dme-mir-929-as- 12- and 20-way alignments

dme-mir-929-as	chr3R:121091-121178 -	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mature strand at position 121141-121161
   star strand at position 121106-121126
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chr3R:121076-121193 -	T--------------------------------GCTCCTCTGTTGTG-TCGCTCCTTTGCAGCTCAATCTGACTCCGTTAGGGAGTCGCTCAT-TAAAGGACTCCCTACTAGAGTCAATTTGAGCTCCACCAGGACTGGTTCCG-------------------------CCATGTCA
droSim1	chr3R:194547-194664 -	T--------------------------------GCTCCTCTGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCAT-TAAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACTGGTTGCG-------------------------CCATGCCA
droSec1	super_6:240419-240536 -	T--------------------------------GCTCCTCTGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCAT-TAAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACTGGTTGCG-------------------------CCATGTCA
droYak2	chr3R:481089-481206 -	T--------------------------------GGTCCTGTGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGTTCAT-TAAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACTGGTTTTG-------------------------CCATTTCA
droEre2	scaffold_4770:471031-471148 -	T--------------------------------GCACCTGTGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTTAT-GGAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACTGGTTCCG-------------------------CCACTTCA
droAna3	Unknown	CCACC----------------------------ACGTAGTCGTTGTC-TCGCTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCTCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGCCAGGATTGGTTGGTTGGTTGGTTGGTGGCTGGGGAAGCTGCATCTCA
dp4	chr2:24810831-24810947 +	C--------------------------------GCTCCACTGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAATTGCCGTG--------------------------CACTTCG
droPer1	super_6:111437-111553 +	T--------------------------------GCTCCACTGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAAATCCCGTG--------------------------CACTTCG
droWil1	Unknown	TCG-----------------------------TGGCTTTTTGTTGTTGTTGTTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTTATATAAAGGACTCCCTACTAGAGTCAATTTGAACTGCCGCAGGAGTTCTCAAG-------------------------CCACTTTA
droVir3	Unknown	C----------------------------------------GTTGTC-TGGGTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGT-GAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGGCAGGACGCGTCGCA-------------------------CTTGGCCT
droMoj3	Unknown	CCACTGTATACCATTATTTGCATTTGTGCTCGCGCTTCTTCGTTGTC-TGGGTCCTCTGAAATTCAATCTGACTCCGTTAGGGAGTCGTTAAAAAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCATGAGGACTCGTAGCGTt------------------------TtTGTtT
droGri2	scaffold_15074:2468171-2468274 +	AC--T----------------------------GGGGCATTGTTGAC-TTGGTCCTTTGTAACTCAATCTGACTCCGTTAGGGAGTCGCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCAGCAGGA------------------------------------------

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:121076-121193 -	NA	T----GCTCCTC-----TGTTGTG-TCGCTCCTTTGCAGCTCAATCTGACTCCGTTAGGGAGTCGCTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTCCACCAGGACT-------------------------------G-GTTC-C-GCCATGT---CA
droSim1	chr3R:194547-194664 -	6	T----GCTCCTC-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTG-C-GCCATGC---CA
droSec1	super_6:240419-240536 -	5	T----GCTCCTC-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTG-C-GCCATGT---CA
droYak2	chr3R:481089-481206 -	2	T----GGTCCTG-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGTTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTT-T-GCCATTT---CA
droEre2	scaffold_4770:471031-471148 -	1	T----GCACCTG-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTTATG-GAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTC-C-GCCACTT---CA
droEug1	scf7180000409759:55732-55851 -	4	T----GCTCCTT-----TGTTGTT--TGCTCCTTTGAAATTCAATCTGACTCCGTTAGGGAGTCGCTCGATATAAGGACTCCCTACTAGAGTCAATTTGAACAGCGTCAGGATT-------------------------------T-GTTATCATCTATAT---CA
droBia1	scf7180000302098:364509-364629 +	1	TT---GCTCCTT-----TGTTGTC-TCGCTCCTTTGAAGTTCAATCTGACTCCGTTAGGGAGTCGCTCATTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGTCAGGACTT------------------------------A-GTTC-T-GTTATGT---CA
droTak1	scf7180000414441:35434-35553 +	1	T----TTCCCTT-----TGTTGTC-TTGGTCCTTTGTAGTTCAATCTGACTCCGTTAGGGAGTCGCTCATTGAAAGGACTCCCTACTAGAGTCAATTTGAGCTGCGCCAGGAATT------------------------------G-GTTC-T-CTTATGT---CA
droEle1	scf7180000491104:1857441-1857554 -	6	CT---GCTC-CC-----CGATGTC-TTGCTCCTTCGAAGCTCAATCTGACTCCGTTAGGGAGTCGCTCGAGAAAAGGACTCCCTACTAGAGTCAATTTGAGCTGCGCCAGGAAGT------------------------------C-CTTCTC-G-C---------
droRho1	scf7180000777910:14060-14170 +	1	T----GCTCCT------TGTTGTC-TCTCTCCTTTGTAGATCAATCTGACTCCGTTAGGGAGTCGCTCATGAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGGCAGGAAGT------------------------------C-GTTT---------T----C
droFic1	scf7180000454096:1242536-1242654 -	6	C----GCTCCCT-----CGATGTC-TCGCTCCTTTGAAGTTCAATCTGACTCCGTTAGGGAGTCGCTCAAGAAAAGGACTCCCTACTAGAGTCAATTTGAGCTGCGTCAGGAAGT------------------------------C-GTTC---TCAAAGT---CG
droKik1	scf7180000302634:767745-767852 -	8	T----C-T-CAC-----TGTTGTC-TCTCTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGTACAAAGGACTCCCTACTAGAGTCAATTTGAACTCCGACAGGAA-------------------------------------------CATGG---CG
droAna3	scaffold_13340:11127706-11127842 -	3	G----CCACCACGTAGTCGTTGTC-TCGCTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCTCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGCCAGGAAGTGGTTGGTTGGTT------------------G-GTTG-G-TTGGTGG---CT
droBip1	scf7180000396691:36372-36522 -	3	A----ACCCCTT--AGTCGTTGTC-TCGCTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGCCAGGAAGTGGTTGGTGGGTTGGTGGAAGGCCGCATCTCA-GTAC----CCTTTT---CA
dp4	chr2:24810831-24810946 +	1	C----GCTCCAC-----TGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAATT----------------------------G-CCGT-----GC-ACTT---C-
droPer1	super_6:111437-111552 +	3	T----GCTCCAC-----TGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAAAT----------------------------C-CCGT-----GC-ACTT----C
droWil1	scaffold_181089:9825565-9825678 +	1	TCGTGGCT-TTT-----TGTTGTTGTTGTTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTTATATAAAGGACTCCCTACTAGAGTCAATTTGAACTGCCGCAGGAAG----------------------------------TTC---------T---CA
droVir3	scaffold_12822:1418795-1418912 -	4	C----------T-----CGTTGTC-TGGGTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGTG-AAAGGACTCCCTACTAGAGTCAATTTGAACTGCGGCAGGAATT----------------------------C-ACGCGT-C-GC-ACTTGGCCT
droMoj3	scaffold_6540:34020273-34020392 -	18	C----GCTTCTT-----CGTTGTC-TGGGTCCTCTGAAATTCAATCTGACTCCGTTAGGGAGTCGTTAAAAAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCATGAGGAAAC----------------------------T-C-GTAG-C-G-TATAT---GT
droGri2	scaffold_15074:2468173-2468294 +	1	T----GGGGCAT-----TGTTGAC-TTGGTCCTTTGTAACTCAATCTGACTCCGTTAGGGAGTCGCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCAGCAGGAAGT----------------------------T-CGGGGG-C-ACACTTT---CA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

T--------------------------------GCTCCTCTGTTGTG-TCGCTCCTTTGCAGCTCAATCTGACTCCGTTAGGGAGTCGCTCAT-TAAAGGACTCCCTACTAGAGTCAATTTGAGCTCCACCAGGACTGGTTCCG-------------------------CCATGTCA

Size

Hit Count

Total Norm

droSim1

T--------------------------------GCTCCTCTGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCAT-TAAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACTGGTTGCG-------------------------CCATGCCA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

T--------------------------------GCTCCTCTGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCAT-TAAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACTGGTTGCG-------------------------CCATGTCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................................................................................................ACAAGGACAGGTTGCG-------------------------CC......	18	2	1.00	0.00	0.50	0.50

droYak2

T--------------------------------GGTCCTGTGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGTTCAT-TAAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACTGGTTTTG-------------------------CCATTTCA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.................................................................AATCTGACTCCGTTAGGGAGT...........................................................................................	21	2	0.50	0.50	0.00	0.00	0.00	0.00
.................................................................AATCTGACTCCGTTAGGGAGTC..........................................................................................	22	2	0.50	0.50	0.00	0.00	0.00	0.00

droEre2

T--------------------------------GCACCTGTGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTTAT-GGAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACTGGTTCCG-------------------------CCACTTCA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................................................TTTGAGCTGCACCAGGACTC.......................................	20	2	0.50	0.00	0.50	0.00	0.00
.................................................................AAGCTGACTCCGTTAGGGAGTC..........................................................................................	22	2	0.50	0.00	0.00	0.50	0.00
....................................................TCCTCTGTAGCTCAATCTG..........................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00

droAna3

CCACC----------------------------ACGTAGTCGTTGTC-TCGCTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCTCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGCCAGGATTGGTTGGTTGGTTGGTTGGTGGCTGGGGAAGCTGCATCTCA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................................................................................................................GTGGGTTGGTGGGTGGGG.............	18	2	90.50	4.00	86.00	0.50	0.00
...................................................................................................................................................TGGGTTGGTGGGTGGGGA............	18	2	3.50	0.00	3.50	0.00	0.00
..................................................................................................................................................GTGGGTTGGTGGGTGGGGA............	19	2	2.50	0.00	2.50	0.00	0.00
................................................................................................................................................TGGGTGGGTGGTGGCTGGG..............	19	2	2.50	0.00	2.50	0.00	0.00
..............................................................................................................................................GTTGGTGGGTTGGTGGCC.................	18	2	2.00	0.00	2.00	0.00	0.00
..................................................................................................................................................GTTGGTTGGTGGGTGGGGC............	19	2	1.50	0.00	1.50	0.00	0.00
..................................................................................................................................................GTTGGTTGGTGGGTGGGG.............	18	3	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................GTTGGTTGGTTGGTTGGGC....................	19	2	1.50	0.00	1.50	0.00	0.00
...........................................................................................................................................TTGGTTGGTTGGTTGGTTG...................	19	4	0.75	0.00	0.75	0.00	0.00
.......................................................................................................................................TTGGTTGGTTGGTTGGTTG.......................	19	4	0.75	0.00	0.75	0.00	0.00
.........................................................................................................................................GGTTGGTTGGTTGGTTGG......................	18	4	0.50	0.00	0.25	0.25	0.00
.......................................................................................................................................TTGGTTGGTTGGTGGGTC........................	18	7	0.29	0.00	0.29	0.00	0.00
...................................................................................................................................................TTGGTTGGTGGGTGGGGC............	18	2	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................TTGGTTGGTTGGTTGGTAGT..................	20	4	0.50	0.00	0.50	0.00	0.00
..........................................................................................................................................GTTGGTTGGTTGGTTGGCTG...................	20	4	0.50	0.00	0.50	0.00	0.00
..........................................................................................................................................TTTGGTTGGTTGGTGGGT.....................	18	7	0.29	0.00	0.29	0.00	0.00
.........................................................................................................................................GGTTGGTTGGTTGGCTGGC.....................	19	2	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................TGGGTGGTTGGGTGGTTGG......................	19	5	0.40	0.00	0.40	0.00	0.00
...........................................................................................................................................TTGGTTGGTTGGTGGGTC....................	18	7	0.29	0.00	0.29	0.00	0.00
......................................................................................................................................TTTGGTTGGTTGGTGGGT.........................	18	7	0.29	0.00	0.29	0.00	0.00
......................................................................................................................................GTTGGCTGGTTGGTTGGTTGG......................	21	2	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................GTTGGTTGGTTGGTTGGCTG.......................	20	4	0.50	0.00	0.50	0.00	0.00
...............................................................................................................................................TTGGTTGGTTGGTGGGTC................	18	7	0.29	0.00	0.29	0.00	0.00
..............................................................................................................................................TTTGGTTGGTTGGTGGGT.................	18	7	0.29	0.00	0.29	0.00	0.00
.......................................................................................................................................TTGGTTGGTTGGTTGGTAGT......................	20	4	0.50	0.00	0.50	0.00	0.00
.....................................................................................................................................GGTTGGTTGGTTGGTTGG..........................	18	4	0.50	0.00	0.25	0.25	0.00
.......................................................................................................................................TTGGxCGGTTGGTTGGTTGG......................	19	2	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................GTTGGTTGGTTGGTTGGTTG.......................	20	4	0.25	0.00	0.25	0.00	0.00
...................................................................................................................................................TGGGTTGGTGGGTGGGG.............	17	2	0.50	0.00	0.00	0.50	0.00
.......................................................................................................................................TTGGCTGGTTGGTTGGTT........................	18	4	0.25	0.00	0.25	0.00	0.00
..................................................................................................................................................GTGGGTTGGTGGATGGGG.............	18	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................................................................TTGGTGGCTGGGGxAGCTG.......	18	2	0.50	0.00	0.00	0.50	0.00
.......................................................................................................................................TTGGTTGGTTGGTTGGTTGGAT....................	22	2	0.50	0.00	0.50	0.00	0.00
..........................................................................................................................................GTTGGTTGGTTGGTTGGTTG...................	20	4	0.25	0.00	0.25	0.00	0.00
.........................................................................................................................................GGTGGGTTGGTGGGTTGGTGG...................	21	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................................................GGGGTTGGTTGGTTGGTTGG......................	20	4	0.25	0.00	0.25	0.00	0.00
.........................................................................................................................................GGTGGGTTGGTTGGATGG......................	18	2	0.50	0.00	0.50	0.00	0.00
..................................................................................................................................................GTAGGTTGGTGGGTGGGG.............	18	2	0.50	0.00	0.50	0.00	0.00
..................................................................................................................................................GTTGGTTGGTGGGTGGGGT............	19	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................TGGGTTGGTGGGTTGGTGG...................	19	2	0.50	0.00	0.50	0.00	0.00
.............................................................................................................................................GGTTGGTTGGTTGGTGCT..................	18	3	0.33	0.00	0.33	0.00	0.00
...........................................................................................................................................TTGGCTGGTTGGTTGGTT....................	18	4	0.25	0.00	0.25	0.00	0.00
.....................................................................................................................................GATTAGCTGGTTGGTTGGT.........................	19	2	0.50	0.50	0.00	0.00	0.00
..........................................................................................................................................GTTGGCTGGTTGGTTGGTTG...................	20	4	0.25	0.00	0.25	0.00	0.00
..............................................................................................................................................GTTGGTGGGTGGGTGGCT.................	18	2	0.50	0.00	0.50	0.00	0.00
...................................................................................................................................GGGGTTGGTTGGTTGGTTGG..........................	20	4	0.25	0.00	0.25	0.00	0.00
...........................................................................................................................................TTGGTTGGTTGGTTGGTAG...................	19	4	0.25	0.00	0.25	0.00	0.00
......................................................................................................................................GTTGGCTGGTTGGTTGGTTG.......................	20	4	0.25	0.00	0.25	0.00	0.00
..................................................................................................................................................GTTGGTTGGTGGATGGTGAA...........	20	2	0.50	0.50	0.00	0.00	0.00
.....................................................................................................................................GGTTGGTTGGTTGGTTGGTTG.......................	21	4	0.25	0.00	0.25	0.00	0.00
.......................................................................................................................................GTGGTTGGTTGGGTGGTTG.......................	19	3	0.33	0.00	0.33	0.00	0.00
................................................................................................................AGTCAATTTGxATTGCG................................................	16	2	0.50	0.00	0.00	0.50	0.00
.........................................................................................................................................GGTTGGTTGGTTGGTTGGTTG...................	21	4	0.25	0.00	0.25	0.00	0.00
........................................................................................................................................................TGGCGGCTGGGGTAGC.........	16	2	0.50	0.00	0.00	0.50	0.00
.......................................................................................................................................TTGGTTGGTTGGTTGGTAG.......................	19	4	0.25	0.00	0.25	0.00	0.00
..................................................................................................................................................GTGGGTTGGTGGTTGGGG.............	18	3	0.33	0.00	0.33	0.00	0.00
.....................................AGTCTTTTTC-TCGCTCCT.........................................................................................................................	18	4	0.25	0.00	0.00	0.25	0.00
..............................................................................................................................................GTTGGTTGGTGGGTGGCC.................	18	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................................................TTGGCTTGTTGGTTGGTTGG......................	20	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................TTGGTTGGTTGGTTGGTGG...................	19	4	0.25	0.00	0.25	0.00	0.00
.......................................................................................................................................TTGGTTGGTTGGTTGGTTGG......................	20	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................................................TTGGTTGGTTGGTTGGTGG.......................	19	4	0.25	0.00	0.25	0.00	0.00
...........................................................................................................................................TTGGTTGGTTGGTTGGTGCT..................	20	2	0.50	0.00	0.50	0.00	0.00
.........................................................................................................................................GGGTGGTTGGGTGGTTGG......................	18	5	0.20	0.00	0.20	0.00	0.00
..................................................................................................................................................GTGGGTTGGTGGCTGTGG.............	18	2	0.50	0.00	0.50	0.00	0.00
........................................................................................................................................TGGTTGGTTGGTTGGATGGTC....................	21	2	0.50	0.00	0.50	0.00	0.00
........................................................................................................................................TGGxGGGTTGGTTGGTTGGT.....................	19	3	0.33	0.00	0.33	0.00	0.00

dp4

C--------------------------------GCTCCACTGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAATTGCCGTG--------------------------CACTTCG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.....................................................................................................................ATTTGAACTGCTGCAGAT..........................................	18	2	0.50	0.00	0.50	0.00	0.00

droPer1

T--------------------------------GCTCCACTGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAAATCCCGTG--------------------------CACTTCG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................................................................AAACTGACTCCCTTAGGGAGTC..........................................................................................	22	2	0.50	0.00	0.00	0.00	0.50	0.00
......................................................................................................................TTTGxACTGCTGCTGGAAAT.......................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00

droWil1

TCG-----------------------------TGGCTTTTTGTTGTTGTTGTTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTTATATAAAGGACTCCCTACTAGAGTCAATTTGAACTGCCGCAGGAGTTCTCAAG-------------------------CCACTTTA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...................................GTTGTTGTTGTTGTTGTT............................................................................................................................	18	3	1.00	0.00	1.00	0.00	0.00
....................................TTGTTGTTGTTGTTGTTG...........................................................................................................................	18	4	0.50	0.00	0.50	0.00	0.00
...................................CTTTTTGTTGTAGTTGTT............................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.....................................TTTTGTTGTTGTTGTACT..........................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
.......................................TTGTTGTTGTTGTTTTTTT.......................................................................................................................	19	6	0.17	0.00	0.00	0.00	0.17
.......................................TTGTTGTTGTTGTTGTTT........................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
...................................ATTTTTGTTGTTGTTGTT............................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
..................................GCTGTGTGTTGTTGTTGT.............................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...........................................TGTTGTTGTTCTTTTGAAA...................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
.....................................TGTTGTTGTTGTTGTTGCT.........................................................................................................................	19	4	0.25	0.25	0.00	0.00	0.00
....................................TTGTTGTTGTTGTTGTTT...........................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
.....................................TTTTGTTGTTGTTGTACC..........................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
......................................TTTGTTGTTGTTGTTGGTTT.......................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
......................................TTTGTTGTTGTTGTTTTT.........................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
................................TAGCTGTTTGTTGTTGTTG..............................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
.....................................TTTTGTTGTTGTTTTTCTTTT.......................................................................................................................	21	3	0.33	0.33	0.00	0.00	0.00
...................................ATTATTGTTGTTGTTGTT............................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
.........................................GTTGTTGTTGTTTATTTG......................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.....................................ATTTGTTGTTGCTGTTCCT.........................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
..................................GTTGTTTGTTGTTGTTGTT............................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
....................................TTTTTGTTGTTGTTGTTGG..........................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00
..................................TCTTGTTGTTGTTGTTGT.............................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
.....................................TGTTGTTGTTGTTGTTGC..........................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
.................................AGCTGTTTGTTGTTGTTGTT............................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
..................................CCTTGTTGTTGTTGTTGTT............................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
.................................GATTTTTTGTTGTTGTTGT.............................................................................................................................	19	3	0.33	0.33	0.00	0.00	0.00
.......................................TTGTTGTTGTTGTTGTTTT.......................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
...................................................................................AGTCGCTTATATxAAGGCC...........................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.TG-----------------------------TGGTTTTTTGTTGTTGT................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
....................................TTATTGTTGTTGTTGTTG...........................................................................................................................	18	4	0.25	0.00	0.00	0.25	0.00
..................................TCTTTTTGTTGTTGCTGTT............................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
....................................TTGTTGTTGCTGTTGTTCCT.........................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
......................................GTTGTTGTTGTTGTTGCT.........................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
.......................................TTGTTGTTGTTGGTACTTTGT.....................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
....................................TTTTTGTTGTTGTTTTTTC..........................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
...................................ATTGTTGTTGTTGTTGTT............................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
..................................ACTTTTTGTTGTAGTTGTT............................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00

droVir3

C----------------------------------------GTTGTC-TGGGTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGT-GAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGGCAGGACGCGTCGCA-------------------------CTTGGCCT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.................................................................AAGCTGACTCCGTTAGGGAGTC..........................................................................................	22	2	0.50	0.00	0.00	0.50	0.00	0.00
G----------------------------------------GTTGTC-TGTGTCCTTTG......................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
...............................................................................AGGGTGGCGCTCGT-GAA................................................................................	17	2	0.50	0.00	0.50	0.00	0.00	0.00

droMoj3

CCACTGTATACCATTATTTGCATTTGTGCTCGCGCTTCTTCGTTGTC-TGGGTCCTCTGAAATTCAATCTGACTCCGTTAGGGAGTCGTTAAAAAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCATGAGGACTCGTAGCGTt------------------------TtTGTtT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.............................................................................TTAGGGAGTxxTTAAAAAAAA...............................................................................	19	2	0.50	0.50	0.00	0.00	0.00

droGri2

AC--T----------------------------GGGGCATTGTTGAC-TTGGTCCTTTGTAACTCAATCTGACTCCGTTAGGGAGTCGCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCAGCAGGA------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image