAGGGAT.....................................

0.20

........................................................................................................................................CAACATGTCTTCGAAGCGA.......

0.08

Species	Coordinate	ID	Alignment
droAna3	scaffold_12947:1463761-1463922 +	dan_152	CCGAAGGTTATTTTGTCAATGCGGCAGCGGGCATCTTCGATCAGTCCATCTTTGGATTCTCTGACAAGGACTTATGACCCTTACTGGAGTCCTTGTCAGAGAATCCAAAGATGGTCAGATCCCCAAGGAAC------GCTGGGCGGTACAGAAGCCTCGCTTGGAGAG
droBip1	scf7180000391825:11401-11521 +		CCAACCGCTCGTTCGCCGAGGTAACGAAGGGAA-----------------------------------------GAACCTTAATTGGAGTCCTGGACAAGGGCTCCAAGGATGGGCTCATCCCCAAGGAACTTTGGCGACGAGTGGTAAACGAGT------TGCATGG

Species

Coordinate

Alignment

droAna3

scaffold_12947:1463761-1463922 +

dan_152

CCGAAGGTTATTTTGTCAATGCGGCAGCGGGCATCTTCGATCAGTCCATCTTTGGATTCTCTGACAAGGACTTATGACCCTTACTGGAGTCCTTGTCAGAGAATCCAAAGATGGTCAGATCCCCAAGGAAC------GCTGGGCGGTACAGAAGCCTCGCTTGGAGAG

droBip1

scf7180000391825:11401-11521 +

CCAACCGCTCGTTCGCCGAGGTAACGAAGGGAA-----------------------------------------GAACCTTAATTGGAGTCCTGGACAAGGGCTCCAAGGATGGGCTCATCCCCAAGGAACTTTGGCGACGAGTGGTAAACGAGT------TGCATGG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droAna3

CCGAAGGTTATTTTGTCAATGCGGCAGCGGGCATCTTCGATCAGTCCATCTTTGGATTCTCTGACAAGGACTTATGACCCTTACTGGAGTCCTTGTCAGAGAATCCAAAGATGGTCAGATCCCCAAGGAAC------GCTGGGCGGTACAGAAGCCTCGCTTGGAGAG	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
..................................................TTTGGATTCTCTGACAAGGACT................................................................................................	22	2	5.50	11	2	1	0	0	0	8
..................................................TTTGGATTCTCTGACAAGGA..................................................................................................	20	2	1.50	3	1	0	0	0	0	2
....................................................TGGATTCTCTGACAAGGACTT...............................................................................................	21	1	1.00	1	0	0	0	0	0	1
...................................................TTGGATTCTCTGACAAGGACTT...............................................................................................	22	1	1.00	1	1	0	0	0	0	0
...................................................TTGGATTCTCTGACAAGGA..................................................................................................	19	2	0.50	1	0	0	0	0	0	1
.................................................CTTTGGATTCTCTGACAAGGACT................................................................................................	23	2	0.50	1	0	0	0	0	1	0
.................................................CTTTGGATTCTCTGACAAGGA..................................................................................................	21	2	0.50	1	1	0	0	0	0	0
..................................................TTTGGATTCTCTGACAAGG...................................................................................................	19	2	0.50	1	1	0	0	0	0	0
................................................TCTTTGGATTCTCTGACAAGG...................................................................................................	21	2	0.50	1	1	0	0	0	0	0
...........................................................................................CTTGTCAGAGAATCCAAAGA.........................................................	20	2	0.50	1	0	1	0	0	0	0
................................................TCTTTGGATTCTCTGACAAGGA..................................................................................................	22	2	0.50	1	1	0	0	0	0	0
....................................................TGGATTCTCTGACAAGGACT................................................................................................	20	2	0.50	1	0	0	0	0	0	1

droBip1

CCAACCGCTCGTTCGCCGAGGTAACGAAGGGAA-----------------------------------------GAACCTTAATTGGAGTCCTGGACAAGGGCTCCAAGGATGGGCTCATCCCCAAGGAACTTTGGCGACGAGTGGTAAACGAGT------TGCATGG	Size	Hit Count	Total Norm	Total
No Reads

dan_152

scaffold_12947:1463811-1463872 +

Candidate

Unknown

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-53.4	-52.8