dpe_310

GGTCGTCACGTCTCCGTGTGGCCGCACGGGGGCCTTTTTAAGGGTCCTTCTTGGTTGCGATAGCTCCTTTTCGCTGCCTTGGGCGCACTCTTCGACAGAGAAGCTTCAAACAGCGAGAAGCGAGTCTGGGTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN *********************************........((...............((((((((((((((((....((((...((((.....))))..))))....)))))))))).))).)))...))......................*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	M021 embryo	V042 embryo	V057 head
..................................................TTGGTTGCGATAGCCCCTTTTCGC....................................................................................................................	24	1	5	18.20	91	89	2	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCGCTG..................................................................................................................	26	1	5	7.40	37	37	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCG.....................................................................................................................	23	1	5	4.00	20	19	0	1	0
..................................................TTGGTTGCGATAGCCCCTTTTCGCTGC.................................................................................................................	27	1	5	2.40	12	12	0	0	0
..................................................TTGGTTGCGATAGCTCCTTTTCGC....................................................................................................................	24	0	5	2.20	11	11	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTC......................................................................................................................	22	1	5	1.80	9	9	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCGCT...................................................................................................................	25	1	5	1.60	8	8	0	0	0
...................................................TGGTTGCGATAGCCCCTTTTCGCTG..................................................................................................................	25	1	6	1.00	6	6	0	0	0
...................................................TGGTTGCGATAGCCCCTTTTCGC....................................................................................................................	23	1	6	1.00	6	6	0	0	0
...................................................TGGTTGCGATAGCCCCTTTTCG.....................................................................................................................	22	1	6	0.83	5	5	0	0	0
..................................................TTGGTTGCAATAGCCCCTTTTCGC....................................................................................................................	24	2	5	0.60	3	3	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCGT....................................................................................................................	24	2	5	0.40	2	2	0	0	0
..................................................TTGGTTGCTATAGCCCCTTTTCGC....................................................................................................................	24	2	5	0.40	2	2	0	0	0
.......................................................TGCGATAGCCCCTTTTCGCTGCCT...............................................................................................................	24	1	5	0.40	2	2	0	0	0
..................................................TTGGTTGCGATAGCTCCTTTTCGCTG..................................................................................................................	26	0	5	0.40	2	2	0	0	0
......................................................TTGCGATAGCCCCTTTTCGCTGCCT...............................................................................................................	25	1	5	0.40	2	2	0	0	0
............................................................TAGCCCCTTTTCGCTGCCTTGGGCGT........................................................................................................	26	2	4	0.25	1	1	0	0	0
..................................................TTGGTTGCGATAGCTCCTTTTCGCT...................................................................................................................	25	0	5	0.20	1	1	0	0	0
..................................................TTGGTTGCAATAGCTCCTTTTCGC....................................................................................................................	24	1	5	0.20	1	1	0	0	0
.........................ACGGGGGCTTTTTTTAGG...................................................................................................................................................	18	2	5	0.20	1	0	0	1	0
.......................................................GGCGATAGCCCCTTTTCGCTGCCT...............................................................................................................	24	2	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATACCCCCTTTTCG.....................................................................................................................	23	2	5	0.20	1	1	0	0	0
..................................................TTGGTTGCTATAGCCCCTTTTCGCT...................................................................................................................	25	2	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCGCAA..................................................................................................................	26	3	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATACCCCCTTTTCGC....................................................................................................................	24	2	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCGTTA..................................................................................................................	26	3	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCACTGC.................................................................................................................	27	2	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATAGCCCCTCTTCGT....................................................................................................................	24	3	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATAGCCCCTTT........................................................................................................................	20	1	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCGA....................................................................................................................	24	2	5	0.20	1	1	0	0	0
................................................TGTTGGTTGCGATAGCCCCTTTT.......................................................................................................................	23	2	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCGATG..................................................................................................................	26	2	5	0.20	1	1	0	0	0
..................................................TTGGTTGCTATAGCCCCTTTTCG.....................................................................................................................	23	2	5	0.20	1	1	0	0	0
.......................................................TGCGATAGACCCTTTTCGCTGCCT...............................................................................................................	24	2	5	0.20	1	1	0	0	0
..................................................TTGGTTGCGATAGCCCCTTTTCGCTGCC................................................................................................................	28	1	5	0.20	1	1	0	0	0
...................................................TGGTTGCGATAGCCCCTTTTCGCTA..................................................................................................................	25	2	6	0.17	1	1	0	0	0
.....................................................GTTGCGATAGCCCCTTTTCG.....................................................................................................................	20	1	6	0.17	1	1	0	0	0
...................................................TGGTTGCGATAGCCCCTTTTC......................................................................................................................	21	1	6	0.17	1	1	0	0	0
...................................................TGGTTGCGGTAGCCCCTTTTCGCTG..................................................................................................................	25	2	6	0.17	1	1	0	0	0
...................................................TGGTTGCGATAGCCCCTTTTCGA....................................................................................................................	23	2	6	0.17	1	1	0	0	0
...................................................TGGTTGCGATAGCCCCTTTTCGCTGC.................................................................................................................	26	1	6	0.17	1	1	0	0	0
.....................................................TTTGCGATAGCCCCTTTTCGCTG..................................................................................................................	23	2	6	0.17	1	1	0	0	0
....................................................GGTTGCGATAGCCCCTTTTCGC....................................................................................................................	22	1	6	0.17	1	1	0	0	0
...................................................TGGTTGCGCTAGCCCCTTTTCGCTG..................................................................................................................	25	2	6	0.17	1	1	0	0	0
...................................................TGGTTGCGATACCCCCTTTTCGCTGC.................................................................................................................	26	2	6	0.17	1	1	0	0	0
..............................................CTGCTTAGTTGCGATAAC..............................................................................................................................	18	3	20	0.05	1	0	0	0	1

CCAGCAGTGCAGAGGCACACCGGCGTGCCCCCGGAAAAATTCCCAGGAAGAACCAACGCTATCGAGGAAAAGCGACGGAACCCGCGTGAGAAGCTGTCTCTTCGAAGTTTGTCGCTCTTCGCTCAGACCCATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN *********************************........((...............((((((((((((((((....((((...((((.....))))..))))....)))))))))).))).)))...))......................*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V057 head
................................................................................................TATCTTCTTAGTTTGTCGCT..........................................................................	20	3	20	0.05	1	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droPer2	scaffold_435:1544-1733 +	dpe_310	GGTCGT------------------------CACGTCTCCGTG-------TGGCCGCACGGGGG------------------CCTTTTTAAGGGTCCTTCTTGGTTG--------CGATAGCTCCTTTTCGCTGCCTTGGGCGCACTCTTCGACAGAGAAGCTTCAAACAGCGAGAAGCGAGTCTGGGTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
dp5	XL_group1a:2208292-2208420 -		GGTCGT------------------------CACGTCTCCGTG-------TGGCCGCAACGGGG------------------CCTTTTTAAGGGTCCT-CTTGGTTG--------CGATAACTCCTTTTCGCTGCCTTGGGCGCACTCTTCGACAGAG-AGCTTCAA-CAGAGAGA-GCGAGTCTGGGTAT---------------------------------------------------------
droWil2	scf2_1100000004521:1948126-1948139 +		GGTCGC------------------------AATGGCTC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	scaffold_13339:179463-179468 +		GGGCGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000393860:3925-3979 -		GGTCCT-------------------GGCGCTGCGG-TCTGTG-------CGGCCATGCTCTGG------------------TCCTTCTTGGGGTTTCTTT---------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000300302:8246-8368 +		GGGCCTTCAGTCGCTTGGCCGATTGGCTGCGGCGG-GTTGGG-------TGCCTTGGATTTGGGCGCGCTGGCCGCGGGTGTCCTTCTTGCGGGAGTTTT----------------------CC------------------------CCTGCTTAGCAGCTTCAGCCGGCGTGGGG----------------------------------------------------------------------
droBia1	scf7180000301361:17562-17650 +		GGGATC-------------------GGAATCACGACTTCGTA-------AGACCCTTTTGGG-------------------GGTTCCTGTGGATTCT-CCTTGTAG--------CTCTGGCGCTTTTCGTCTGCGTTGAGCAC--------------------------------------------------------------------------------------------------------
droTak1	scf7180000413585:9036-9115 -		GGAACC--------------------------------CGTG-------GGGCCCTTTAGGGT------------------GGTTCCTTCGGGTGCT-CCTGGAAG--------CGTTGGTGCGTTCCTGCTGCATAGGGCGCATT-----------------------------------------------------------------------------------------------------
droEug1	scf7180000409005:627974-627995 -		TGACGT------------------------TGCGGT-CTGTG-------CGGCC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_3220:6401-6506 -		GCTTGC------------------------CACGACTCTGAGTTTCAGCTTGCTGTGCCGTGG------------------CCTTCTCCGCTGTCCTCGCCTGCCGCTTTGGAGGGCTGGCTCTC---TTCTCCCTCGGCCTCACCCTCTG------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

GGTCGT------------------------CACGTCTCCGTG-------TGGCCGCACGGGGG------------------CCTTTTTAAGGGTCCTTCTTGGTTG--------CGATAGCTCCTTTTCGCTGCCTTGGGCGCACTCTTCGACAGAGAAGCTTCAAACAGCGAGAAGCGAGTCTGGGTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
...................................................................................................TTGGTTG--------CGATAGCTCCTTTTCGC....................................................................................................................	24	5	2.20	11	0	11	0	0	0	0
...................................................................................................TTGGTTG--------CGATAGCTCCTTTTCGCTG..................................................................................................................	26	5	0.40	2	0	2	0	0	0	0
...................................................................................................TTGGTTG--------CGATAGCTCCTTTTCGCT...................................................................................................................	25	5	0.20	1	0	1	0	0	0	0

dp5

GGTCGT------------------------CACGTCTCCGTG-------TGGCCGCAACGGGG------------------CCTTTTTAAGGGTCCT-CTTGGTTG--------CGATAACTCCTTTTCGCTGCCTTGGGCGCACTCTTCGACAGAG-AGCTTCAA-CAGAGAGA-GCGAGTCTGGGTAT---------------------------------------------------------	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
......................................................................................................GTTG--------CGATAACTCCTTTTCGCTGCC................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....................................TCCGTG-------TGGCCGCAACGGGG------------------CCTT..................................................................................................................................................................	24	4	0.75	3	0	3	0	0	0	0	0	0	0	0
..............................CACGTCTCCGTG-------TGGCCGCAACGG..........................................................................................................................................................................................	24	3	0.33	1	0	1	0	0	0	0	0	0	0	0
................................CGTCTCCGTG-------TGGCCGCAACGG..........................................................................................................................................................................................	22	3	0.33	1	0	1	0	0	0	0	0	0	0	0
................................CGTCTCCGTG-------TGGCCGCAACG...........................................................................................................................................................................................	21	3	0.33	1	0	1	0	0	0	0	0	0	0	0
..............................CACGTCTCCGTG-------TGGCCGCAACGGG.........................................................................................................................................................................................	25	3	0.33	1	0	1	0	0	0	0	0	0	0	0
..............................CACGTCTCCGTG-------TGGCCGCAACG...........................................................................................................................................................................................	23	3	0.33	1	0	1	0	0	0	0	0	0	0	0
................................CGTCTCCGTG-------TGGCCGCAACGT..........................................................................................................................................................................................	22	3	0.33	1	0	1	0	0	0	0	0	0	0	0
................................CGTCTCCGTG-------TGGCCGCAAC............................................................................................................................................................................................	20	3	0.33	1	0	1	0	0	0	0	0	0	0	0
....................................TCCGTG-------TGGCCGCAACGGGA------------------......................................................................................................................................................................	20	4	0.25	1	0	1	0	0	0	0	0	0	0	0
....................................TCCGTG-------TGGCCGCAACGGGT------------------......................................................................................................................................................................	20	4	0.25	1	0	1	0	0	0	0	0	0	0	0
....................................TCCGTG-------TGGCCGCAACGGGA------------------AA....................................................................................................................................................................	22	4	0.25	1	0	1	0	0	0	0	0	0	0	0
...................................CTCCGTG-------TGGCCGCAACGGGG------------------CCTT..................................................................................................................................................................	25	4	0.25	1	0	1	0	0	0	0	0	0	0	0
..................................TCTCCGTG-------TGGCCGCAACGGGG------------------CCT...................................................................................................................................................................	25	4	0.25	1	0	1	0	0	0	0	0	0	0	0
........................................TG-------TGGCCGCAACGGGG------------------CCTTTTTAAGG...........................................................................................................................................................	27	4	0.25	1	0	1	0	0	0	0	0	0	0	0
....................................TCCGTG-------TGGCCGCAACGGGG------------------CCTTT.................................................................................................................................................................	25	4	0.25	1	0	1	0	0	0	0	0	0	0	0
....................................TCCGTG-------TGGCCGCAACGGGG------------------CCTTTT................................................................................................................................................................	26	4	0.25	1	0	1	0	0	0	0	0	0	0	0
....................................TCCGTG-------TGGCCGCAACGGGG------------------......................................................................................................................................................................	20	4	0.25	1	0	1	0	0	0	0	0	0	0	0
......................................................................................TTAAGGGTCCT-CTTGGTTG--------CG...................................................................................................................................	21	5	0.20	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................TCCTTTTCGCTGCCTTGGGCG.........................................................................................................	21	5	0.20	1	0	1	0	0	0	0	0	0	0	0
.................................................TGGCCGCAACGGGG------------------CCTTTTTAAGG...........................................................................................................................................................	25	6	0.17	1	0	1	0	0	0	0	0	0	0	0
.....................................................CGCAACGGGG------------------CCTTTTTAAGGGTCC.......................................................................................................................................................	25	6	0.17	1	0	1	0	0	0	0	0	0	0	0
.................................................TGGCCGCAACGGGG------------------CCTTTTTAAGGGT.........................................................................................................................................................	27	6	0.17	1	0	1	0	0	0	0	0	0	0	0
.................................................TGGCCGCAACGGGG------------------CCTTTTTAAGGGTA........................................................................................................................................................	28	6	0.17	1	0	1	0	0	0	0	0	0	0	0
.......................................................CAACGGGG------------------CCTTTTTAAGGGT.........................................................................................................................................................	21	6	0.17	1	0	0	1	0	0	0	0	0	0	0

droWil2

GGTCGC------------------------AATGGCTC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
No Reads

droAna3

GGGCGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droBip1

GGTCCT-------------------GGCGCTGCGG-TCTGTG-------CGGCCATGCTCTGG------------------TCCTTCTTGGGGTTTCTTT---------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

GGGCCTTCAGTCGCTTGGCCGATTGGCTGCGGCGG-GTTGGG-------TGCCTTGGATTTGGGCGCGCTGGCCGCGGGTGTCCTTCTTGCGGGAGTTTT----------------------CC------------------------CCTGCTTAGCAGCTTCAGCCGGCGTGGGG----------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GGGATC-------------------GGAATCACGACTTCGTA-------AGACCCTTTTGGG-------------------GGTTCCTGTGGATTCT-CCTTGTAG--------CTCTGGCGCTTTTCGTCTGCGTTGAGCAC--------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GGAACC--------------------------------CGTG-------GGGCCCTTTAGGGT------------------GGTTCCTTCGGGTGCT-CCTGGAAG--------CGTTGGTGCGTTCCTGCTGCATAGGGCGCATT-----------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEug1

TGACGT------------------------TGCGGT-CTGTG-------CGGCC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEre2

GCTTGC------------------------CACGACTCTGAGTTTCAGCTTGCTGTGCCGTGG------------------CCTTCTCCGCTGTCCTCGCCTGCCGCTTTGGAGGGCTGGCTCTC---TTCTCCCTCGGCCTCACCCTCTG------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
..........................................TTTCAGCTTGCTGTGCCGTGG------------------C.....................................................................................................................................................................	22	9	0.11	1	1	0	0	0	0	0	0
...TGC------------------------CACGACTCTGAGTTTCAGCTTGC..................................................................................................................................................................................................	26	20	0.10	2	2	0	0	0	0	0	0
..........................................TTTCAGCTTGCTGTGCCGTGG------------------......................................................................................................................................................................	21	10	0.10	1	1	0	0	0	0	0	0
.............................................................................................................TGGAGGGCTGGCTCTC---TTCTCCC................................................................................................................	23	14	0.07	1	1	0	0	0	0	0	0
......................................TGAGTTTCAGCTTGCTGTGCCG...........................................................................................................................................................................................	22	20	0.05	1	1	0	0	0	0	0	0
...TGC------------------------CACGACTCTGAGTTTCAGCTTG...................................................................................................................................................................................................	25	20	0.05	1	1	0	0	0	0	0	0
...TGC------------------------CACGACTCTGAGTTTCAGCTTGCT.................................................................................................................................................................................................	27	20	0.05	1	1	0	0	0	0	0	0
..............................CACGACTCTGAGTTTCAGCTTGCTG................................................................................................................................................................................................	25	20	0.05	1	1	0	0	0	0	0	0
.....................................................................................................TGCCGCTTTGGAGGGCTGGCTC............................................................................................................................	22	20	0.05	1	1	0	0	0	0	0	0

-29.2	-29.2	-29.1	-29.1

dpe_310

scaffold_435:1594-1683 +

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