dpe_308

GCGTCAGCCACCTTAGGGTTAAGTCGTCGTTGCACTTTAGGATTTTAATCCCATTTAGCCACCTAGCACCATCGAAAGAGGGCATTGGGGCTGCGGGACTTCCTCCATGTGCGCAAACAGTGCGTGACGTTCCTGCACCAGCTTCCACT *********************************...((((......((((...(((((.((..((.((.((....))))))...))))))).))))..))))..........*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	M021 embryo	V057 head
..................................................CCATTTAGCCACCTAGCACCATCG...........................................................................	24	0	3	3.67	11	11	0	0
..................................................CCATTTAGCCACCTAGCACCATCGA..........................................................................	25	0	3	1.67	5	4	1	0
..................................................CCATTTAGCCACCTAGCACCATC............................................................................	23	0	4	0.50	2	2	0	0
..................................................................................................................AAACAGTGAGTGACGTTCCTGCACC..........	25	1	2	0.50	1	1	0	0
..................................................CCATTTAGCCACCTAGCACCATCGAA.........................................................................	26	0	3	0.33	1	1	0	0
...................................................CATTTAGCAACCTAGCACCATCGA..........................................................................	24	1	3	0.33	1	1	0	0
.............................................CAAATCCATTTAGCCACCTAGCACCATCG...........................................................................	29	3	3	0.33	1	1	0	0
...................................................CATTTAGCCACCTAGCACCATCGA..........................................................................	24	0	3	0.33	1	1	0	0
..................................................CCATTTAGCCACCTAGCACCAACG...........................................................................	24	1	3	0.33	1	1	0	0
..................................................CCATTTAGGCACCTAGCACCATC............................................................................	23	1	4	0.25	1	1	0	0
...................................................CATTTAGCCACCTAGCACCAT.............................................................................	21	0	4	0.25	1	1	0	0
....................................................................................TTGGGGCTGGGGGACCTC...............................................	18	2	10	0.10	1	0	0	1
.......................TCTTCGTTGCACTTTAGG............................................................................................................	18	1	20	0.05	1	1	0	0

CGCAGTCGGTGGAATCCCAATTCAGCAGCAACGTGAAATCCTAAAATTAGGGTAAATCGGTGGATCGTGGTAGCTTTCTCCCGTAACCCCGACGCCCTGAAGGAGGTACACGCGTTTGTCACGCACTGCAAGGACGTGGTCGAAGGTGA *********************************...((((......((((...(((((.((..((.((.((....))))))...))))))).))))..))))..........*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body
..........................................................................................GACGCCCTGAAGGAGGGACACGCGT..................................	25	1	2	0.50	1	1
..CAGTCGGTGGAATCCCAA.................................................................................................................................	18	0	20	0.05	1	1

Species	Coordinate	ID	Alignment
droPer2	scaffold_220:10768-10916 -	dpe_308	GCGTCAGCCACCTTAGGGTTAAGTCGTCGTTGCACTTTAGGATTTTAATCCCATTTAGCCACCTAGCACCATCGAAAGAGGGCATTGGGGCTGCGGGA--CTTCCTCCATGTGCGCAAACAGTG------CGTGACGTTCCTGCACCAGCTTCCACT
dp5	Unknown_group_85:27432-27580 -		GCGTCAGCCACCTTAGGGTTAAGTCGTCGTTGCACTTTAGGATTTTAATCCCATTTAGCCACCCAGCACCATCGAAAGAGGGCATTGGGGCTGCGG-A-ACTTCCTCCATGTGCGCAAACAGTG------CGTGACTTTCCTGCACCAGCTTCCACT
droWil2	scf2_1100000004967:2589543-2589680 -		----CACCCACTGCATGGTCGGGTCAACCTTGCATTTCAGAATTTAATCGCCATTGGATCATCCCGCTCAATCGAATGTGTGCGGTGGTGATCCTGGCGTTCGCTCTTATCTCCACTAACAACAAC---------------TCCACTACTTTCGACT
droVir3	scaffold_12963:5335170-5335322 -		TAGAGAGCCATTTCATGGCGTGGTCATCTCCGCAACCGATAAGCTTGACCCCAGTTTGCCAACCGGCATCGTCAAA-GCGGGCGGGTATGCTGTCGGG---TTTGGCCATGCTTTGGAGCAGGGCATCCACCAGCTTGGTCTCGACCAACTGCCATT
droKik1	scf7180000302695:307212-307360 -		GCGTCAGCCACTTC-TCGTCGGGTCATCCATGCACTTTAGGATTTTGACCCCATTTAGCCACCCAGCGCCATCGAAGGTGGGCATGGGAGCTTCGGGA-TCATCCTCCATCCGTGTGT------ACTCAACGAGCCACGCATGCACCATCTTCCACT
droFic1	scf7180000452125:11441-11578 +		GCGTCAGCCATCCCAGAGTTGGGTCGTTCCAGCACTTCAGGACTTTGAC---ATTCCGCCACCCA---------------GGCATGGGAGCTGTTAGG-GCCTCATCCATCCGTGCGAGCAGCGATTCCACAAGTCGCGCGTACACTGTCTTCCACC
droEle1	scf7180000488370:31659-31794 +		GCGTC----ACTTCAAGGCCGGATCGTTGTTGCACGTGACAATTTTTACCCCGTTGAGCCACCCTGCACCATCGAATGTGGACATGGGAGCGGTGGGA-TCTTCCTCCATCCGCGCAAAGAGGGATTCG---------------ACCAGCCGCCA-T
droBia1	scf7180000302042:30401-30538 -		GCGTCACCCACTTCCTGGTCGGATCTTTGTTGCCCTTAAG-GTTTTGACTCTGTTCAACCACCCTGCGCCACTGAATGTGGACATGGGTGCC-------------TCTAT-----TAAAGAGAGACTCAACGAGTCGTGCATGGACGATCATCCAGC
droTak1	scf7180000413931:3382-3537 +		GCGTCAGCCACTTCCTGGCCAGATCGTCGTTGCACTTCAGGATTTTCACGCCGTTCAACCACCCTGCACCATCGAATGTGGGCATGGGGGCTGTGGGT-AATTCATCCATCTGTGCAAAGAGAGACTCGATCAGTCGCGCATGGACGATCTTCCAGC
droYak3	chr2h:269521-269674 +		GCGTCAGCCACTTTCTCGTCGGGTCATCCATGCACTTCAGGATTTTCACCCCGTTCAGCCACCCGGCAACATCAAAAGTGGGCATGGGGGCCTCAGGA-GCTTCCTCCATCCGTGCAAACAG--ACTCAAAGAGTCGTGCATGCACCAACTTCCACC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

GCGTCAGCCACCTTAGGGTTAAGTCGTCGTTGCACTTTAGGATTTTAATCCCATTTAGCCACCTAGCACCATCGAAAGAGGGCATTGGGGCTGCGGGA--CTTCCTCCATGTGCGCAAACAGTG------CGTGACGTTCCTGCACCAGCTTCCACT	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
..................................................CCATTTAGCCACCTAGCACCATCG...................................................................................	24	3	3.67	11	0	11	0	0	0	0
..................................................CCATTTAGCCACCTAGCACCATCGA..................................................................................	25	3	1.67	5	1	4	0	0	0	0
..................................................CCATTTAGCCACCTAGCACCATC....................................................................................	23	4	0.50	2	0	2	0	0	0	0
..................................................CCATTTAGCCACCTAGCACCATCGAA.................................................................................	26	3	0.33	1	0	1	0	0	0	0
...................................................CATTTAGCCACCTAGCACCATCGA..................................................................................	24	3	0.33	1	0	1	0	0	0	0
...................................................CATTTAGCCACCTAGCACCAT.....................................................................................	21	4	0.25	1	0	1	0	0	0	0

dp5

GCGTCAGCCACCTTAGGGTTAAGTCGTCGTTGCACTTTAGGATTTTAATCCCATTTAGCCACCCAGCACCATCGAAAGAGGGCATTGGGGCTGCGG-A-ACTTCCTCCATGTGCGCAAACAGTG------CGTGACTTTCCTGCACCAGCTTCCACT	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
.............................TTGCACTTTAGGATTTTAATCCCATT......................................................................................................	26	1	6.00	6	0	2	0	0	1	0	0	3	0	0
.............................TTGCACTTTAGGATTTTAAT............................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...................TAAGTCGTCGTTGCACTTTAGGATTT................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................TTAATCCCATTTAGCCACCCAGCACCA......................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..............................................................................AGGGCATTGGGGCTGCGG-A-ACTTCCTC..................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.......................................................TAGCCACCCAGCACCATCGAA.................................................................................	21	18	0.44	8	0	7	1	0	0	0	0	0	0	0
.............................TTGCACTTTAGGATTTTAAAA...........................................................................................................	21	7	0.43	3	0	3	0	0	0	0	0	0	0	0
.......................................................TAGCCACCCAGCACCATCGAAAG...............................................................................	23	5	0.20	1	0	1	0	0	0	0	0	0	0	0
..........................TCGTTGCACTTTAGGATT.................................................................................................................	18	6	0.17	1	0	1	0	0	0	0	0	0	0	0
..................................................CCATTTAGCCACCCAGCACCATCGA..................................................................................	25	20	0.15	3	0	3	0	0	0	0	0	0	0	0
.......................................................TAGCCACCCAGCACCATCG...................................................................................	19	20	0.15	3	0	3	0	0	0	0	0	0	0	0
.......................................................TAGCCACCCAGCACCATCGA..................................................................................	20	20	0.10	2	0	2	0	0	0	0	0	0	0	0
......................................................TTAGCCACCCAGCACCATCGA..................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
..................................................CCATTTAGCCACCCAGCACCATCG...................................................................................	24	20	0.10	2	0	2	0	0	0	0	0	0	0	0
.............................TTGCACTTTAGGATTA................................................................................................................	16	11	0.09	1	0	0	0	0	0	0	0	1	0	0
.........................GTCGTTGCACTTTAGGAT..................................................................................................................	18	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droWil2

----CACCCACTGCATGGTCGGGTCAACCTTGCATTTCAGAATTTAATCGCCATTGGATCATCCCGCTCAATCGAATGTGTGCGGTGGTGATCCTGGCGTTCGCTCTTATCTCCACTAACAACAAC---------------TCCACTACTTTCGACT	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.....................................................................AATCGAATGTGTGCGGTGGTG...................................................................	21	1	1.00	1	0	0	0	1	0
.......................................................................TCGAATGTGTGCGGTGGTG...................................................................	19	1	1.00	1	0	0	0	1	0
.......................................................GGATCATCCCGCTCAAGG....................................................................................	18	2	0.50	1	0	1	0	0	0

droVir3

TAGAGAGCCATTTCATGGCGTGGTCATCTCCGCAACCGATAAGCTTGACCCCAGTTTGCCAACCGGCATCGTCAAA-GCGGGCGGGTATGCTGTCGGG---TTTGGCCATGCTTTGGAGCAGGGCATCCACCAGCTTGGTCTCGACCAACTGCCATT

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

No Reads

droKik1

GCGTCAGCCACTTC-TCGTCGGGTCATCCATGCACTTTAGGATTTTGACCCCATTTAGCCACCCAGCGCCATCGAAGGTGGGCATGGGAGCTTCGGGA-TCATCCTCCATCCGTGTGT------ACTCAACGAGCCACGCATGCACCATCTTCCACT	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GCGTCAGCCATCCCAGAGTTGGGTCGTTCCAGCACTTCAGGACTTTGAC---ATTCCGCCACCCA---------------GGCATGGGAGCTGTTAGG-GCCTCATCCATCCGTGCGAGCAGCGATTCCACAAGTCGCGCGTACACTGTCTTCCACC	Size	Hit Count	Total Norm	Total
No Reads

droEle1

GCGTC----ACTTCAAGGCCGGATCGTTGTTGCACGTGACAATTTTTACCCCGTTGAGCCACCCTGCACCATCGAATGTGGACATGGGAGCGGTGGGA-TCTTCCTCCATCCGCGCAAAGAGGGATTCG---------------ACCAGCCGCCA-T	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GCGTCACCCACTTCCTGGTCGGATCTTTGTTGCCCTTAAG-GTTTTGACTCTGTTCAACCACCCTGCGCCACTGAATGTGGACATGGGTGCC-------------TCTAT-----TAAAGAGAGACTCAACGAGTCGTGCATGGACGATCATCCAGC	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GCGTCAGCCACTTCCTGGCCAGATCGTCGTTGCACTTCAGGATTTTCACGCCGTTCAACCACCCTGCACCATCGAATGTGGGCATGGGGGCTGTGGGT-AATTCATCCATCTGTGCAAAGAGAGACTCGATCAGTCGCGCATGGACGATCTTCCAGC	Size	Hit Count	Total Norm	Total
No Reads

droYak3

GCGTCAGCCACTTTCTCGTCGGGTCATCCATGCACTTCAGGATTTTCACCCCGTTCAGCCACCCGGCAACATCAAAAGTGGGCATGGGGGCCTCAGGA-GCTTCCTCCATCCGTGCAAACAG--ACTCAAAGAGTCGTGCATGCACCAACTTCCACC	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
..............................TGCACTTCAGGATTTTCACCCCGTT......................................................................................................	25	1	3.00	3	0	3	0	0	0	0	0	0	0	0	0
...............................GCACTTCAGGATTTTCACCCCGTTC.....................................................................................................	25	1	2.00	2	0	2	0	0	0	0	0	0	0	0	0
..............................TGCACTTCAGGATTTTCACCCCGTTCAG...................................................................................................	28	1	2.00	2	0	2	0	0	0	0	0	0	0	0	0
..............................TGCACTTCAGGATTTTCACCCCGTTC.....................................................................................................	26	1	2.00	2	0	2	0	0	0	0	0	0	0	0	0
..............................................................................................................................TCAAAGAGTCGTGCATGCACCAAC.......	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.......................................................................TCAAAAGTGGGCATGGGGGCCTCAGG............................................................	26	2	1.00	2	0	2	0	0	0	0	0	0	0	0	0
..............................TGCACTTCAGGATTTTCACCCCGTTCA....................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
..............................TGCACTTCAGGATTTTCACCCCGT.......................................................................................................	24	2	0.50	1	0	1	0	0	0	0	0	0	0	0	0
..................TCGGGTCATCCATGCACTTCAGGATT.................................................................................................................	26	3	0.33	1	0	1	0	0	0	0	0	0	0	0	0
..............................................................................TGGGCATGGGGGCCTCAGGA-GCTTCCT...................................................	27	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................................TGGGGGCCTCAGGA-GCTTCCTCCA................................................	24	8	0.13	1	0	1	0	0	0	0	0	0	0	0	0

dpe_308

scaffold_220:10818-10866 -

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

-22.1	-21.6