dmo_1216

exon [dmoj_GLEANR_5865:5]; CDS [Dmoj\GI21059-cds]; CDS [Dmoj\GI21059-cds]; exon [dmoj_GLEANR_5865:4]; intron [Dmoj\GI21059-in]

Name	Class	Family	Strand
AT_rich	Low_complexity	Low_complexity	+

Name

Class

Family

Strand

AT_rich

Low_complexity

##################################################----------------------------------------------------------################################################## TCGACATCACCAGCTGAATTAGATGAAGAGGTTGCAGGGGCAAGCGCAGAGTAAGTGCTGAAATATCTATTGTAATTTATAATAATAATAATAATGGTGTATATTCAGGCATGAGTCGCCTCCTGGCGCCGTAGAGGAGCATCTACCGGACGTCGTGC ************************************************.......((((((((((((((((.(((.........))).))))))).)))).)))))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V110 male body	M046 female body
....................................................................................................ATATCGAGGCATGAGTCGC.......................................	19	2	1	1.00	1	1	0
........................................................................CAATTTATAATAATAATAATATTG..............................................................	24	2	6	0.17	1	0	1
..........................................................................ATTTATAATAATAATAATAAT...............................................................	21	0	19	0.05	1	0	1
...............GAATTAGGTGATGGGGTTG............................................................................................................................	19	3	20	0.05	1	1	0

##################################################----------------------------------------------------------##################################################
TCGACATCACCAGCTGAATTAGATGAAGAGGTTGCAGGGGCAAGCGCAGAGTAAGTGCTGAAATATCTATTGTAATTTATAATAATAATAATAATGGTGTATATTCAGGCATGAGTCGCCTCCTGGCGCCGTAGAGGAGCATCTACCGGACGTCGTGC
**************************************************.......((((((((((((((((.(((.........))).))))))).)))).)))))**************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

V110
male body

M046
female body

....................................................................................................ATATCGAGGCATGAGTCGC.......................................

1.00

........................................................................CAATTTATAATAATAATAATATTG..............................................................

0.17

..........................................................................ATTTATAATAATAATAATAAT...............................................................

0.05

...............GAATTAGGTGATGGGGTTG............................................................................................................................

0.05

AGCTGTAGTGGTCGACTTAATCTACTTCTCCAACGTCCCCGTTCGCGTCTCATTCACGACTTTATAGATAACATTAAATATTATTATTATTATTACCACATATAAGTCCGTACTCAGCGGAGGACCGCGGCATCTCCTCGTAGATGGCCTGCAGCACG ************************************************.......((((((((((((((((.(((.........))).))))))).)))).)))))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V049 head
..........................................................................................................................................CGTAGATGGTCTGCGGAAC.	19	3	10	0.10	1	1
..........................................................................................................................................CGTAGGTGGCTTGCAGGA..	18	3	20	0.05	1	1

AGCTGTAGTGGTCGACTTAATCTACTTCTCCAACGTCCCCGTTCGCGTCTCATTCACGACTTTATAGATAACATTAAATATTATTATTATTATTACCACATATAAGTCCGTACTCAGCGGAGGACCGCGGCATCTCCTCGTAGATGGCCTGCAGCACG
**************************************************.......((((((((((((((((.(((.........))).))))))).)))).)))))**************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

V049
head

..........................................................................................................................................CGTAGATGGTCTGCGGAAC.

0.10

..........................................................................................................................................CGTAGGTGGCTTGCAGGA..

0.05

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6496:20558998-20559155 +	dmo_1216	TCGACATC-ACCAGCTGA----ATTAGATGAAGAGGTTGCAGGGGCAAGCGCAGAGTAAGTGCTGAAATATCTATTGTAATTTATAATAATAATAATAATGGTGTATATTCAGGCATGAGTCGCCTCCTGGCGCCGTAGAGGAGCATCTA------------CCGGACGTCGTGC
droVir3	scaffold_12875:13270044-13270172 +		TTGACACAAACCAGCCCAGCATACAAGATGAAGACATTGCAATGGAATCCGATGAGTATGAGTTCAAATA---------------------------------------------AAGCATCGCTTACT-GCGCTATAGTTGTTAATCAATTTTTCAGAAATCAGCCCGTCGTTC

Species

Coordinate

Alignment

droMoj3

scaffold_6496:20558998-20559155 +

dmo_1216

TCGACATC-ACCAGCTGA----ATTAGATGAAGAGGTTGCAGGGGCAAGCGCAGAGTAAGTGCTGAAATATCTATTGTAATTTATAATAATAATAATAATGGTGTATATTCAGGCATGAGTCGCCTCCTGGCGCCGTAGAGGAGCATCTA------------CCGGACGTCGTGC

droVir3

scaffold_12875:13270044-13270172 +

TTGACACAAACCAGCCCAGCATACAAGATGAAGACATTGCAATGGAATCCGATGAGTATGAGTTCAAATA---------------------------------------------AAGCATCGCTTACT-GCGCTATAGTTGTTAATCAATTTTTCAGAAATCAGCCCGTCGTTC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

TCGACATC-ACCAGCTGA----ATTAGATGAAGAGGTTGCAGGGGCAAGCGCAGAGTAAGTGCTGAAATATCTATTGTAATTTATAATAATAATAATAATGGTGTATATTCAGGCATGAGTCGCCTCCTGGCGCCGTAGAGGAGCATCTA------------CCGGACGTCGTGC	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
...............................................................................ATTTATAATAATAATAATAAT...........................................................................	21	19	0.05	1	1	0	0	0	0	0

droVir3

TTGACACAAACCAGCCCAGCATACAAGATGAAGACATTGCAATGGAATCCGATGAGTATGAGTTCAAATA---------------------------------------------AAGCATCGCTTACT-GCGCTATAGTTGTTAATCAATTTTTCAGAAATCAGCCCGTCGTTC	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
...............................................................................................................................CT-GCGCTATAGTTGTTAATC...........................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................AGCATACAAGATGAAGACATTGC.......................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

dmo_1216

scaffold_6496:20559048-20559105 +

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

-8.1	-7.2	-7.2