dme-mir-4986- Best orthologs

dme-mir-4986	chr3L:9726758-9726880 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 9726828-9726850
   star strand at position 9726788-9726809
   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	chr3L:9726743-9726895 -		1	AGACTGCCAACTGGGTTCTGCC----GCTT---TTGCTGTGGCTTCTCTGCATGGG-ATTCCCCAT--TCTGCA-TGGCGCCGATCTCTGCCAGCCCATCGGATGGCGGAACTTCCAGTGCAGCGAGGTCGCTTCTCTGCAGGATCTGGTGGACTTGGGCG---------CCG
droSim1	chr3L:9107366-9107518 -	LASTZ	5	CAACTGCCAACTGGGTTCTGCC----GCTT---TTGCTGTGGCTTCTCTGCGTGGG-ATTCCCCAT--ACTGCA-TGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGATGGATTTGGGCG---------CCG
droSec1	super_0:1960228-1960380 -	LASTZ	5	CAACTGCCAACTGGGTTCTGTC----GCTT---TTGCTGTGCCTTCTCTGCGTGGG-ATTCCCCAT--CCTGCA-TGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGCAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGGTGGACCTGGGCG---------CCG
droYak2	chr3L:9698225-9698377 -	LASTZ	4	CAACTGCCAATTGGGTTCTGCC----GCTT---TTTCTGTGGCTTCTCTGCGCGGG-ATTCCCCAG--CCTGCA-TGGTGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGAATTGGGCG---------CCG
droEre2	scaffold_4784:9713780-9713932 -	LASTZ	4	CAACTGCCAATTGGGTTCTGCC----GCTC---TTTCTGTGCCTTCTCTGCGCGGG-ATTCCCCAG--CCTGCA-TGGAGCTGATCTCTGCCAGCCCGTCGGGTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGACCTGGGCG---------CCG
droEug1	scf7180000409711:1583067-1583219 -	LASTZ	4	TGACTGCCAAGTGGGTTCTGCC----GCTT---TTGCTATGGCTCTCTCTTGGGGG-ATTTCCCTT--GTTAAA-CGGCGTCGATCTCTGCCAGCCCATCGGTTGGCGGAATTTCCAGTGCAACGAGGTCGCATCTCTGCAGGATCTGGTAGATTTGGGAG---------CTG
droBia1	scf7180000302428:8053551-8053703 +	LASTZ	5	CCGCTGCAAATAGGGTTCTGCC----ACTT---TTTCTGCTGCTTTTCTGCGGGGG-ATTCCCCGT--CCCGAA-CGCAGCCGATCTCTGCCAGCCCCTTGGCTGGCGGAACTTCCAGTGCAACGAGATCGCTTCCCTGCAGGATCTGGTGGACTTGGGGG---------CCG
droTak1	scf7180000415741:49485-49637 +	LASTZ	5	TGACTGCCAATTGGGTTCTGCC----GCTT---TTTCTGTGGCTCTTCTATGGGGG-ATTTCCCCA--TGTGAG-CGGCGCCGATCTCTGCGAGCCCCTTGGATGGCGGAATTACCAGTGCAATGAGATCGCTTCCCTGCAGGATCTGGTGGATTTGGGAG---------CGG
droEle1	scf7180000490564:510103-510255 -	LASTZ	5	TGACTGCCAATTGGTTTCTGCC----GCTT---TTTCTGTGGCTCGGCTGCGGGGG-ATTCCCCTC--GCTGAA-CGGAGCCGATCTCTGCCAGCCCGTTGGTTGGCGCAACTTCCAGTGCAACGAGGTGGCCTCTCTGCAGGATCTGGTGGATTTGGGAG---------CCG
droRho1	scf7180000778255:38347-38499 -	LASTZ	5	TTTCTGCCAATTGGTTTCTTAC----GCTC---TTTCTGTGGCTCGGCTGCGGGGG-ATTCCCCTC--CCTAAA-CGGAGCCGATCTCTGCCAGCCCATAGGTTGGCGCAATTTCCAGTGCAGCGAGGTGGCCTCCTTGCAGGATCTGGTGGATCTAGGAG---------CCG
droFic1	scf7180000453807:871186-871338 -	LASTZ	5	CCACTGCCAATTGGGTTGTGCC----GCTT---TTTCTGTGGTTCCTCTGCGGGGG-AATTCCCTT--TCTGGA-TGGCGCCGATCTGTGCCAGCCCATCGGTTGGCGGAACTTCCAGTGCAACGAGGTGGCTTCCCTACAGGATCTGGTGGATTTGGGGG---------CAG
droKik1	scf7180000302486:2298206-2298349 -	LASTZ	5	CAACTGCCGG----GTTCTG------GCTT---CTGCCGTCGATTCTCTGG---GG-AATTCCCTA--CCTGGC-TGCCGCCGATCTTTGCCAGCCGGTGGGATGGCGCAGCTTTGAGTGCAACGAGGTGGCTTCGTTACAGGATCTGGTGGGTTTGGGGG---------CAG
droAna3	scaffold_13337:3652327-3652482 +	LASTZ	5	TGCCAGTCAAATGGACTCTGTT----GCCTTGCTTTTTGTGGCTCTTCTCGAAGGG-GCTTCCCTC--CACAAG-AGCTCAAGATCTTTGCCAGCCCCGAGGTTGGCGCAACTTCGAGTGCCTTGAAGTGGCTTCTCTGCAGGATCTAGTGGATTTGGGGG---------CCG
droBip1	scf7180000395954:52966-53124 +	LASTZ	5	TGACAGTCAAATGGATTCTGTT----GGCTGGCTTTTTGTGGCTTTTCCCGAAGGGGCTTTTTCCCGGCACAAG-AGCTCAAGATCTTTGCCAGCCCCGGGGTTGGCGCAATTTCGAGTGCCTTGAAGTGGCCTCTCTGGAGGATCTAGTGGATCTGGGGG---------CCG
dp4	chrXR_group6:9932877-9933023 +	LASTZ	5	TGAATGCCAATTGGGTTTTGTC----CG------CTCTGTGGCTCTGCTGCAGGGG-CTTCCCCCA-----GGT-CGGGGCTCTTCCCTGCCGGACTCTGGCCTGGCGCAGCTTCGAGTGTCGTGAATTAGCCAGTCTGCAGGATCTGTCTGATGTGGGGG---------CCG
droPer1	super_61:212952-213098 +	LASTZ	5	TGAATGCCAATTGGGTTTTGTC----CG------CTCTGTGGCTCTGCTGCAGGGG-CTTCCCCCA-----GGT-CGGGGCTCTTCCCTGCCGGACTCTGGCCTGGCGCAGCTTCGAGTGTCGTGAATTAGCCAGTCTGCAGGATCTGTCTGATGTGGGGG---------CCG
droWil1	scaffold_180949:1195301-1195459 +	LASTZ	5	CGAATTTCCAGTGGTTTTGGCC----GTTG---GCTTTATGGCTTGTATGTCGGTG-CTTCCCGC---GGTGCA-CA--GCTCAAGTCTGTAATCCCCGCGGCTGGCGTAACTACGAATGCAGCGAATTGGCTAGTCTAGAGGATTTAATAAATTCTGAAGGCTTGTCCACTG
droVir3	scaffold_13049:8736379-8736540 +	LASTZ	5	CGAATGCCAAACAG-TTCTGGACTTGGTCA---GTTCTCTGGCTGCTCTGCTGGGC-TGTGCCCCG--TG--CGTTG--GCGCAGTTGTGCGAGGCGCAGGGCTGGCGCAGCTTTGAGTGCCGCGAGCTGGGCAGCCTGCAGGAGCTGATCAATGAGAAGGCCTTGCCCACTG
droMoj3	scaffold_6680:6608267-6608428 -	LASTZ	5	TGAATGCGCAACCT-TTGCGCCTAGGTCCA---GTCCTCTGGCTGCTGTGCTGCGG-CCTTTCCCA--GGTG-C-TG--AGTCAGATATGCGAGGCTCAAGGCTGGCGCAGCTTCGAGTGTCGTGAGCTGAGCAGCCTGAAGGAGCTGAAGAACGTTAGGAACTTTCCCAAAG
droGri2	scaffold_15110:4482444-4482593 +	LASTZ	5	TGTTCTACACTTGG-------------CCA---ATTCTTTGCCTGCTCTGCTTTGG-GTTTTCCC----CTGGATTG--GCTGTGGTCTGTGAGGCTCAAGGCTGGCGTAGTTTTGAGTGCCGCGAATTGAGCAGCCTGCAGGAGCTGATCGATGTGAAGGCATTTCCCACCG

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	AGACTGCCAACTGGGTTCTGCC----GCTT---TTGCTGTGGCTTCTCTGCATGGG-ATTCCCCAT--TCTGCA-TGGCGCCGATCTCTGCCAGCCCATCGGATGGCGGAACTTCCAGTGCAGCGAGGTCGCTTCTCTGCAGGATCTGGTGGACTTGGGCG---------CCG
droSim1	CAACTGCCAACTGGGTTCTGCC----GCTT---TTGCTGTGGCTTCTCTGCGTGGG-ATTCCCCAT--ACTGCA-TGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGATGGATTTGGGCG---------CCG
droSec1	CAACTGCCAACTGGGTTCTGTC----GCTT---TTGCTGTGCCTTCTCTGCGTGGG-ATTCCCCAT--CCTGCA-TGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGCAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGGTGGACCTGGGCG---------CCG
droYak2	CAACTGCCAATTGGGTTCTGCC----GCTT---TTTCTGTGGCTTCTCTGCGCGGG-ATTCCCCAG--CCTGCA-TGGTGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGAATTGGGCG---------CCG
droEre2	CAACTGCCAATTGGGTTCTGCC----GCTC---TTTCTGTGCCTTCTCTGCGCGGG-ATTCCCCAG--CCTGCA-TGGAGCTGATCTCTGCCAGCCCGTCGGGTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGACCTGGGCG---------CCG
droEug1	TGACTGCCAAGTGGGTTCTGCC----GCTT---TTGCTATGGCTCTCTCTTGGGGG-ATTTCCCTT--GTTAAA-CGGCGTCGATCTCTGCCAGCCCATCGGTTGGCGGAATTTCCAGTGCAACGAGGTCGCATCTCTGCAGGATCTGGTAGATTTGGGAG---------CTG
droBia1	CCGCTGCAAATAGGGTTCTGCC----ACTT---TTTCTGCTGCTTTTCTGCGGGGG-ATTCCCCGT--CCCGAA-CGCAGCCGATCTCTGCCAGCCCCTTGGCTGGCGGAACTTCCAGTGCAACGAGATCGCTTCCCTGCAGGATCTGGTGGACTTGGGGG---------CCG
droTak1	TGACTGCCAATTGGGTTCTGCC----GCTT---TTTCTGTGGCTCTTCTATGGGGG-ATTTCCCCA--TGTGAG-CGGCGCCGATCTCTGCGAGCCCCTTGGATGGCGGAATTACCAGTGCAATGAGATCGCTTCCCTGCAGGATCTGGTGGATTTGGGAG---------CGG
droEle1	TGACTGCCAATTGGTTTCTGCC----GCTT---TTTCTGTGGCTCGGCTGCGGGGG-ATTCCCCTC--GCTGAA-CGGAGCCGATCTCTGCCAGCCCGTTGGTTGGCGCAACTTCCAGTGCAACGAGGTGGCCTCTCTGCAGGATCTGGTGGATTTGGGAG---------CCG
droRho1	TTTCTGCCAATTGGTTTCTTAC----GCTC---TTTCTGTGGCTCGGCTGCGGGGG-ATTCCCCTC--CCTAAA-CGGAGCCGATCTCTGCCAGCCCATAGGTTGGCGCAATTTCCAGTGCAGCGAGGTGGCCTCCTTGCAGGATCTGGTGGATCTAGGAG---------CCG
droFic1	CCACTGCCAATTGGGTTGTGCC----GCTT---TTTCTGTGGTTCCTCTGCGGGGG-AATTCCCTT--TCTGGA-TGGCGCCGATCTGTGCCAGCCCATCGGTTGGCGGAACTTCCAGTGCAACGAGGTGGCTTCCCTACAGGATCTGGTGGATTTGGGGG---------CAG
droKik1	CAACTGCCGG----GTTCTG------GCTT---CTGCCGTCGATTCTCTGG---GG-AATTCCCTA--CCTGGC-TGCCGCCGATCTTTGCCAGCCGGTGGGATGGCGCAGCTTTGAGTGCAACGAGGTGGCTTCGTTACAGGATCTGGTGGGTTTGGGGG---------CAG
droAna3	TGCCAGTCAAATGGACTCTGTT----GCCTTGCTTTTTGTGGCTCTTCTCGAAGGG-GCTTCCCTC--CACAAG-AGCTCAAGATCTTTGCCAGCCCCGAGGTTGGCGCAACTTCGAGTGCCTTGAAGTGGCTTCTCTGCAGGATCTAGTGGATTTGGGGG---------CCG
droBip1	TGACAGTCAAATGGATTCTGTT----GGCTGGCTTTTTGTGGCTTTTCCCGAAGGGGCTTTTTCCCGGCACAAG-AGCTCAAGATCTTTGCCAGCCCCGGGGTTGGCGCAATTTCGAGTGCCTTGAAGTGGCCTCTCTGGAGGATCTAGTGGATCTGGGGG---------CCG
dp4	TGAATGCCAATTGGGTTTTGTC----CG------CTCTGTGGCTCTGCTGCAGGGG-CTTCCCCCA-----GGT-CGGGGCTCTTCCCTGCCGGACTCTGGCCTGGCGCAGCTTCGAGTGTCGTGAATTAGCCAGTCTGCAGGATCTGTCTGATGTGGGGG---------CCG
droPer1	TGAATGCCAATTGGGTTTTGTC----CG------CTCTGTGGCTCTGCTGCAGGGG-CTTCCCCCA-----GGT-CGGGGCTCTTCCCTGCCGGACTCTGGCCTGGCGCAGCTTCGAGTGTCGTGAATTAGCCAGTCTGCAGGATCTGTCTGATGTGGGGG---------CCG
droWil1	CGAATTTCCAGTGGTTTTGGCC----GTTG---GCTTTATGGCTTGTATGTCGGTG-CTTCCCGC---GGTGCA-CA--GCTCAAGTCTGTAATCCCCGCGGCTGGCGTAACTACGAATGCAGCGAATTGGCTAGTCTAGAGGATTTAATAAATTCTGAAGGCTTGTCCACTG
droVir3	CGAATGCCAAACAG-TTCTGGACTTGGTCA---GTTCTCTGGCTGCTCTGCTGGGC-TGTGCCCCG--TG--CGTTG--GCGCAGTTGTGCGAGGCGCAGGGCTGGCGCAGCTTTGAGTGCCGCGAGCTGGGCAGCCTGCAGGAGCTGATCAATGAGAAGGCCTTGCCCACTG
droMoj3	TGAATGCGCAACCT-TTGCGCCTAGGTCCA---GTCCTCTGGCTGCTGTGCTGCGG-CCTTTCCCA--GGTG-C-TG--AGTCAGATATGCGAGGCTCAAGGCTGGCGCAGCTTCGAGTGTCGTGAGCTGAGCAGCCTGAAGGAGCTGAAGAACGTTAGGAACTTTCCCAAAG
droGri2	TGTTCTACACTTGG-------------CCA---ATTCTTTGCCTGCTCTGCTTTGG-GTTTTCCC----CTGGATTG--GCTGTGGTCTGTGAGGCTCAAGGCTGGCGTAGTTTTGAGTGCCGCGAATTGAGCAGCCTGCAGGAGCTGATCGATGTGAAGGCATTTCCCACCG

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

CAACTGCCAACTGGGTTCTGCC----GCTT---TTGCTGTGGCTTCTCTGCGTGGG-ATTCCCCAT--ACTGCA-TGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGATGGATTTGGGCG---------CCG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................................................................................................GATCTGATxGATTTCGGCG---------C..	19	1	2.00	0.00	0.00	0.00	2.00
..ACTGCCAACTGGGTTCTGCC----GCT................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................GCAGGATCTGAAGGATCT.................	18	1	1.00	0.00	1.00	0.00	0.00
.................................TTGGTGGGGCTTCTCTGC..........................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

CAACTGCCAACTGGGTTCTGTC----GCTT---TTGCTGTGCCTTCTCTGCGTGGG-ATTCCCCAT--CCTGCA-TGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGCAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGGTGGACCTGGGCG---------CCG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.AACTGCCAACTGGGTTCTGTC----GCTT---TT..........................................................................................................................................	27	1	1.00	1.00	0.00	0.00
.......................................................................................................................................GCTGCAGGATCTGGAGGC....................	18	1	1.00	0.00	1.00	0.00
.........................................................................................................................................TGCAGGATCTGGTCGACA..................	18	1	1.00	0.00	1.00	0.00
........................................................................................................................................ATGCAGGATCTGGTCGAC...................	18	1	1.00	0.00	1.00	0.00
....................................................................................................................................CTCTCTGCTGGATCTGGT.......................	18	1	1.00	0.00	1.00	0.00
.......................................................................................................................................GCTGCAGGATCTGGAGGCC...................	19	1	1.00	0.00	1.00	0.00
........................................................................CA-CGGCGCCGAACTCTGC..................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

CAACTGCCAATTGGGTTCTGCC----GCTT---TTTCTGTGGCTTCTCTGCGCGGG-ATTCCCCAG--CCTGCA-TGGTGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGAATTGGGCG---------CCG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................................................................................................CTTCGCTGCAGGATCTGGGC......................	20	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

CAACTGCCAATTGGGTTCTGCC----GCTC---TTTCTGTGCCTTCTCTGCGCGGG-ATTCCCCAG--CCTGCA-TGGAGCTGATCTCTGCCAGCCCGTCGGGTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGACCTGGGCG---------CCG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
................................................................AG--CCTGCA-TGGAGCTGCC........................................................................................	18	1	4.00	0.00	0.00	0.00	4.00
................................................................AG--CCTGCA-TGGAGCTGACAT......................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................TCCAGTGCAACGAGGTCGCT........................................	20	1	1.00	0.00	0.00	0.00	1.00
.............................................................CGTAG--CCTGCA-TGGAGCT...........................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................CTCTCTGCTGGATCTGGT.......................	18	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................TCCAGCGCxACGAGGTCGC.........................................	18	1	1.00	1.00	0.00	0.00	0.00

droEug1

TGACTGCCAAGTGGGTTCTGCC----GCTT---TTGCTATGGCTCTCTCTTGGGGG-ATTTCCCTT--GTTAAA-CGGCGTCGATCTCTGCCAGCCCATCGGTTGGCGGAATTTCCAGTGCAACGAGGTCGCATCTCTGCAGGATCTGGTAGATTTGGGAG---------CTG

Size

Hit Count

Total Norm

droBia1

CCGCTGCAAATAGGGTTCTGCC----ACTT---TTTCTGCTGCTTTTCTGCGGGGG-ATTCCCCGT--CCCGAA-CGCAGCCGATCTCTGCCAGCCCCTTGGCTGGCGGAACTTCCAGTGCAACGAGATCGCTTCCCTGCAGGATCTGGTGGACTTGGGGG---------CCG

Size

Hit Count

Total Norm

droTak1

TGACTGCCAATTGGGTTCTGCC----GCTT---TTTCTGTGGCTCTTCTATGGGGG-ATTTCCCCA--TGTGAG-CGGCGCCGATCTCTGCGAGCCCCTTGGATGGCGGAATTACCAGTGCAATGAGATCGCTTCCCTGCAGGATCTGGTGGATTTGGGAG---------CGG

Size

Hit Count

Total Norm

droEle1

TGACTGCCAATTGGTTTCTGCC----GCTT---TTTCTGTGGCTCGGCTGCGGGGG-ATTCCCCTC--GCTGAA-CGGAGCCGATCTCTGCCAGCCCGTTGGTTGGCGCAACTTCCAGTGCAACGAGGTGGCCTCTCTGCAGGATCTGGTGGATTTGGGAG---------CCG

Size

Hit Count

Total Norm

droRho1

TTTCTGCCAATTGGTTTCTTAC----GCTC---TTTCTGTGGCTCGGCTGCGGGGG-ATTCCCCTC--CCTAAA-CGGAGCCGATCTCTGCCAGCCCATAGGTTGGCGCAATTTCCAGTGCAGCGAGGTGGCCTCCTTGCAGGATCTGGTGGATCTAGGAG---------CCG

Size

Hit Count

Total Norm

droFic1

CCACTGCCAATTGGGTTGTGCC----GCTT---TTTCTGTGGTTCCTCTGCGGGGG-AATTCCCTT--TCTGGA-TGGCGCCGATCTGTGCCAGCCCATCGGTTGGCGGAACTTCCAGTGCAACGAGGTGGCTTCCCTACAGGATCTGGTGGATTTGGGGG---------CAG

Size

Hit Count

Total Norm

droKik1

CAACTGCCGG----GTTCTG------GCTT---CTGCCGTCGATTCTCTGG---GG-AATTCCCTA--CCTGGC-TGCCGCCGATCTTTGCCAGCCGGTGGGATGGCGCAGCTTTGAGTGCAACGAGGTGGCTTCGTTACAGGATCTGGTGGGTTTGGGGG---------CAG

Size

Hit Count

Total Norm

droAna3

TGCCAGTCAAATGGACTCTGTT----GCCTTGCTTTTTGTGGCTCTTCTCGAAGGG-GCTTCCCTC--CACAAG-AGCTCAAGATCTTTGCCAGCCCCGAGGTTGGCGCAACTTCGAGTGCCTTGAAGTGGCTTCTCTGCAGGATCTAGTGGATTTGGGGG---------CCG

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

TGACAGTCAAATGGATTCTGTT----GGCTGGCTTTTTGTGGCTTTTCCCGAAGGGGCTTTTTCCCGGCACAAG-AGCTCAAGATCTTTGCCAGCCCCGGGGTTGGCGCAATTTCGAGTGCCTTGAAGTGGCCTCTCTGGAGGATCTAGTGGATCTGGGGG---------CCG

Size

Hit Count

Total Norm

dp4

TGAATGCCAATTGGGTTTTGTC----CG------CTCTGTGGCTCTGCTGCAGGGG-CTTCCCCCA-----GGT-CGGGGCTCTTCCCTGCCGGACTCTGGCCTGGCGCAGCTTCGAGTGTCGTGAATTAGCCAGTCTGCAGGATCTGTCTGATGTGGGGG---------CCG

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TGAATGCCAATTGGGTTTTGTC----CG------CTCTGTGGCTCTGCTGCAGGGG-CTTCCCCCA-----GGT-CGGGGCTCTTCCCTGCCGGACTCTGGCCTGGCGCAGCTTCGAGTGTCGTGAATTAGCCAGTCTGCAGGATCTGTCTGATGTGGGGG---------CCG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..................................CTCTGTGGCTCTGCTGGG.........................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

CGAATTTCCAGTGGTTTTGGCC----GTTG---GCTTTATGGCTTGTATGTCGGTG-CTTCCCGC---GGTGCA-CA--GCTCAAGTCTGTAATCCCCGCGGCTGGCGTAACTACGAATGCAGCGAATTGGCTAGTCTAGAGGATTTAATAAATTCTGAAGGCTTGTCCACTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........................................................................................................................................TAGAGAATTTATTAAATT..................	18	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................CGAATTGGCTGGTGTAGAG...............................	19	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................CGAATGCAGTGxATTGGCT........................................	18	1	1.00	0.00	1.00	0.00	0.00
..........................GTTG---GCTTTATGGCTTGTATGTCGG.......................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................AGAGGATTTAATGAAGTCT................	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

CGAATGCCAAACAG-TTCTGGACTTGGTCA---GTTCTCTGGCTGCTCTGCTGGGC-TGTGCCCCG--TG--CGTTG--GCGCAGTTGTGCGAGGCGCAGGGCTGGCGCAGCTTTGAGTGCCGCGAGCTGGGCAGCCTGCAGGAGCTGATCAATGAGAAGGCCTTGCCCACTG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.....GCCAAACAG-TTCTGGACT.....................................................................................................................................................	18	1	4.00	0.00	0.00	0.00	0.00	4.00
.........................................................................................................................................TGAAGGAGCTGGTCAATGA.................	19	1	2.00	2.00	0.00	0.00	0.00	0.00
...............................................................................................................................................AGCTGATCATTGAGAAAG............	18	1	2.00	0.00	0.00	0.00	2.00	0.00
...............................................................................................................................................AGCTGATCATCGAGAAGG............	18	1	1.00	0.00	0.00	0.00	1.00	0.00
............AG-TGCTGGCCTTGGTCA---G...........................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................GTTCTCTGGCTGCTCTGCTGGGC-TGTGC...............................................................................................................	28	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................................................................AGGAGCTGATCAATGAGAAGGC...........	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................A---GTTCTCTGGCTGCTCTGCTGGG......................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
..AACGCCAAACAA-TTCTGGA.......................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................................................CTGGCGCAGCTTTGAGTG.....................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
..........................................................................................................................................GCAGGAGATGATCAAGGA.................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
......................................CTGGCTGCAGTGCTGGGC-....................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

TGAATGCGCAACCT-TTGCGCCTAGGTCCA---GTCCTCTGGCTGCTGTGCTGCGG-CCTTTCCCA--GGTG-C-TG--AGTCAGATATGCGAGGCTCAAGGCTGGCGCAGCTTCGAGTGTCGTGAGCTGAGCAGCCTGAAGGAGCTGAAGAACGTTAGGAACTTTCCCAAAG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........................................................................................................................................TGAAGAAGCTGAAGAACCTT................	20	1	1.00	1.00	0.00	0.00	0.00

droGri2

TGTTCTACACTTGG-------------CCA---ATTCTTTGCCTGCTCTGCTTTGG-GTTTTCCC----CTGGATTG--GCTGTGGTCTGTGAGGCTCAAGGCTGGCGTAGTTTTGAGTGCCGCGAATTGAGCAGCCTGCAGGAGCTGATCGATGTGAAGGCATTTCCCACCG	Size	Hit Count	Total Norm	V109 Male body
..............................................................................................................................ATTGAGAAGCCTGCTGGAG............................	19	1	1.00	1.00

Generated: 04/20/2012 at 05:19:54 EDT

dme-mir-4986

chr3L:9726758-9726880 -

Known_mirbase

CDS

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