dme-mir-1015- Best orthologs

dme-mir-1015	chr3R:20164954-20165017 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 20164996-20165017
   star strand at position 20164954-20164975
   mutations
   read mismatches

Notes: The miRNA appears lost in dp4 - droGri2. The orthologs for these species look confident however they've accumulated too many substitutions to fold nicely.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3R:20164939-20165032 +		1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGGCTGAGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAG
droSim1	chr3R:19998542-19998635 +	LASTZ	1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGGCTGAGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droSec1	super_0:20503496-20503589 +	LASTZ	1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGTCTGAGTGAG-A--------C----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droYak2	chr3R:26340571-26340664 -	LASTZ	1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGACTGGGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAC
droEre2	scaffold_4820:7895693-7895786 -	LASTZ	1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTGAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAAATCCTAAAAC
droEug1	scf7180000409798:215829-215922 -	LASTZ	5	TAATGGGCTACAATGGTGAGTG----ATGCTCCAGATAGCTTCGCAAAGTAAG-G--------A----TA------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAGAC
droBia1	scf7180000302136:526695-526788 +	LASTZ	4	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATGGCTGGGCTAAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAGC
droTak1	scf7180000415769:2262017-2262110 -	LASTZ	4	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGCTGGCTTGGCAAAGCGTG-G--------A----TC------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTCAAGC
droEle1	scf7180000491008:477705-477804 +	LASTZ	4	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGAAAGCTTGGCCAAGTGAC-C--------A----CCCATACTTAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCTGAAGC
droRho1	scf7180000779477:268222-268317 +	LASTZ	4	TCATGGGATACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTAAGTGAG-G--------A----TTAA----TAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCTGAAGC
droFic1	scf7180000453912:1339925-1340020 +	LASTZ	5	TCATGGGCTACCAAGGTGAGTG----ATGCTCCAGATAACTTGGAAAAGTGGG-A--------ATACGGA------TAAGTCC--GGAC-----TTCTCTCTTGCAGTCAAGATTCTGAAAT
droKik1	scf7180000302387:55058-55154 +	LASTZ	4	TGATGGGCTATGACGGTGAGTG----ATGCTCCAGATAGCTTAGTTTAAAAAAAG--------A----TTCA----AAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAGC
droAna3	scaffold_13088:204245-204339 +	LASTZ	1	TCATGGGCTACGACAGTGAGTG----ATGCTCCAGATAGGTTGGCTTAGGAAGTC--------A----TT------AAAGCCCTGGGAT-----GTCTCTCTTGCAGTTAAGATCCTGAAAC
droBip1	scf7180000396413:258464-258558 +	LASTZ	4	TCATGGGCTACGATAGTGAGTG----ATGCTCTAGATAGGTTAGCTGATGAAG-T--------C---TTT------CAAGCCCTAGGTC-----ATCTCTCTTGCAGTTAAAATCCTGAAAC
dp4	chr2:18646206-18646298 -	LASTZ	5	TGATGGGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTT-CTTTCTTTTGCAGTCAAGATACTAAAGC
droPer1	super_3:1376406-1376498 -	LASTZ	5	TGATGGGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTC-CTTTCTTTTGCAGTCAAGATCCTAAAGC
droWil1	scaffold_181108:4541725-4541808 -	LASTZ	5	TAATGGGTTATGACAGTAAGTTA--GCTGGTAAAGTTGATTTCT------------------------TT------TAACTAATGT-GT-----ATATTTACTGTAGTAAGAATTTTAAAGC
droVir3	scaffold_13047:3497490-3497590 +	LASTZ	5	TTGTGGGCTACGAAAGTAAGTA----T-TTACTTGATAACTCGTT------AA-ACCTAAAGTC----TGTT----AACCACTCTTATAACTATG-CATCTAAACAGTTAAGGTACTAAAGA
droMoj3	scaffold_6540:20508341-20508431 +	LASTZ	5	TAATGGGCTACGATGGTAAATG-CTGATGTTCATGAATATTTATCCAAGTAAT-T--------T----------------CTTTACGTT-----GTCTTCTTAACAGTTAAGGTTTTGAAAA
droGri2	scaffold_14906:156637-156731 +	LASTZ	5	TGGTGGGCTATGATAGTGAGTTG---ATTCTATTGT--AATAATC-AAATC-G-T--------T----TTTG----TTATTTTATAAAC---ATGCCATTTTAACAGTCAAGATACTCAAGA

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	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGGCTGAGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAG
droSim1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGGCTGAGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droSec1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGTCTGAGTGAG-A--------C----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droYak2	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGACTGGGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAC
droEre2	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTGAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAAATCCTAAAAC
droEug1	TAATGGGCTACAATGGTGAGTG----ATGCTCCAGATAGCTTCGCAAAGTAAG-G--------A----TA------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAGAC
droBia1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATGGCTGGGCTAAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAGC
droTak1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGCTGGCTTGGCAAAGCGTG-G--------A----TC------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTCAAGC
droEle1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGAAAGCTTGGCCAAGTGAC-C--------A----CCCATACTTAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCTGAAGC
droRho1	TCATGGGATACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTAAGTGAG-G--------A----TTAA----TAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCTGAAGC
droFic1	TCATGGGCTACCAAGGTGAGTG----ATGCTCCAGATAACTTGGAAAAGTGGG-A--------ATACGGA------TAAGTCC--GGAC-----TTCTCTCTTGCAGTCAAGATTCTGAAAT
droKik1	TGATGGGCTATGACGGTGAGTG----ATGCTCCAGATAGCTTAGTTTAAAAAAAG--------A----TTCA----AAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAGC
droAna3	TCATGGGCTACGACAGTGAGTG----ATGCTCCAGATAGGTTGGCTTAGGAAGTC--------A----TT------AAAGCCCTGGGAT-----GTCTCTCTTGCAGTTAAGATCCTGAAAC
droBip1	TCATGGGCTACGATAGTGAGTG----ATGCTCTAGATAGGTTAGCTGATGAAG-T--------C---TTT------CAAGCCCTAGGTC-----ATCTCTCTTGCAGTTAAAATCCTGAAAC
dp4	TGATGGGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTT-CTTTCTTTTGCAGTCAAGATACTAAAGC
droPer1	TGATGGGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTC-CTTTCTTTTGCAGTCAAGATCCTAAAGC
droWil1	TAATGGGTTATGACAGTAAGTTA--GCTGGTAAAGTTGATTTCT------------------------TT------TAACTAATGT-GT-----ATATTTACTGTAGTAAGAATTTTAAAGC
droVir3	TTGTGGGCTACGAAAGTAAGTA----T-TTACTTGATAACTCGTT------AA-ACCTAAAGTC----TGTT----AACCACTCTTATAACTATG-CATCTAAACAGTTAAGGTACTAAAGA
droMoj3	TAATGGGCTACGATGGTAAATG-CTGATGTTCATGAATATTTATCCAAGTAAT-T--------T----------------CTTTACGTT-----GTCTTCTTAACAGTTAAGGTTTTGAAAA
droGri2	TGGTGGGCTATGATAGTGAGTTG---ATTCTATTGT--AATAATC-AAATC-G-T--------T----TTTG----TTATTTTATAAAC---ATGCCATTTTAACAGTCAAGATACTCAAGA

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

TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGGCTGAGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGT..............	23	1	34.00	1.00	0.00	33.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAG...............	22	1	28.00	1.00	0.00	25.00	2.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGTT.............	24	1	5.00	0.00	0.00	5.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGC.................	20	1	4.00	0.00	0.00	4.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCA................	21	1	2.00	0.00	0.00	1.00	1.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGG..............	23	1	2.00	0.00	0.00	1.00	1.00
...............GTGAGTG----ATGCTCCAGTTAGCT.................................................................................	22	1	2.00	1.00	0.00	1.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGTTT............	25	1	1.00	0.00	0.00	1.00	0.00
..................................................................................CTGGGAC-----ATCTCTCTTGCAGTT.............	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAA...............	22	1	1.00	0.00	0.00	1.00	0.00
.........................................TGGCTGAGTGAG-G--------A----TT------TAAG..........................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAC...............	22	1	1.00	0.00	0.00	1.00	0.00
................................................................................TCCTTGGAC-----ATCTCTCTTGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGC..............	23	1	1.00	0.00	0.00	1.00	0.00
...............GTGAGTG----ATGCTCCCGTTAGCTTG...............................................................................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................AGTCCTGGGAC-----ATCTCTCTTGC.................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGAAA...............	22	1	1.00	0.00	0.00	1.00	0.00

droSec1

TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGTCTGAGTGAG-A--------C----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGT..............	23	1	18.00	18.00	0.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAG...............	22	1	11.00	10.00	1.00	0.00
...............GTGAGTG----ATGCTCCAGTTAGCT.................................................................................	22	1	11.00	5.00	6.00	0.00
...............GTGAGTG----ATGCTCCAGTTAGCTTG...............................................................................	24	1	8.00	7.00	1.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGA..............	23	1	6.00	6.00	0.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCA................	21	1	3.00	1.00	1.00	1.00
...............GTGAGTG----ATGCTCCAGTTAGCTT................................................................................	23	1	3.00	3.00	0.00	0.00
..............................................................................AGTCCTGGGAC-----ATCTCTCTTGC.................	22	1	2.00	0.00	2.00	0.00
...............GTGAGTG----ATGCTCCAGTTAGC..................................................................................	21	1	2.00	2.00	0.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTACAGA..............	23	1	1.00	1.00	0.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTACAGT..............	23	1	1.00	1.00	0.00	0.00
............................................................................TAAGTxCTGGGAC-----AACTCTCT....................	20	1	1.00	0.00	0.00	1.00

droYak2

TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGACTGGGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...............GTGAGTG----ATGCTCCAGATAGCTTG...............................................................................	24	1	7.00	0.00	1.00	6.00	0.00	0.00
...............GTGAGTG----ATGCTCCAGATAGCTT................................................................................	23	1	6.00	0.00	1.00	5.00	0.00	0.00
...............GTGAGTG----ATGCTCCAGATAGCT.................................................................................	22	1	4.00	0.00	1.00	3.00	0.00	0.00
...............GTGAGTG----ATGCTCCAGATAGCTTGT..............................................................................	25	1	3.00	1.00	0.00	2.00	0.00	0.00
...............GTGAGTG----ATGCTCCAGATAG...................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGT..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCATT..............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................GACTGGGTGAG-G--------A----TT------TGC...........................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTG----ATGCTCCAGATAGCTTGTT.............................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTGAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAAATCCTAAAAC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............GTGAGTG----ATGCTCCAGATAGCT.................................................................................	22	1	7.00	0.00	0.00	0.00	7.00
...............GTGAGTG----ATGCTCCAGATAGCTT................................................................................	23	1	4.00	0.00	0.00	0.00	4.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGT..............	23	1	3.00	0.00	0.00	0.00	3.00
...............GTGAGTG----ATGCTCCAGATAGCTTG...............................................................................	24	1	2.00	0.00	0.00	0.00	2.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCCTGGGAC-----ATCTCTCTTG..................	19	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCCTGGGAC-----ATCCCTCTTGCAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
.........................................TGGCTGAGTGAG-G--------A----CT------TAAG..........................................	20	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCCTTGGAC-----ATCTCTCTTGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCCTGGGAC-----ATCTCTCTTGCAGC..............	23	1	1.00	0.00	0.00	0.00	1.00
..............................................................................AGTCCTGGGAC-----ATCTCTCTTGC.................	22	1	1.00	0.00	0.00	0.00	1.00
...............GTGAGTG----ATGCCCCAGATAGCT.................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............GTGAGTG----ATGCTCCAGATATCT.................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................TCCTGGGAC-----ATCTCTCTTGC.................	20	1	1.00	0.00	0.00	0.00	1.00

droEug1

TAATGGGCTACAATGGTGAGTG----ATGCTCCAGATAGCTTCGCAAAGTAAG-G--------A----TA------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAGAC

Size

Hit Count

Total Norm

droBia1

TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATGGCTGGGCTAAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAGC

Size

Hit Count

Total Norm

droTak1

TCATGGGCTACGACGGTGAGTG----ATGCTCCAGCTGGCTTGGCAAAGCGTG-G--------A----TC------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTCAAGC

Size

Hit Count

Total Norm

droEle1

TCATGGGCTACGACGGTGAGTG----ATGCTCCAGAAAGCTTGGCCAAGTGAC-C--------A----CCCATACTTAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCTGAAGC

Size

Hit Count

Total Norm

droRho1

TCATGGGATACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTAAGTGAG-G--------A----TTAA----TAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCTGAAGC

Size

Hit Count

Total Norm

droFic1

TCATGGGCTACCAAGGTGAGTG----ATGCTCCAGATAACTTGGAAAAGTGGG-A--------ATACGGA------TAAGTCC--GGAC-----TTCTCTCTTGCAGTCAAGATTCTGAAAT

Size

Hit Count

Total Norm

droKik1

TGATGGGCTATGACGGTGAGTG----ATGCTCCAGATAGCTTAGTTTAAAAAAAG--------A----TTCA----AAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAGC

Size

Hit Count

Total Norm

droAna3

TCATGGGCTACGACAGTGAGTG----ATGCTCCAGATAGGTTGGCTTAGGAAGTC--------A----TT------AAAGCCCTGGGAT-----GTCTCTCTTGCAGTTAAGATCCTGAAAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............GTGAGTG----ATGCTCCAGATAGGT.................................................................................	22	1	2.00	1.00	1.00	0.00	0.00
...............GTGAGTG----ATGCTCCAGATAGGTTGGCT............................................................................	27	1	1.00	1.00	0.00	0.00	0.00
...............GTGAGTG----ATGCTCCAGATAGGTTGGC.............................................................................	26	1	1.00	1.00	0.00	0.00	0.00
................................................................................CCCTGGGAT-----GTCTCTCTTGCA................	21	1	1.00	0.00	1.00	0.00	0.00

droBip1

TCATGGGCTACGATAGTGAGTG----ATGCTCTAGATAGGTTAGCTGATGAAG-T--------C---TTT------CAAGCCCTAGGTC-----ATCTCTCTTGCAGTTAAAATCCTGAAAC

Size

Hit Count

Total Norm

dp4

TGATGGGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTT-CTTTCTTTTGCAGTCAAGATACTAAAGC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TGATGGGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTC-CTTTCTTTTGCAGTCAAGATCCTAAAGC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TAATGGGTTATGACAGTAAGTTA--GCTGGTAAAGTTGATTTCT------------------------TT------TAACTAATGT-GT-----ATATTTACTGTAGTAAGAATTTTAAAGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..............................................................................................ATATTTACTGTAGGAATA..........	18	1	157.00	1.00	66.00	3.00	87.00
........................................................................................T-----ATATTTACTGTAGGAATA..........	19	1	149.00	7.00	39.00	1.00	102.00
........................................................................................T-----ATATTTACTGTAGGAAT...........	18	1	39.00	0.00	5.00	0.00	34.00
.......................................................................................AT-----ATATTTACTGTAGGAA............	18	1	6.00	0.00	2.00	0.00	4.00
................................................................................................ATTTACTGTAGTAGGACT........	18	1	3.00	0.00	0.00	0.00	3.00
..............................................................................................ATATTTACTGTAGGAACA..........	18	1	2.00	0.00	1.00	0.00	1.00
........................................................................................T-----ATATTTACTGTAGGAAAAA.........	20	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................ATATTTACTGTAGAAATA..........	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................TATTTACTGTAGTAGGACT........	19	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................TATTTACTGTAGGAAAAA.........	18	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................ATATTTACTGTAGTAATA..........	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................TATTTACTGTAGGAGGAA.........	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................T-----ATATTTACTGTAGTAATA..........	19	1	1.00	0.00	0.00	0.00	1.00
........................................................................................T-----ATATTTACTGTAGGAAA...........	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................GA-----ATATTTACTGTAGGAA............	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................TATTTACTGTAGTAGGAAT........	19	1	1.00	0.00	0.00	0.00	1.00

droVir3

TTGTGGGCTACGAAAGTAAGTA----T-TTACTTGATAACTCGTT------AA-ACCTAAAGTC----TGTT----AACCACTCTTATAACTATG-CATCTAAACAGTTAAGGTACTAAAGA

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TAATGGGCTACGATGGTAAATG-CTGATGTTCATGAATATTTATCCAAGTAAT-T--------T----------------CTTTACGTT-----GTCTTCTTAACAGTTAAGGTTTTGAAAA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TGGTGGGCTATGATAGTGAGTTG---ATTCTATTGT--AATAATC-AAATC-G-T--------T----TTTG----TTATTTTATAAAC---ATGCCATTTTAACAGTCAAGATACTCAAGA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:52 EDT

dme-mir-1015

chr3R:20164954-20165017 +

Known_mirbase

mirtron

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