dwi_3904

Name	Class	Family	Strand
BEL-10_DWil-I-int	LTR	Pao	+
BEL-10_DWil-LTR	LTR	Pao	+

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------################################################## GGAAATCTCTCTTCACTTTTTCGTTTATTCATTTTTCTAGTTGAACTAAATCTAGCTTATTTAAGAGCTTAATAAGCCCCGCCTGGAGCGAAGTGTGGGGAGTTCTTGGGGTGGTGGCATCATCAGGAGAGCGGCGCAAGGTGAAAGCTCTCGCCTCCCTTAACCCTTAAACTCATAAACGTGCTCCACCCCCCCTTGCAGGAGTGCAAGACCAGGAAGCCGAAGACTGTGCGCATCGCGATTGGCCGACC ********************************************************************************.....(((..((.....(((((...(((((((.(((........((((((..(((...)))...))))))))).))....)))))..)))))....)).)))*****************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M045 female body	V117 male body	V118 embryo	V119 head
................................................................................CGCTGGAGCGAAGTGTGGGGAGTTCTT................................................................................................................................................	27	2	1	2.00	2	2	0	0	0
.....................................................................................................................................................................................................GCAGGAGTGCAAGACCAGGAAGCCGA............................	26	0	1	1.00	1	1	0	0	0
..............................................................................................................................................................CTTAACCCTTAAACTCATAAACGTGC...................................................................	26	0	1	1.00	1	1	0	0	0
...............................................................................................................................................................................................................................AGACTGTGCGCATCGCGATTGGCCGT..	26	1	1	1.00	1	0	0	1	0
..................................................................................CTGGAGCGAAGTGTGGGGA......................................................................................................................................................	19	0	1	1.00	1	0	1	0	0
........................................................................................................................................CAAGGTGAAAGCCATCGCCTGC.............................................................................................	22	3	1	1.00	1	1	0	0	0
.............................................................................................GGTGGGGAGTTTCTGGGGTGG.........................................................................................................................................	21	3	2	0.50	1	1	0	0	0
.....................................................................TAATAAGCGGCGCCTGGAGCA.................................................................................................................................................................	21	3	2	0.50	1	0	1	0	0
.............................................................................................................................................TGAAAGCTCTCGCCTCCCTTAACCCT....................................................................................	26	0	2	0.50	1	1	0	0	0
...................................................................................TGGAGCGAAGTGTGGGGAGTTC..................................................................................................................................................	22	0	20	0.45	9	9	0	0	0
..............................................................................................GTGGGGAGTTTCTGGGGCGG.........................................................................................................................................	20	3	5	0.40	2	2	0	0	0
................................................................................................GGGGAGTTCCTGGGGCGG.........................................................................................................................................	18	2	3	0.33	1	1	0	0	0
.............................................................................................................................GGAGAGCGGCGCAAGGTGAAAGCTC.....................................................................................................	25	0	4	0.25	1	1	0	0	0
..............................................................................................GTGGGGAGTTGCTGGGGCGG.........................................................................................................................................	20	3	16	0.25	4	2	2	0	0
..................................................................................CTGGAGCAAAGTGTGGGG.......................................................................................................................................................	18	1	4	0.25	1	0	0	1	0
...................................................................................TGGAGCAAAGTGTGGGGAGTTCTTG...............................................................................................................................................	25	1	4	0.25	1	1	0	0	0
.............................................................................................GGTGGGGAGTTTTTGGGGCGG.........................................................................................................................................	21	3	6	0.17	1	1	0	0	0
....................................................................................................................................................................................................TGCAGGAGTGCAAGACCAGGA..................................	21	0	7	0.14	1	0	0	1	0
...................................................................................................................................................................................................TTGCAGGAGTGCAAGACCAGGA..................................	22	0	7	0.14	1	0	0	0	1
..............................................................................CCGCCGGTAGCTAAGTGTG..........................................................................................................................................................	19	3	8	0.13	1	0	1	0	0
..............................................................................................................................................GAAAGGTCTCGCCTTCCTG..........................................................................................	19	3	16	0.06	1	1	0	0	0
.................................................................................CCTGGGGTGAAGTGTGGGGG......................................................................................................................................................	20	3	16	0.06	1	0	1	0	0
...................................................................................TAGAGCGAAGTGTGGGGAGTTCT.................................................................................................................................................	23	1	20	0.05	1	1	0	0	0
...................................................................................TGGAGCGAAGTGTGGGGACG....................................................................................................................................................	20	2	20	0.05	1	1	0	0	0
...............................................................................................................................ACAGGGGCGCATGGTGAA..........................................................................................................	18	3	20	0.05	1	1	0	0	0

CCTTTAGAGAGAAGTGAAAAAGCAAATAAGTAAAAAGATCAACTTGATTTAGATCGAATAAATTCTCGAATTATTCGGGGCGGACCTCGCTTCACACCCCTCAAGAACCCCACCACCGTAGTAGTCCTCTCGCCGCGTTCCACTTTCGAGAGCGGAGGGAATTGGGAATTTGAGTATTTGCACGAGGTGGGGGGGAACGTCCTCACGTTCTGGTCCTTCGGCTTCTGACACGCGTAGCGCTAACCGGCTGG *****************************************************************.....(((..((.....(((((...(((((((.(((........((((((..(((...)))...))))))))).))....)))))..)))))....)).)))********************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M045 female body	V117 male body	V118 embryo
.......................................................................................................................................................................................................TCCTCACGTTGTGCTCCTG.................................	19	3	20	1.15	23	22	1	0
.............................................................................................................CCACCACCGTAGTAGTCCTCTCGCCG....................................................................................................................	26	0	1	1.00	1	1	0	0
..................................................................................GACCTCGCTTCACACCCCTCA....................................................................................................................................................	21	0	1	1.00	1	1	0	0
.......................................................................................................................................................................................................TCCTCACGTTGTGCTCCT..................................	18	2	9	0.33	3	3	0	0
...................................................................................................................................................................................GCACGAGGTGGGGCGCAAA.....................................................	19	3	6	0.33	2	1	1	0
...................................................................................................................................................................................................................................AGACGCGTAGTGCTAACCGC....	20	3	5	0.20	1	0	1	0
....................................................................................................................................................AAAGCGGAGGGAATTGGGAA...................................................................................	20	1	8	0.13	1	1	0	0
........................................................................................................................................................................................................CCTCACGTTGTGCTCCTG.................................	18	3	20	0.10	2	2	0	0
.........................................................................................................................................TTCCACTCGCGAGAGCAGA...............................................................................................	19	3	10	0.10	1	1	0	0
........................................................................TTTCGGGGCCGACCGCGC.................................................................................................................................................................	18	3	15	0.07	1	1	0	0
.............................................................................................................................................................................................GGGGGGAACGTCCTCACGTTC.........................................	21	0	20	0.05	1	1	0	0
........................................................................................GCTTCACACCCCTCAAGAA................................................................................................................................................	19	0	20	0.05	1	0	0	1
............................................................................................................................................................................................GGGGGGGAACGTCCTCACGTTCTG.......................................	24	0	20	0.05	1	1	0	0
...................................................................................ACCTCGCTTCACACCCCT......................................................................................................................................................	18	0	20	0.05	1	1	0	0

Species	Coordinate	ID	Alignment
droWil2	scf2_1100000004961:4866122-4866372 -	dwi_3904	GGAAATCTCTCTTCACTTTTTCGTTTATTCATTTTTCTAGTTGAACTAAATCTAGCTTATTTAAGAGCTTAATAAGCCCCGCCTGGAGCGAAGTGTGGGGAGTTCTTGGGGT----GGTGGCATCATCAGGAGAGCG---GCGCAAGGTGAAAGCTCTCGCCTCCCTTAACCCTTAAACTCATAAACGTGCTCCACCCCCCCTTGCAG-------GAGTGC---A----------------------------AGACCAGGAAGCCGAAGACTGTGCGCATCGCGATTGGCCGACC----------
dp5	Unknown_group_6:40258-40351 -		--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAACATCCTCCACCCC--CTTGCAG-------GATTGC---A--------AGGCTGAGTGCACGCCCCCGGCAGGATCCATCCAAACACGGTGCTCTGAGCCACCGGCAGGCC----------
droPer2	scaffold_43:209119-209212 -		--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAACATCCTCCACCCC--CTTGCAG-------GATTGC---A--------AGGTTGAGTGCACGCCCCCGGCAGGATCCATCCAAACACGGTGCTCTGAGCCACCGGCAGGCC----------
droFic1	scf7180000453500:1301-1455 -		GA-------------------------------------------------------------------------GTGCGGTGTGGGGTAAAGCTCCGGGAG-------------------------AGGGAGAGCG---GGAGAGG-------------------------------C--CTGAACATT--CCGCCCC--CTTGCAACCGCTGGCGTTGC---AAATAACTAGCCCTGGTTGCAGGCGCCCGACAGGATCCAGCCGAAGATGGTCTTCTGAGCTACTGGCAATCC----------
droRho1	scf7180000768343:5402-5499 +		C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCC--CCTGCGG-------GAGAGTTCC-TTGAAGCAGGACTGACGGCAGGCTCCCGACACGATCCATCCAAACGCCGTGCTCTGAGCGACGGGCAGCCC----------
droSec2	scaffold_1949:3883-3954 -		C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGAACATTCTCCCCCCC--C------------------------------------------CCGCTCCAGAAACGGTCCATCCGAACACCGTGTTCAGCGCGACGGGCAACCC----------
droYak3	v2_chrUn_003:300769-300944 -		GC-------------------------------------------------------------------------G---------------------GAGACTCCTTGGAGACTCTGTGGTGAAGAGCGAGAGAGCGTAAGAGGAAGCGGAGAGCGGGTGACAGTCCAAACCCCGTAAC--TTGAACATTCCGC-CCCC--CTTGCAATCACTGGGGTTGC---A----------------------------ACAACAAAAACCCAAAAACAGTTTTCTGGGTGACCGGCATTCCCTCTTCGAAG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droWil2

GGAAATCTCTCTTCACTTTTTCGTTTATTCATTTTTCTAGTTGAACTAAATCTAGCTTATTTAAGAGCTTAATAAGCCCCGCCTGGAGCGAAGTGTGGGGAGTTCTTGGGGT----GGTGGCATCATCAGGAGAGCG---GCGCAAGGTGAAAGCTCTCGCCTCCCTTAACCCTTAAACTCATAAACGTGCTCCACCCCCCCTTGCAG-------GAGTGC---A----------------------------AGACCAGGAAGCCGAAGACTGTGCGCATCGCGATTGGCCGACC----------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
............................................................................................................................................................................................................GCAG-------GAGTGC---A----------------------------AGACCAGGAAGCCGA......................................	26	1	1.00	1	0	1	0	0	0
.....................................................................................................................................................................CTTAACCCTTAAACTCATAAACGTGC...................................................................................................................	26	1	1.00	1	0	1	0	0	0
............................................................................................................................................................................................................................................................................AGACTGTGCGCATCGCGATTGGCCGT............	26	1	1.00	1	0	0	0	1	0
..................................................................................CTGGAGCGAAGTGTGGGGA.............................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0	0
....................................................................................................................................................TGAAAGCTCTCGCCTCCCTTAACCCT....................................................................................................................................	26	2	0.50	1	0	1	0	0	0
...................................................................................TGGAGCGAAGTGTGGGGAGTTC.........................................................................................................................................................................................................	22	20	0.45	9	0	9	0	0	0
.................................................................................................................................GGAGAGCG---GCGCAAGGTGAAAGCTC.....................................................................................................................................................	25	4	0.25	1	0	1	0	0	0
...........................................................................................................................................................................................................TGCAG-------GAGTGC---A----------------------------AGACCAGGA............................................	21	7	0.14	1	0	0	0	1	0
..........................................................................................................................................................................................................TTGCAG-------GAGTGC---A----------------------------AGACCAGGA............................................	22	7	0.14	1	0	0	0	0	1
...................................................................................TGGAGCGAAGTGTGGGGACG...........................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0

dp5

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAACATCCTCCACCCC--CTTGCAG-------GATTGC---A--------AGGCTGAGTGCACGCCCCCGGCAGGATCCATCCAAACACGGTGCTCTGAGCCACCGGCAGGCC----------	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
...................................................................................................................................................................................................................................................................TCCATCCAAACACGGTGCTCTGAGCC.....................	26	4	2.00	8	0	8	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................TCCATCCAAACACGGTGCTCTGAG.......................	24	4	1.50	6	0	3	0	0	0	0	0	3	0	0
...................................................................................................................................................................................................................................................................TCCATCCAAACACGGTGCTCTGAGCCA....................	27	4	1.50	6	1	5	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................TGCAG-------GATTGC---A--------AGGCTGAGTGCACGC..........................................................	27	3	0.67	2	0	0	0	0	0	0	2	0	0	0
...................................................................................................................................................................................................................................................................TCCATCCAAACACGGTGCTCTGAGC......................	25	4	0.50	2	0	2	0	0	0	0	0	0	0	0
......................................................................................................................................................................................TGAACATCCTCCACCCC--CTTGCAG-------...........................................................................................	24	4	0.25	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................ATCCATCCAAACACGGTGCTCTGAGCCA....................	28	4	0.25	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................TCCATCCAAACACGGTGCTCTGA........................	23	4	0.25	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................TGAGTGCACGCCCCCGGCAGGATCCATC.........................................	28	4	0.25	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................CCATCCAAACACGGTGCTCTGAGCCAC...................	27	4	0.25	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................ATCCATCCAAACACGGTGCTCTGAGC......................	26	4	0.25	1	0	1	0	0	0	0	0	0	0	0

droPer2

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAACATCCTCCACCCC--CTTGCAG-------GATTGC---A--------AGGTTGAGTGCACGCCCCCGGCAGGATCCATCCAAACACGGTGCTCTGAGCCACCGGCAGGCC----------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
...................................................................................................................................................................................................................................................................TCCATCCAAACACGGTGCTCTGAGCC.....................	26	1	3.00	3	2	1	0	0	0	0
...................................................................................................................................................................................................................................................................TCCATCCAAACACGGTGCTCTGAGC......................	25	1	2.00	2	0	2	0	0	0	0

droFic1

GA-------------------------------------------------------------------------GTGCGGTGTGGGGTAAAGCTCCGGGAG-------------------------AGGGAGAGCG---GGAGAGG-------------------------------C--CTGAACATT--CCGCCCC--CTTGCAACCGCTGGCGTTGC---AAATAACTAGCCCTGGTTGCAGGCGCCCGACAGGATCCAGCCGAAGATGGTCTTCTGAGCTACTGGCAATCC----------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCC--CCTGCGG-------GAGAGTTCC-TTGAAGCAGGACTGACGGCAGGCTCCCGACACGATCCATCCAAACGCCGTGCTCTGAGCGACGGGCAGCCC----------	Size	Hit Count	Total Norm	Total
No Reads

droSec2

C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGAACATTCTCCCCCCC--C------------------------------------------CCGCTCCAGAAACGGTCCATCCGAACACCGTGTTCAGCGCGACGGGCAACCC----------	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
...............................................................................................................................................................................................................................................................ACGGTCCATCCGAACACCGTG..............................	21	20	0.10	2	2	0	0	0
..............................................................................................................................................................................................................................................................AACGGTCCATCCGAACACCGTGTTC...........................	25	20	0.05	1	1	0	0	0
..............................................................................................................................................................................................................................................................AACGGTCCATCCGAACACCGTG..............................	22	20	0.05	1	1	0	0	0

droYak3

GC-------------------------------------------------------------------------G---------------------GAGACTCCTTGGAGACTCTGTGGTGAAGAGCGAGAGAGCGTAAGAGGAAGCGGAGAGCGGGTGACAGTCCAAACCCCGTAAC--TTGAACATTCCGC-CCCC--CTTGCAATCACTGGGGTTGC---A----------------------------ACAACAAAAACCCAAAAACAGTTTTCTGGGTGACCGGCATTCCCTCTTCGAAG	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
.......................................................................................................................GTGAAGAGCGAGAGAGCGTAAGAGG..................................................................................................................................................................	25	20	1.55	31	0	18	0	0	0	0	2	0	0	0	11
.......................................................................................................................GTGAAGAGCGAGAGAGCGTAAGAG...................................................................................................................................................................	24	20	0.45	9	0	9	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................TCCGC-CCCC--CTTGCAATCACTGGGGT........................................................................................	26	20	0.25	5	0	5	0	0	0	0	0	0	0	0	0
...................................................................................................................TGTGGTGAAGAGCGAGAGAGCGTA.......................................................................................................................................................................	24	20	0.20	4	0	1	0	0	0	0	0	0	0	0	3
.......................................................................................................................GTGAAGAGCGAGAGAGCGTAAGA....................................................................................................................................................................	23	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................CCC--CTTGCAATCACTGGGGTTGC---A----------------------------A....................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TTCCGC-CCCC--CTTGCAATCACTGGG..........................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
........................................................................................................................TGAAGAGCGAGAGAGCGTAAGAGG..................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.................................................................................................GAGACTCCTTGGAGACTCTGTGGT.........................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................................................................................GCGGAGAGCGGGTGACAGTCCAAAC.......................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TTCCGC-CCCC--CTTGCAATCACTGGGGT........................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
......................................................................................................TCCTTGGAGACTCTGTGGTGAAG.....................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

dwi_3904

scf2_1100000004961:4866172-4866322 -

Candidate

Unknown

Predicted structure

Flybase annnotation

Repeatable elements

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-28.6	-28.5	-28.3