dan_970

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GGATGGGGAAACTGGGTTCCGTCGCCATCAAAGATAGTGTGGAAGAAGTCGTAAATTTAATAAATAATTTGCGCTTAAAAAACAAATTGGCCGGCGCGGTGGCGGACAAATGTCCATCAAACCAGGAGGCAATAGCCTTCTTACAACAAAAACAAGTACCGGTCTTGTATGACCTACATCATTTTTGTGGTACTTTACTAAGATTAGGTCATGTTGATAACATTTTAATGCACCTCTATATTGATGTGTCA *************************************************************************.............((((((.(((((((.((((....)))).))..)))(((((((....)))))))..............)).))))))*************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M044 female body	M058 embryo	V105 male body	V039 embryo	V055 head
............................................................................................................................................TTACAACAAAAACAAGTACCGGTC.......................................................................................	24	0	1	7.00	7	6	1	0	0	0
.....................................................................................................................................................................................................CTAAGATTAGGTCATGTTGATAACA.............................	25	0	1	2.00	2	2	0	0	0	0
....................................................................................................................................................................................................ACTAAGATTAGGTCATGTTGATAACA.............................	26	0	1	2.00	2	2	0	0	0	0
....................................................................................................................................................................................................ACTAAGATTAGGTCATGTTGATAAC..............................	25	0	1	2.00	2	2	0	0	0	0
............................................................................................................................................TTACAACAAAAACAAGTACCGGTCTTG....................................................................................	27	0	1	2.00	2	2	0	0	0	0
...........................................................................TAAAAAACAAATTGGCCGGCGCGG........................................................................................................................................................	24	0	2	1.50	3	1	1	1	0	0
.GATGGGGAAACTGGGTTCCGTCG...................................................................................................................................................................................................................................	23	0	1	1.00	1	1	0	0	0	0
....................................................................................................................................................................................................ACTAAGATGAGGTCATGTTGATAACAT............................	27	1	1	1.00	1	1	0	0	0	0
..................................................................................................................CATCAAACCAGGAGGCAATAGCCTT................................................................................................................	25	0	1	1.00	1	1	0	0	0	0
............................................................................................................................................TTACAACAAAAACAAGTACCTGTCTT.....................................................................................	26	1	1	1.00	1	0	0	1	0	0
.....................................TGTGGAAGAAGTCGTAAATTTAATA.............................................................................................................................................................................................	25	0	1	1.00	1	1	0	0	0	0
..........................................................................................CCGGCGCGGTGGCGGACAAATGTCCATC.....................................................................................................................................	28	0	1	1.00	1	1	0	0	0	0
............................................................................................................................................TTACAACAAAAACAAGTACCGGTCT......................................................................................	25	0	1	1.00	1	1	0	0	0	0
............................................................................................................................................TTACAACAAAAACAAGGACCGGTCTTG....................................................................................	27	1	1	1.00	1	1	0	0	0	0
.................................................................................................................................................................................................................CATGTTGATAACATTTTAATGCACCTC...............	27	0	1	1.00	1	1	0	0	0	0
...TGGGGAAACTGGGTTCCGTCGCC.................................................................................................................................................................................................................................	23	0	1	1.00	1	0	1	0	0	0
........................................................................................................GACAAATGTCCATCAAACCAGGAGGCAA.......................................................................................................................	28	0	1	1.00	1	1	0	0	0	0
......................................................................GCGCTTAAAAAACAAATTGGCCGGCT...........................................................................................................................................................	26	1	2	0.50	1	1	0	0	0	0
...........................................................................TAAAAAACAACTTGGCCGGCGCGGTGGCT...................................................................................................................................................	29	2	2	0.50	1	0	1	0	0	0
......GGAAACTGGGTTCCGTCGCCATC..............................................................................................................................................................................................................................	23	0	2	0.50	1	1	0	0	0	0
............................................................................AAAAAACAAATTGGCCGGCGCGGTGG.....................................................................................................................................................	26	0	2	0.50	1	1	0	0	0	0
.........AACTGGGTTCCGTCGCCATCAA............................................................................................................................................................................................................................	22	0	2	0.50	1	1	0	0	0	0
.......................................................................CGCTTAAAAAACAAATTGGCCGGCGCGG........................................................................................................................................................	28	0	2	0.50	1	1	0	0	0	0
............................................................................................................................................TTACAACAAAAACAAGTACCGGT........................................................................................	23	0	2	0.50	1	1	0	0	0	0
.................TCCGTCGCCATCAACGATAGTGTG..................................................................................................................................................................................................................	24	1	2	0.50	1	0	0	0	1	0
........................................................................GCTTAAAAAACAAATTGGCCGGC............................................................................................................................................................	23	0	2	0.50	1	1	0	0	0	0
............................................................................................................................................TTACAACAAAAACAAGTACCGGC........................................................................................	23	1	2	0.50	1	0	1	0	0	0
..........................................................................................................................................TCTTACAAGAAAAACAAGTACCGG.........................................................................................	24	1	2	0.50	1	1	0	0	0	0
........................................................................................GGCCGGCGGAGTGGCGGACAAATGT..........................................................................................................................................	25	2	2	0.50	1	1	0	0	0	0
...........................................................................TAAAAAACAAATTGGCCGGCGCGGTGGC....................................................................................................................................................	28	0	2	0.50	1	1	0	0	0	0
...............................................................................AAACAAATTGGCCGGCGCGGTGGCG...................................................................................................................................................	25	0	2	0.50	1	0	0	1	0	0
..........................................................................TTAAAAAACAAATTGGCCGGCGCG.........................................................................................................................................................	24	0	2	0.50	1	1	0	0	0	0
...........................................................................TAAAAAACAAATTGGCCGGCGCGGGGGC....................................................................................................................................................	28	1	2	0.50	1	0	1	0	0	0
...........................................................................TAAAAAACAAATTGGCCGGCGC..........................................................................................................................................................	22	0	3	0.33	1	1	0	0	0	0
..ACGGGGAAACTGGGGTCC.......................................................................................................................................................................................................................................	18	2	5	0.20	1	0	0	0	0	1
.............................................................................AAAAACCAATTGGCGGGC............................................................................................................................................................	18	2	18	0.06	1	0	0	0	0	1
....................................................................................................................................................AAAGCAAGTACCGGTCTCT....................................................................................	19	3	20	0.05	1	1	0	0	0	0

##################################################---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
GGATGGGGAAACTGGGTTCCGTCGCCATCAAAGATAGTGTGGAAGAAGTCGTAAATTTAATAAATAATTTGCGCTTAAAAAACAAATTGGCCGGCGCGGTGGCGGACAAATGTCCATCAAACCAGGAGGCAATAGCCTTCTTACAACAAAAACAAGTACCGGTCTTGTATGACCTACATCATTTTTGTGGTACTTTACTAAGATTAGGTCATGTTGATAACATTTTAATGCACCTCTATATTGATGTGTCA
***************************************************************************.............((((((.(((((((.((((....)))).))..)))(((((((....)))))))..............)).))))))***************************************************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

M044
female body

M058
embryo

V105
male body

V039
embryo

V055
head

............................................................................................................................................TTACAACAAAAACAAGTACCGGTC.......................................................................................

7.00

.....................................................................................................................................................................................................CTAAGATTAGGTCATGTTGATAACA.............................

2.00

....................................................................................................................................................................................................ACTAAGATTAGGTCATGTTGATAACA.............................

2.00

....................................................................................................................................................................................................ACTAAGATTAGGTCATGTTGATAAC..............................

2.00

............................................................................................................................................TTACAACAAAAACAAGTACCGGTCTTG....................................................................................

2.00

...........................................................................TAAAAAACAAATTGGCCGGCGCGG........................................................................................................................................................

1.50

.GATGGGGAAACTGGGTTCCGTCG...................................................................................................................................................................................................................................

1.00

....................................................................................................................................................................................................ACTAAGATGAGGTCATGTTGATAACAT............................

1.00

..................................................................................................................CATCAAACCAGGAGGCAATAGCCTT................................................................................................................

1.00

............................................................................................................................................TTACAACAAAAACAAGTACCTGTCTT.....................................................................................

1.00

.....................................TGTGGAAGAAGTCGTAAATTTAATA.............................................................................................................................................................................................

1.00

..........................................................................................CCGGCGCGGTGGCGGACAAATGTCCATC.....................................................................................................................................

1.00

............................................................................................................................................TTACAACAAAAACAAGTACCGGTCT......................................................................................

1.00

............................................................................................................................................TTACAACAAAAACAAGGACCGGTCTTG....................................................................................

1.00

.................................................................................................................................................................................................................CATGTTGATAACATTTTAATGCACCTC...............

1.00

...TGGGGAAACTGGGTTCCGTCGCC.................................................................................................................................................................................................................................

1.00

........................................................................................................GACAAATGTCCATCAAACCAGGAGGCAA.......................................................................................................................

1.00

......................................................................GCGCTTAAAAAACAAATTGGCCGGCT...........................................................................................................................................................

0.50

...........................................................................TAAAAAACAACTTGGCCGGCGCGGTGGCT...................................................................................................................................................

0.50

......GGAAACTGGGTTCCGTCGCCATC..............................................................................................................................................................................................................................

0.50

............................................................................AAAAAACAAATTGGCCGGCGCGGTGG.....................................................................................................................................................

0.50

.........AACTGGGTTCCGTCGCCATCAA............................................................................................................................................................................................................................

0.50

.......................................................................CGCTTAAAAAACAAATTGGCCGGCGCGG........................................................................................................................................................

0.50

............................................................................................................................................TTACAACAAAAACAAGTACCGGT........................................................................................

0.50

.................TCCGTCGCCATCAACGATAGTGTG..................................................................................................................................................................................................................

0.50

........................................................................GCTTAAAAAACAAATTGGCCGGC............................................................................................................................................................

0.50

............................................................................................................................................TTACAACAAAAACAAGTACCGGC........................................................................................

0.50

..........................................................................................................................................TCTTACAAGAAAAACAAGTACCGG.........................................................................................

0.50

........................................................................................GGCCGGCGGAGTGGCGGACAAATGT..........................................................................................................................................

0.50

...........................................................................TAAAAAACAAATTGGCCGGCGCGGTGGC....................................................................................................................................................

0.50

...............................................................................AAACAAATTGGCCGGCGCGGTGGCG...................................................................................................................................................

0.50

..........................................................................TTAAAAAACAAATTGGCCGGCGCG.........................................................................................................................................................

0.50

...........................................................................TAAAAAACAAATTGGCCGGCGCGGGGGC....................................................................................................................................................

0.50

...........................................................................TAAAAAACAAATTGGCCGGCGC..........................................................................................................................................................

0.33

..ACGGGGAAACTGGGGTCC.......................................................................................................................................................................................................................................

0.20

.............................................................................AAAAACCAATTGGCGGGC............................................................................................................................................................

0.06

....................................................................................................................................................AAAGCAAGTACCGGTCTCT....................................................................................

0.05

CCTACCCCTTTGACCCAAGGCAGCGGTAGTTTCTATCACACCTTCTTCAGCATTTAAATTATTTATTAAACGCGAATTTTTTGTTTAACCGGCCGCGCCACCGCCTGTTTACAGGTAGTTTGGTCCTCCGTTATCGGAAGAATGTTGTTTTTGTTCATGGCCAGAACATACTGGATGTAGTAAAAACACCATGAAATGATTCTAATCCAGTACAACTATTGTAAAATTACGTGGAGATATAACTACACAGT *************************************************************************************.............((((((.(((((((.((((....)))).))..)))(((((((....)))))))..............)).))))))*************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M044 female body	M058 embryo	V039 embryo	V055 head	V106 head
............................................................................................................................CCTCCGTTATCGGAAGAATGTTGTTT.....................................................................................................	26	0	2	2.50	5	2	3	0	0	0
..........................TAGTTTCTATCACACCTTCTTCAGCAT......................................................................................................................................................................................................	27	0	1	2.00	2	2	0	0	0	0
.............................................................................................................................CTCCGTTATCGGAAGAATGTTGTTT.....................................................................................................	25	0	2	1.50	3	2	0	1	0	0
..........................TAGTTTCTATCACACCTTCTTCAGCA.......................................................................................................................................................................................................	26	0	1	1.00	1	1	0	0	0	0
.........................GTAGTTTCTATCACACCTTCTTCAGCAT......................................................................................................................................................................................................	28	0	1	1.00	1	1	0	0	0	0
..........................TAGTTTCTATCACACCTTCTTCAGC........................................................................................................................................................................................................	25	0	1	1.00	1	1	0	0	0	0
.........................GTAGTTTCTATCACACCTTGTTCAGCAT......................................................................................................................................................................................................	28	1	1	1.00	1	1	0	0	0	0
..........................................................................................GGCCGCGCCACCGCCTGTTTACAGGT.......................................................................................................................................	26	0	1	1.00	1	1	0	0	0	0
............................................................................................CCGCGCCACCGCCTGTTTACAGGTAGTTT..................................................................................................................................	29	0	1	1.00	1	0	1	0	0	0
............ACCCAAGGCAGCGGTAGTTTCTAT.......................................................................................................................................................................................................................	24	0	1	1.00	1	1	0	0	0	0
........................GGTAGTTTCTATCACACCTTCTTCA..........................................................................................................................................................................................................	25	0	1	1.00	1	1	0	0	0	0
....CCCCTTTGACCCAAGGCAGCGGTAG..............................................................................................................................................................................................................................	25	0	1	1.00	1	0	1	0	0	0
..................GGCAGCGGTAGTTTCTATCACACCTTCT.............................................................................................................................................................................................................	28	0	1	1.00	1	1	0	0	0	0
.....................................................TTAAATTATTTATTAAACGCGAATTTGT..........................................................................................................................................................................	28	1	2	0.50	1	0	1	0	0	0
..........................................................................................................................GTCCTCCGTTATCGGAAGAATGTTGT.......................................................................................................	26	0	2	0.50	1	1	0	0	0	0
.................................................................................................................................GTTATCGGAAGAATGTTGTTTTTGTT................................................................................................	26	0	2	0.50	1	1	0	0	0	0
..........................................................................................................................GTCCTCCGTTATCGGAAGAATGTCG........................................................................................................	25	1	2	0.50	1	1	0	0	0	0
...........................................................................................................................TCCTCCGTTATCGGAAGAATGTTGTTT.....................................................................................................	27	0	2	0.50	1	1	0	0	0	0
.................................................................................................................................GTTATCGGAAGAATGTTGTTTTTGT.................................................................................................	25	0	2	0.50	1	1	0	0	0	0
......CCTTTGACCCAAGGCAGCGGTAGT.............................................................................................................................................................................................................................	24	0	2	0.50	1	0	0	1	0	0
...................................................................................................................................TATCGGAAGAATGTTGTTTTTGTTCAT.............................................................................................	27	0	2	0.50	1	0	0	1	0	0
.....................................................................................TAACCGGCCGCGGCACCGCCT.................................................................................................................................................	21	1	3	0.33	1	1	0	0	0	0
.................................................................................................................................................................CTGAAGATAATGGATGTAGTAA....................................................................	22	3	10	0.10	1	0	0	0	1	0
........................................................................................................................TGGTCGTCCGTTAAGGGAAG...............................................................................................................	20	3	10	0.10	1	0	0	0	0	1
.......................................ACCTTCGGCATCATTTAAAT................................................................................................................................................................................................	20	3	13	0.08	1	0	1	0	0	0

CCTACCCCTTTGACCCAAGGCAGCGGTAGTTTCTATCACACCTTCTTCAGCATTTAAATTATTTATTAAACGCGAATTTTTTGTTTAACCGGCCGCGCCACCGCCTGTTTACAGGTAGTTTGGTCCTCCGTTATCGGAAGAATGTTGTTTTTGTTCATGGCCAGAACATACTGGATGTAGTAAAAACACCATGAAATGATTCTAATCCAGTACAACTATTGTAAAATTACGTGGAGATATAACTACACAGT
***************************************************************************************.............((((((.(((((((.((((....)))).))..)))(((((((....)))))))..............)).))))))***************************************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

M044
female body

M058
embryo

V039
embryo

V055
head

V106
head

............................................................................................................................CCTCCGTTATCGGAAGAATGTTGTTT.....................................................................................................

2.50

..........................TAGTTTCTATCACACCTTCTTCAGCAT......................................................................................................................................................................................................

2.00

.............................................................................................................................CTCCGTTATCGGAAGAATGTTGTTT.....................................................................................................

1.50

..........................TAGTTTCTATCACACCTTCTTCAGCA.......................................................................................................................................................................................................

1.00

.........................GTAGTTTCTATCACACCTTCTTCAGCAT......................................................................................................................................................................................................

1.00

..........................TAGTTTCTATCACACCTTCTTCAGC........................................................................................................................................................................................................

1.00

.........................GTAGTTTCTATCACACCTTGTTCAGCAT......................................................................................................................................................................................................

1.00

..........................................................................................GGCCGCGCCACCGCCTGTTTACAGGT.......................................................................................................................................

1.00

............................................................................................CCGCGCCACCGCCTGTTTACAGGTAGTTT..................................................................................................................................

1.00

............ACCCAAGGCAGCGGTAGTTTCTAT.......................................................................................................................................................................................................................

1.00

........................GGTAGTTTCTATCACACCTTCTTCA..........................................................................................................................................................................................................

1.00

....CCCCTTTGACCCAAGGCAGCGGTAG..............................................................................................................................................................................................................................

1.00

..................GGCAGCGGTAGTTTCTATCACACCTTCT.............................................................................................................................................................................................................

1.00

.....................................................TTAAATTATTTATTAAACGCGAATTTGT..........................................................................................................................................................................

0.50

..........................................................................................................................GTCCTCCGTTATCGGAAGAATGTTGT.......................................................................................................

0.50

.................................................................................................................................GTTATCGGAAGAATGTTGTTTTTGTT................................................................................................

0.50

..........................................................................................................................GTCCTCCGTTATCGGAAGAATGTCG........................................................................................................

0.50

...........................................................................................................................TCCTCCGTTATCGGAAGAATGTTGTTT.....................................................................................................

0.50

.................................................................................................................................GTTATCGGAAGAATGTTGTTTTTGT.................................................................................................

0.50

......CCTTTGACCCAAGGCAGCGGTAGT.............................................................................................................................................................................................................................

0.50

...................................................................................................................................TATCGGAAGAATGTTGTTTTTGTTCAT.............................................................................................

0.50

.....................................................................................TAACCGGCCGCGGCACCGCCT.................................................................................................................................................

0.33

.................................................................................................................................................................CTGAAGATAATGGATGTAGTAA....................................................................

0.10

........................................................................................................................TGGTCGTCCGTTAAGGGAAG...............................................................................................................

0.10

.......................................ACCTTCGGCATCATTTAAAT................................................................................................................................................................................................

0.08

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droAna3	scaffold_12943:4661561-4661811 +	dan_970	GG--ATGGGGAAACTGGGTTCCGTCGCCATCAAAGATAGTGTGGAAGAAGT-----CGTAAATTTAATAAATAATTTGCGCTTAAAAAACAAATTGGC-----CGGCGCGGTGGCGGACAAATGTCCATCAAACCAGGAGGCAATAGCCTTCTTACAACAAAAACAAGTACCGGTCTTGTATGACCTACATCATTTTTGTGGTACTTTACTAAGATTAGGTCATGTTGATAACATTTTAATGCACCTCTATATTGATGTGTCA------
droBip1	scf7180000396707:954790-955043 -		GC--ATAGAGAAAATGGGATCCGCTGCTATTTTGGAAGGGGTGAAAATGGTATTGGCGAGCATTCGAAAAAG-CCCCGAGGT-TGCCACCAAATTGGC-----CGGTGCGGTGGCTGATAATTGCGCCGCCAATTTGGAGGCCATTCAATACCTCAATCAAAATGGAGTCCCAGTCCTATATGATCTGCGGCACTTCTGCGGCACAATCAGAAGATTGGGATTTGTGGACTTGTTAAATACAAGTTTGTATACAATCCCAACG------
droKik1	scf7180000302643:16571-16630 +		CC--T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCAGTCTTTGTGGTCCCTTGCAAAAGTTTCCTCATGGTGATATTTTTTTTGCGC-------------------------A
droFic1	scf7180000454107:689536-689567 +		AA--ATTTAATAAATTA---------------------------------------------------------TTTAAACTCGAAAAAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A
droEle1	scf7180000490456:21432-21519 -		ATCATTTCTGTGTCAAT---------------------------------------------------------TTTTTCAGATTCGATCTTATTTACAACGTTTGCCGTTGAGTCTA----------------------------------------------------------------------------------------------------------------------------CCTCTTTAAATTGTTTTTTTAATTGAT
droRho1	scf7180000759948:31532-31612 +		AA--ACTGAGAGACTAG---------------------------------------------------------TTTGCGAGAAACAAACAGACGGAC-----AGACGGGCAGACGGACATGGCTATATCAACTCAGGAGGTGA----------------------------------------------------------------------------------------------------------------------------T
droBia1	scf7180000302291:250983-251004 +		GA--ATCGGAACATGGAGTTGCGT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droTak1	scf7180000415786:189452-189518 +		TT--G--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACTACAAAACTAAAATTATAACACGAGTATAACGTATGTATGTATATACATACATTTGTACGC------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droAna3

GG--ATGGGGAAACTGGGTTCCGTCGCCATCAAAGATAGTGTGGAAGAAGT-----CGTAAATTTAATAAATAATTTGCGCTTAAAAAACAAATTGGC-----CGGCGCGGTGGCGGACAAATGTCCATCAAACCAGGAGGCAATAGCCTTCTTACAACAAAAACAAGTACCGGTCTTGTATGACCTACATCATTTTTGTGGTACTTTACTAAGATTAGGTCATGTTGATAACATTTTAATGCACCTCTATATTGATGTGTCA------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
........................................................................................................................................................TTACAACAAAAACAAGTACCGGTC.............................................................................................	24	1	7.00	7	6	1	0	0	0	0
.................................................................................................................................................................................................................CTAAGATTAGGTCATGTTGATAACA...................................	25	1	2.00	2	2	0	0	0	0	0
................................................................................................................................................................................................................ACTAAGATTAGGTCATGTTGATAACA...................................	26	1	2.00	2	2	0	0	0	0	0
................................................................................................................................................................................................................ACTAAGATTAGGTCATGTTGATAAC....................................	25	1	2.00	2	2	0	0	0	0	0
........................................................................................................................................................TTACAACAAAAACAAGTACCGGTCTTG..........................................................................................	27	1	2.00	2	2	0	0	0	0	0
..................................................................................TAAAAAACAAATTGGC-----CGGCGCGG..............................................................................................................................................................	24	2	1.50	3	1	1	0	0	1	0
.G--ATGGGGAAACTGGGTTCCGTCG...................................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0
..............................................................................................................................CATCAAACCAGGAGGCAATAGCCTT......................................................................................................................	25	1	1.00	1	1	0	0	0	0	0
.......................................TGTGGAAGAAGT-----CGTAAATTTAATA........................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0
.................................................................................................C-----CGGCGCGGTGGCGGACAAATGTCCATC...........................................................................................................................................	28	1	1.00	1	1	0	0	0	0	0
........................................................................................................................................................TTACAACAAAAACAAGTACCGGTCT............................................................................................	25	1	1.00	1	1	0	0	0	0	0
.............................................................................................................................................................................................................................CATGTTGATAACATTTTAATGCACCTC.....................	27	1	1.00	1	1	0	0	0	0	0
.....TGGGGAAACTGGGTTCCGTCGCC.................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0
....................................................................................................................GACAAATGTCCATCAAACCAGGAGGCAA.............................................................................................................................	28	1	1.00	1	1	0	0	0	0	0
.............................................................................GCGCTTAAAAAACAAATTGGC-----CGGCT.................................................................................................................................................................	26	2	0.50	1	1	0	0	0	0	0
........GGAAACTGGGTTCCGTCGCCATC..............................................................................................................................................................................................................................................	23	2	0.50	1	1	0	0	0	0	0
...................................................................................AAAAAACAAATTGGC-----CGGCGCGGTGG...........................................................................................................................................................	26	2	0.50	1	1	0	0	0	0	0
...........AACTGGGTTCCGTCGCCATCAA............................................................................................................................................................................................................................................	22	2	0.50	1	1	0	0	0	0	0
..............................................................................CGCTTAAAAAACAAATTGGC-----CGGCGCGG..............................................................................................................................................................	28	2	0.50	1	1	0	0	0	0	0
........................................................................................................................................................TTACAACAAAAACAAGTACCGGT..............................................................................................	23	2	0.50	1	1	0	0	0	0	0
...............................................................................GCTTAAAAAACAAATTGGC-----CGGC..................................................................................................................................................................	23	2	0.50	1	1	0	0	0	0	0
........................................................................................................................................................TTACAACAAAAACAAGTACCGGC..............................................................................................	23	2	0.50	1	0	1	0	0	0	0
..................................................................................TAAAAAACAAATTGGC-----CGGCGCGGTGGC..........................................................................................................................................................	28	2	0.50	1	1	0	0	0	0	0
......................................................................................AAACAAATTGGC-----CGGCGCGGTGGCG.........................................................................................................................................................	25	2	0.50	1	0	0	0	0	1	0
.................................................................................TTAAAAAACAAATTGGC-----CGGCGCG...............................................................................................................................................................	24	2	0.50	1	1	0	0	0	0	0
..................................................................................TAAAAAACAAATTGGC-----CGGCGC................................................................................................................................................................	22	3	0.33	1	1	0	0	0	0	0

droBip1

GC--ATAGAGAAAATGGGATCCGCTGCTATTTTGGAAGGGGTGAAAATGGTATTGGCGAGCATTCGAAAAAG-CCCCGAGGT-TGCCACCAAATTGGC-----CGGTGCGGTGGCTGATAATTGCGCCGCCAATTTGGAGGCCATTCAATACCTCAATCAAAATGGAGTCCCAGTCCTATATGATCTGCGGCACTTCTGCGGCACAATCAGAAGATTGGGATTTGTGGACTTGTTAAATACAAGTTTGTATACAATCCCAACG------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

CC--T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCAGTCTTTGTGGTCCCTTGCAAAAGTTTCCTCATGGTGATATTTTTTTTGCGC-------------------------A	Size	Hit Count	Total Norm	Total
No Reads

droFic1

AA--ATTTAATAAATTA---------------------------------------------------------TTTAAACTCGAAAAAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A	Size	Hit Count	Total Norm	Total
No Reads

droEle1

ATCATTTCTGTGTCAAT---------------------------------------------------------TTTTTCAGATTCGATCTTATTTACAACGTTTGCCGTTGAGTCTA----------------------------------------------------------------------------------------------------------------------------CCTCTTTAAATTGTTTTTTTAATTGAT	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AA--ACTGAGAGACTAG---------------------------------------------------------TTTGCGAGAAACAAACAGACGGAC-----AGACGGGCAGACGGACATGGCTATATCAACTCAGGAGGTGA----------------------------------------------------------------------------------------------------------------------------T	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GA--ATCGGAACATGGAGTTGCGT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TT--G--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACTACAAAACTAAAATTATAACACGAGTATAACGTATGTATGTATATACATACATTTGTACGC------	Size	Hit Count	Total Norm	Total
No Reads

dan_970

scaffold_12943:4661611-4661761 +

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

-26.9	-26.4	-26.2