dme-mir-929-as- Best orthologs

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

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

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

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	T----GCTCCTC-----TGTTGTG-TCGCTCCTTTGCAGCTCAATCTGACTCCGTTAGGGAGTCGCTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTCCACCAGGACT-------------------------------G-GTTC-C-GCCATGT---CA
droSim1	T----GCTCCTC-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTG-C-GCCATGC---CA
droSec1	T----GCTCCTC-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTG-C-GCCATGT---CA
droYak2	T----GGTCCTG-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGTTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTT-T-GCCATTT---CA
droEre2	T----GCACCTG-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTTATG-GAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTC-C-GCCACTT---CA
droEug1	T----GCTCCTT-----TGTTGTT--TGCTCCTTTGAAATTCAATCTGACTCCGTTAGGGAGTCGCTCGATATAAGGACTCCCTACTAGAGTCAATTTGAACAGCGTCAGGATT-------------------------------T-GTTATCATCTATAT---CA
droBia1	TT---GCTCCTT-----TGTTGTC-TCGCTCCTTTGAAGTTCAATCTGACTCCGTTAGGGAGTCGCTCATTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGTCAGGACTT------------------------------A-GTTC-T-GTTATGT---CA
droTak1	T----TTCCCTT-----TGTTGTC-TTGGTCCTTTGTAGTTCAATCTGACTCCGTTAGGGAGTCGCTCATTGAAAGGACTCCCTACTAGAGTCAATTTGAGCTGCGCCAGGAATT------------------------------G-GTTC-T-CTTATGT---CA
droEle1	CT---GCTC-CC-----CGATGTC-TTGCTCCTTCGAAGCTCAATCTGACTCCGTTAGGGAGTCGCTCGAGAAAAGGACTCCCTACTAGAGTCAATTTGAGCTGCGCCAGGAAGT------------------------------C-CTTCTC-G-C---------
droRho1	T----GCTCCT------TGTTGTC-TCTCTCCTTTGTAGATCAATCTGACTCCGTTAGGGAGTCGCTCATGAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGGCAGGAAGT------------------------------C-GTTT---------T----C
droFic1	C----GCTCCCT-----CGATGTC-TCGCTCCTTTGAAGTTCAATCTGACTCCGTTAGGGAGTCGCTCAAGAAAAGGACTCCCTACTAGAGTCAATTTGAGCTGCGTCAGGAAGT------------------------------C-GTTC---TCAAAGT---CG
droKik1	T----C-T-CAC-----TGTTGTC-TCTCTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGTACAAAGGACTCCCTACTAGAGTCAATTTGAACTCCGACAGGAA-------------------------------------------CATGG---CG
droAna3	G----CCACCACGTAGTCGTTGTC-TCGCTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCTCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGCCAGGAAGTGGTTGGTTGGTT------------------G-GTTG-G-TTGGTGG---CT
droBip1	A----ACCCCTT--AGTCGTTGTC-TCGCTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGCCAGGAAGTGGTTGGTGGGTTGGTGGAAGGCCGCATCTCA-GTAC----CCTTTT---CA
dp4	C----GCTCCAC-----TGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAATT----------------------------G-CCGT-----GC-ACTT---C-
droPer1	T----GCTCCAC-----TGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAAAT----------------------------C-CCGT-----GC-ACTT----C
droWil1	TCGTGGCT-TTT-----TGTTGTTGTTGTTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTTATATAAAGGACTCCCTACTAGAGTCAATTTGAACTGCCGCAGGAAG----------------------------------TTC---------T---CA
droVir3	C----------T-----CGTTGTC-TGGGTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGTG-AAAGGACTCCCTACTAGAGTCAATTTGAACTGCGGCAGGAATT----------------------------C-ACGCGT-C-GC-ACTTGGCCT
droMoj3	C----GCTTCTT-----CGTTGTC-TGGGTCCTCTGAAATTCAATCTGACTCCGTTAGGGAGTCGTTAAAAAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCATGAGGAAAC----------------------------T-C-GTAG-C-G-TATAT---GT
droGri2	T----GGGGCAT-----TGTTGAC-TTGGTCCTTTGTAACTCAATCTGACTCCGTTAGGGAGTCGCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCAGCAGGAAGT----------------------------T-CGGGGG-C-ACACTTT---CA

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

Small RNA-seq read pileup

Species

Alignment

droSim1

T----GCTCCTC-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTG-C-GCCATGC---CA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

T----GCTCCTC-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTG-C-GCCATGT---CA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................................................................ACAAGGACA-------------------------------G-GTTG-C-GCC.........	18	2	1.00	0.00	0.50	0.50

droYak2

T----GGTCCTG-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGTTCATT-AAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTT-T-GCCATTT---CA	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----GCACCTG-----TGTTGTC-TCGCTCCTTTGTAGCTCAATCTGACTCCGTTAGGGAGTCGCTTATG-GAAGGACTCCCTACTAGAGTCAATTTGAGCTTCACCAGGACT-------------------------------G-GTTC-C-GCCACTT---CA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................................................................................TTTGAGCTGCACCAGGACT-------------------------------C-...................	20	2	0.50	0.00	0.50	0.00	0.00

droEug1

T----GCTCCTT-----TGTTGTT--TGCTCCTTTGAAATTCAATCTGACTCCGTTAGGGAGTCGCTCGATATAAGGACTCCCTACTAGAGTCAATTTGAACAGCGTCAGGATT-------------------------------T-GTTATCATCTATAT---CA

Size

Hit Count

Total Norm

droBia1

TT---GCTCCTT-----TGTTGTC-TCGCTCCTTTGAAGTTCAATCTGACTCCGTTAGGGAGTCGCTCATTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGTCAGGACTT------------------------------A-GTTC-T-GTTATGT---CA

Size

Hit Count

Total Norm

droTak1

T----TTCCCTT-----TGTTGTC-TTGGTCCTTTGTAGTTCAATCTGACTCCGTTAGGGAGTCGCTCATTGAAAGGACTCCCTACTAGAGTCAATTTGAGCTGCGCCAGGAATT------------------------------G-GTTC-T-CTTATGT---CA

Size

Hit Count

Total Norm

droEle1

CT---GCTC-CC-----CGATGTC-TTGCTCCTTCGAAGCTCAATCTGACTCCGTTAGGGAGTCGCTCGAGAAAAGGACTCCCTACTAGAGTCAATTTGAGCTGCGCCAGGAAGT------------------------------C-CTTCTC-G-C---------

Size

Hit Count

Total Norm

droRho1

T----GCTCCT------TGTTGTC-TCTCTCCTTTGTAGATCAATCTGACTCCGTTAGGGAGTCGCTCATGAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGGCAGGAAGT------------------------------C-GTTT---------T----C

Size

Hit Count

Total Norm

droFic1

C----GCTCCCT-----CGATGTC-TCGCTCCTTTGAAGTTCAATCTGACTCCGTTAGGGAGTCGCTCAAGAAAAGGACTCCCTACTAGAGTCAATTTGAGCTGCGTCAGGAAGT------------------------------C-GTTC---TCAAAGT---CG

Size

Hit Count

Total Norm

droKik1

T----C-T-CAC-----TGTTGTC-TCTCTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGTACAAAGGACTCCCTACTAGAGTCAATTTGAACTCCGACAGGAA-------------------------------------------CATGG---CG

Size

Hit Count

Total Norm

droAna3

G----CCACCACGTAGTCGTTGTC-TCGCTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCTCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGCCAGGAAGTGGTTGGTTGGTT------------------G-GTTG-G-TTGGTGG---CT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.................................................................................................................GTGGGTGGTTGGGT------------------G-GTTG-..............	19	2	107.50	4.50	100.00	2.50	0.50
.................................................................................................................GTGGGTGGTTGGGT------------------G-GTT................	18	2	9.00	0.00	9.00	0.00	0.00
.................................................................................................................GTGGGTGGTTGGGT------------------G-GTTG-G-............	20	2	8.00	0.00	8.00	0.00	0.00
.................................................................................................................GTGGTTGGTTGGGT------------------G-GGT................	18	2	3.00	0.50	2.50	0.00	0.00
....................................................................................................................GTTGGxTGGTT------------------G-GGTG-G-TTG.........	19	2	2.50	0.00	2.50	0.00	0.00
....................................................................................................................GTTGGTTGGTG------------------G-GTCG-G-TTG.........	20	2	2.00	0.00	2.00	0.00	0.00
............................................................................................................................GTT------------------G-GTGG-G-TTGGTGG---CC	18	2	2.00	0.00	2.00	0.00	0.00
.................................................................................................................GTGGGTGGTTGGTT------------------G-GGT................	18	2	2.00	0.50	1.50	0.00	0.00
....................................................................................................................GTTGGTTGGTT------------------G-GTTG-G-GC..........	19	4	0.75	0.00	0.75	0.00	0.00
................................................................................................................AGTGGTTGGTGGGTG------------------G-GT.................	18	2	1.50	0.00	1.50	0.00	0.00
.................................................................................................................GTGGTTGGGTGGTT------------------G-GGTG-G-............	20	2	1.50	0.00	1.50	0.00	0.00
........................................................................................................................GTTGGTT------------------G-GTTG-G-TTGGGC......	19	4	0.75	0.00	0.75	0.00	0.00
.........................................................................................................................TTGGTT------------------G-GTTG-G-TTGGTTG---..	19	6	0.50	0.00	0.50	0.00	0.00
.....................................................................................................................TTGGTTGGTT------------------G-GTTG-G-TTG.........	19	6	0.50	0.00	0.50	0.00	0.00
.................................................................................................................TTGGTTGGTTGGTT------------------G-GTTG-..............	19	6	0.50	0.00	0.50	0.00	0.00

droBip1

A----ACCCCTT--AGTCGTTGTC-TCGCTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCGCCAGGAAGTGGTTGGTGGGTTGGTGGAAGGCCGCATCTCA-GTAC----CCTTTT---CA

Size

Hit Count

Total Norm

dp4

C----GCTCCAC-----TGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAATT----------------------------G-CCGT-----GC-ACTT---C-	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----GCTCCAC-----TGTTGTC-T-GTTCCTTGGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCAATAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCTGCAGGAAAT----------------------------C-CCGT-----GC-ACTT----C	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

TCGTGGCT-TTT-----TGTTGTTGTTGTTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTTATATAAAGGACTCCCTACTAGAGTCAATTTGAACTGCCGCAGGAAG----------------------------------TTC---------T---CA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
......CT-TTT-----TGTTGTAGTTGTT........................................................................................................................................	18	51	0.02	0.00	0.02	0.00	0.00
...........T-----TGTTGTTGTTGGTACTTTGT.................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
.....................................................................................................ATGGCGCAGGAAG----------------------------------TTC---------T---C.	18	2	0.50	0.00	0.00	0.00	0.50
............................................................AGTCGCTTATATxAAGGCC.......................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.....TCT-TTT-----TGTTGTTGCTGTT........................................................................................................................................	19	51	0.02	0.00	0.02	0.00	0.00
.....GCT-GTG-----TGTTGTTGTTGT.........................................................................................................................................	18	15	0.07	0.00	0.07	0.00	0.00
.........ATT-----TGTTGTTGCTGTTCCT.....................................................................................................................................	19	22	0.05	0.00	0.00	0.00	0.05
.....GTT-GTT-----TGTTGTTGTTGTT........................................................................................................................................	19	49	0.02	0.00	0.02	0.00	0.00
.....ACT-TTT-----TGTTGTAGTTGTT........................................................................................................................................	19	27	0.04	0.00	0.04	0.00	0.00
....................TGTTGTTGTTCTTTTGAAA...............................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
.........TTT-----TGTTGTTGTTGTACC......................................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25

droVir3

C----------T-----CGTTGTC-TGGGTCCTTTGTAATTCAATCTGACTCCGTTAGGGAGTCGCTCGTG-AAAGGACTCCCTACTAGAGTCAATTTGAACTGCGGCAGGAATT----------------------------C-ACGCGT-C-GC-ACTTGGCCT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
........................................................AGGGTGGCGCTCGTG-AA............................................................................................	17	2	0.50	0.00	0.50	0.00	0.00	0.00
.................GGTTGTC-TGTGTCCTTTG..................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
..........................................AAGCTGACTCCGTTAGGGAGTC......................................................................................................	22	2	0.50	0.00	0.00	0.50	0.00	0.00

droMoj3

C----GCTTCTT-----CGTTGTC-TGGGTCCTCTGAAATTCAATCTGACTCCGTTAGGGAGTCGTTAAAAAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCATGAGGAAAC----------------------------T-C-GTAG-C-G-TATAT---GT	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

T----GGGGCAT-----TGTTGAC-TTGGTCCTTTGTAACTCAATCTGACTCCGTTAGGGAGTCGCTCGTTAAAAGGACTCCCTACTAGAGTCAATTTGAACTGCAGCAGGAAGT----------------------------T-CGGGGG-C-ACACTTT---CA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:19:48 EDT

dme-mir-929-as

chr3R:121091-121178 -

Novel

antisense_to_intron

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup