dmo_1636

Name	Class	Family	Strand
Gypsy3-LTR_Dmoj	LTR	Gypsy	+

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------################################################## ATACATATATTTTTCCGCTTCAATGCGGCCGCTTCGCTTGTCACAAAAGTACTAAAAACTGAATCTGAATAGAGAGAGAAAGGTAAGAAGAGATCATAAAGAGAGAGAGACTTAACGGGCTCTGCTTTGTAGGCGTCGATTACTGCTTAGCATCTTGGCGCTGGCTCCCACATGTATAATATATTTATTATTTTCACACAGCTTACAGGACTATGAAAATTTTTATAAGAGTGCTTTATTGAGCCGGCAAA ************************************************........(((.......((((((((((.....((((......((.......))......)))).....)))).))))))..(((((((....(((...)))..)))))))(((...))).....((((((....)))))).......)))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body	M060 embryo	V041 embryo	V110 male body
................................................................................................................TAACGGGCTCTGCTTTGTAGGCGTC..................................................................................................................	25	0	10	0.40	4	4	0	0	0
.............................................................................................................................................................................................GTGTTGACACAGCTTACAGG..........................................	20	3	3	0.33	1	1	0	0	0
...............................................................................................................TTAACGGGCTCTGCTTTGTAGGCGTC..................................................................................................................	26	0	10	0.20	2	2	0	0	0
..........................................................................................................................TGATTTGGAGGCGTCGATTTCTGC.........................................................................................................	24	3	7	0.14	1	0	0	1	0
................................................................................................................TAACGGGCTCTGCTTTGTAGGCG....................................................................................................................	23	0	10	0.10	1	1	0	0	0
...............................................................................................................TTAACGGGCTCTGCTTTGTAGGCGTCG.................................................................................................................	27	0	10	0.10	1	1	0	0	0
...............................................................................................................TTAACGTGCTCTGCTTTGTAGGCGTC..................................................................................................................	26	1	10	0.10	1	0	1	0	0
................................................................................................................TAATGGGCTCTGCTTTGTAGGCGTCGT................................................................................................................	27	2	10	0.10	1	0	1	0	0
..................................................................................................................ACGGGCTCTGCTTTGTAGA......................................................................................................................	19	1	10	0.10	1	1	0	0	0
........................................................................................................................TCTACTTTGTAGGCGTGGAC...............................................................................................................	20	3	16	0.06	1	0	1	0	0
........................................................................................................................TCTGCTTTGTAGGCGTGGGTA..............................................................................................................	21	3	17	0.06	1	0	0	0	1
........................................................................................................................TCTTCTTTGTAGGCGTAGGT...............................................................................................................	20	3	20	0.05	1	0	1	0	0
........................................................................................................................TCTTCTTTGTAGGCGTGG.................................................................................................................	18	2	20	0.05	1	0	1	0	0

TATGTATATAAAAAGGCGAAGTTACGCCGGCGAAGCGAACAGTGTTTTCATGATTTTTGACTTAGACTTATCTCTCTCTTTCCATTCTTCTCTAGTATTTCTCTCTCTCTGAATTGCCCGAGACGAAACATCCGCAGCTAATGACGAATCGTAGAACCGCGACCGAGGGTGTACATATTATATAAATAATAAAAGTGTGTCGAATGTCCTGATACTTTTAAAAATATTCTCACGAAATAACTCGGCCGTTT ************************************************........(((.......((((((((((.....((((......((.......))......)))).....)))).))))))..(((((((....(((...)))..)))))))(((...))).....((((((....)))))).......)))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body	M060 embryo	V056 head
..........................CCGGCGAAGCGAACAGTGTTTT...........................................................................................................................................................................................................	22	0	2	2.00	4	2	2	0
.........................GCCGGCGAAGCGAACAGTGTTT............................................................................................................................................................................................................	22	0	2	0.50	1	1	0	0
.......................ACGCCGGCGAAGCGAACAGTGTTTT...........................................................................................................................................................................................................	25	0	2	0.50	1	1	0	0
..........................................................................TCTCTTTCCATTCTTCAGTAAT...........................................................................................................................................................	22	3	2	0.50	1	0	0	1
..............................................................................................................................................................................................AAAAGTGTGGTGAATGGCCTG........................................	21	3	3	0.33	1	1	0	0
.......................................................................................................................................................................................................................TTTTTAAAATGGTCTCACGAA...............	21	3	6	0.17	1	0	0	1

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6500:23891610-23891860 -	dmo_1636	ATA-----CATATAT---------------------TTTTCCGCTTCAATGCGGCCGCTTCGCTTG---------TCACAAAAGTACTAAAAACT-------GAATCTGAATAGA---------------------------GAGAGAAAGGTAAGAAGAGATCATAAAGAGAGAGAGACTTAACGGGCTCTGCTTTGTAGGCGTCGATTACTGCTTA--GCATCTTGGCGCTGGCTCCCACAT---GTATAATATATTTATT------ATTTTCACACAGCTTACAGGACTATGA----------AAATTTTTATAAGAGTGCTTTATTGAGCCGGCAAA
droVir3	scaffold_12963:19316011-19316236 +		GTAATCGATGTAAAC---------------------TTTTCAATTCCCATTTATCGGCTTTTTATAATTTAGAAAATACAAATTCATTCAAAATC-------G------A----------------------------------------------------TTATAGATATATAGATCGTTGACT---------------CCATATATTCCTATTTGAGACATTTCTTCTCCCTTCTCTACTA---GAATAATATAAT-ATTGTATAAGCTTTCACGCAGCTTACAGGATTATGA----------TGCATTCTACAAGAGTGCCTTGTTGGCCCGTCAAC
droGri2	scaffold_15252:7192179-7192231 +		--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGCTCGACGGACTATGA----------GATTTTTTATAAGATCGCATTACTGTCGCGCGAAC
droWil2	scf2_1100000004967:1699779-1700008 +		ATG-----CATATAT---------------------CTTTCCGCTCCAATGCAG--------ATTG---------ACACAAATATACTTAA-ACT-------AAATTCGAG-------------------------------GAGAGAGAGATAATAAGAGATCTTA----GAGAAAAAATTAAAGTGCTCTGCTCTGTA-GCGTCGATTGCCGCTTA--ACATCTCAGTGCTGGTTGCCACACCCTGCAT----------------------TATCAAGACTTAAAGGGATATGATTATAAACTAGAAGTTTTACAAAAAGGGTTTGGAAAGAAGGTAAA
droYak3	v2_chrUn_4786:1298-1496 +		ACA-----CAACCACAATTTAGATCGTCAACTTATTTATTACACTTCGATGTGATTGCTTCCAAAG---------TCAAAGTCAGACTAATAACTACGAATTAAGTATGTATAACAAAAGAGTACAGTCAAGTAAAGTGTGTGAGAGA-------------------AAGAGAGAGAG---------------------AGCCGTCGATCCTCTCTCA--GCATCGTGGTGCTGGTTCCCACAC---ATATAATGTAT-----------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

ATA-----CATATAT---------------------TTTTCCGCTTCAATGCGGCCGCTTCGCTTG---------TCACAAAAGTACTAAAAACT-------GAATCTGAATAGA---------------------------GAGAGAAAGGTAAGAAGAGATCATAAAGAGAGAGAGACTTAACGGGCTCTGCTTTGTAGGCGTCGATTACTGCTTA--GCATCTTGGCGCTGGCTCCCACAT---GTATAATATATTTATT------ATTTTCACACAGCTTACAGGACTATGA----------AAATTTTTATAAGAGTGCTTTATTGAGCCGGCAAA	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.....................................................................................................................................................................................TAACGGGCTCTGCTTTGTAGGCGTC.......................................................................................................................................	25	10	0.40	4	4	0	0	0	0	0
....................................................................................................................................................................................TTAACGGGCTCTGCTTTGTAGGCGTC.......................................................................................................................................	26	10	0.20	2	2	0	0	0	0	0
.....................................................................................................................................................................................TAACGGGCTCTGCTTTGTAGGCG.........................................................................................................................................	23	10	0.10	1	1	0	0	0	0	0
....................................................................................................................................................................................TTAACGGGCTCTGCTTTGTAGGCGTCG......................................................................................................................................	27	10	0.10	1	1	0	0	0	0	0
.......................................................................................................................................................................................ACGGGCTCTGCTTTGTAGA...........................................................................................................................................	19	10	0.10	1	1	0	0	0	0	0

droVir3

GTAATCGATGTAAAC---------------------TTTTCAATTCCCATTTATCGGCTTTTTATAATTTAGAAAATACAAATTCATTCAAAATC-------G------A----------------------------------------------------TTATAGATATATAGATCGTTGACT---------------CCATATATTCCTATTTGAGACATTTCTTCTCCCTTCTCTACTA---GAATAATATAAT-ATTGTATAAGCTTTCACGCAGCTTACAGGATTATGA----------TGCATTCTACAAGAGTGCCTTGTTGGCCCGTCAAC	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
...........................................................................................................................................................................................................................................................................................TACAGGATTATGA----------TGCATTCTACAA.......................	25	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

droGri2

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGCTCGACGGACTATGA----------GATTTTTTATAAGATCGCATTACTGTCGCGCGAAC	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

ATG-----CATATAT---------------------CTTTCCGCTCCAATGCAG--------ATTG---------ACACAAATATACTTAA-ACT-------AAATTCGAG-------------------------------GAGAGAGAGATAATAAGAGATCTTA----GAGAAAAAATTAAAGTGCTCTGCTCTGTA-GCGTCGATTGCCGCTTA--ACATCTCAGTGCTGGTTGCCACACCCTGCAT----------------------TATCAAGACTTAAAGGGATATGATTATAAACTAGAAGTTTTACAAAAAGGGTTTGGAAAGAAGGTAAA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
No Reads

droYak3

ACA-----CAACCACAATTTAGATCGTCAACTTATTTATTACACTTCGATGTGATTGCTTCCAAAG---------TCAAAGTCAGACTAATAACTACGAATTAAGTATGTATAACAAAAGAGTACAGTCAAGTAAAGTGTGTGAGAGA-------------------AAGAGAGAGAG---------------------AGCCGTCGATCCTCTCTCA--GCATCGTGGTGCTGGTTCCCACAC---ATATAATGTAT-----------------------------------------------------------------------------------	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
..........................................................................................................................TACAGTCAAGTAAAGTGTGTGAGAG..................................................................................................................................................................................................	25	9	3.56	32	0	3	0	0	0	0	0	0	0	0	29
..........................................................................................................................TACAGTCAAGTAAAGTGTGTGAGAGA-------------------..............................................................................................................................................................................	26	9	2.89	26	0	3	3	0	0	0	2	0	0	0	18
.................................................TGTGATTGCTTCCAAAG---------TCAAAGTCA.................................................................................................................................................................................................................................................................	26	13	1.15	15	0	11	0	0	0	0	0	0	0	0	4
...............................................................................................................TAACAAAAGAGTACAGTCAAGTAAAG............................................................................................................................................................................................................	26	9	0.89	8	0	5	0	0	0	0	3	0	0	0	0
.................................................TGTGATTGCTTCCAAAG---------TCAAAGTC..................................................................................................................................................................................................................................................................	25	13	0.77	10	0	2	1	0	0	0	0	0	0	0	7
............................................................................................................................................................................................................TCGATCCTCTCTCA--GCATCGTGGTGC.............................................................................................................	26	13	0.54	7	0	5	2	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................TCCTCTCTCA--GCATCGTGGTGCTGGT.........................................................................................................	26	14	0.50	7	0	6	1	0	0	0	0	0	0	0	0
..........................................................................................................................TACAGTCAAGTAAAGTGTGTGAGA...................................................................................................................................................................................................	24	10	0.40	4	0	1	0	0	0	0	0	0	0	0	3
...................TAGATCGTCAACTTATTTATTACACTTCGA....................................................................................................................................................................................................................................................................................................	30	11	0.27	3	0	0	0	0	0	0	0	0	0	0	3
..............................................................................................................................................................................................................GATCCTCTCTCA--GCATCGTGGTGC.............................................................................................................	24	13	0.23	3	0	1	2	0	0	0	0	0	0	0	0
...............................................................................................................TAACAAAAGAGTACAGTCAAGTA...............................................................................................................................................................................................................	23	9	0.22	2	0	1	0	0	0	0	1	0	0	0	0
..........................TCAACTTATTTATTACACTTCGATG..................................................................................................................................................................................................................................................................................................	25	11	0.18	2	0	2	0	0	0	0	0	0	0	0	0
.......................................TACACTTCGATGTGATTGCTTCCAAAG---------..........................................................................................................................................................................................................................................................................	27	12	0.17	2	0	2	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................GTCGATCCTCTCTCA--GCATCGTGG................................................................................................................	24	13	0.15	2	0	2	0	0	0	0	0	0	0	0	0
...............................................................................................................TAACAAAAGAGTACAGTCAAGTAAAGT...........................................................................................................................................................................................................	27	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................ACAGTCAAGTAAAGTGTGTGAGAG..................................................................................................................................................................................................	24	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
...............................................................................................................TAACAAAAGAGTACAGTCAAGTAAAGTG..........................................................................................................................................................................................................	28	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................CAGACTAATAACTACGAATTAAGTATG........................................................................................................................................................................................................................................	27	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................ACAGTCAAGTAAAGTGTGTGAGAGA-------------------..............................................................................................................................................................................	25	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................AACAAAAGAGTACAGTCAAGTAAAGTG..........................................................................................................................................................................................................	27	10	0.10	1	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................AACAAAAGAGTACAGTCAAGTAAAG............................................................................................................................................................................................................	25	10	0.10	1	0	1	0	0	0	0	0	0	0	0	0
..........................TCAACTTATTTATTACACTTCGATGTGAT..............................................................................................................................................................................................................................................................................................	29	11	0.09	1	0	1	0	0	0	0	0	0	0	0	0
................................TATTTATTACACTTCGATGTGAT..............................................................................................................................................................................................................................................................................................	23	11	0.09	1	0	1	0	0	0	0	0	0	0	0	0
...............................TTATTTATTACACTTCGATGTGAT..............................................................................................................................................................................................................................................................................................	24	11	0.09	1	0	1	0	0	0	0	0	0	0	0	0
..................TTAGATCGTCAACTTATTTATTACACT........................................................................................................................................................................................................................................................................................................	27	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.............................................TCGATGTGATTGCTTCCAAAG---------TCAAAGT...................................................................................................................................................................................................................................................................	28	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
...................................................TGATTGCTTCCAAAG---------TCAAAGTCAGACT.............................................................................................................................................................................................................................................................	28	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
........................................................GCTTCCAAAG---------TCAAAGTCAGACTAA...........................................................................................................................................................................................................................................................	25	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.................TTTAGATCGTCAACTTATTTATTACAC.........................................................................................................................................................................................................................................................................................................	27	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.................................................................................TCAGACTAATAACTACGAATTAAGT...........................................................................................................................................................................................................................................	25	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.................TTTAGATCGTCAACTTATTTATTACACT........................................................................................................................................................................................................................................................................................................	28	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
..................TTAGATCGTCAACTTATTTATTACAC.........................................................................................................................................................................................................................................................................................................	26	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
............................................TTCGATGTGATTGCTTCCAAAG---------TCAAAG....................................................................................................................................................................................................................................................................	28	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.................................................................................TCAGACTAATAACTACGAATTAAGTA..........................................................................................................................................................................................................................................	26	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.......................TCGTCAACTTATTTATTACACTT.......................................................................................................................................................................................................................................................................................................	23	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................AGCCGTCGATCCTCTCTCA--GCATCGTGG................................................................................................................	28	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
................................................ATGTGATTGCTTCCAAAG---------TCAAAGTC..................................................................................................................................................................................................................................................................	26	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.................................................TGTGATTGCTTCCAAAG---------TCAAAG....................................................................................................................................................................................................................................................................	23	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................GCCGTCGATCCTCTCTCA--GCATCG...................................................................................................................	24	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................AGCCGTCGATCCTCTCTCA--GCATCG...................................................................................................................	25	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................TCGATCCTCTCTCA--GCATCGTGGT...............................................................................................................	24	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.................................................TGTGATTGCTTCCAAAG---------TCAAAGTCAGA...............................................................................................................................................................................................................................................................	28	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................TCTCTCA--GCATCGTGGTGCTGG..........................................................................................................	22	14	0.07	1	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................TCCTCTCTCA--GCATCGTGGTGCTGG..........................................................................................................	25	14	0.07	1	0	0	0	1	0	0	0	0	0	0	0

dmo_1636

scaffold_6500:23891660-23891810 -

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

-22.4	-22.3	-22.2