dme-mir-4947- Best orthologs

dme-mir-4947	chr3R:24834474-24834574 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 24834532-24834554
   star strand at position 24834496-24834516
   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:24834459-24834589 -		1	TAAAGTAAT------AATATGAAAGCGACCCACC------C-ATT------CCCCTTC--CG-C---------------------C------CATATTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GTGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCGCACTGGGT-------AGCGGGTA
droSim1	chr3R:24520998-24521128 -	LASTZ	4	TAAAGTAAT------AATATGAAAGCGACCCACC------C-ATT------CGCCGCC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GGGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCGCTCTGGGT-------AGCGGGTA
droSec1	super_4:3696490-3696620 -	LASTZ	4	TAAAGTAAT------AATATGAAAGCGACCCACC------C-ATT------CGCCGCC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GGGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCGCACTGGGT-------AGCGGGTA
droYak2	chr3R:21664594-21664723 +	LASTZ	5	TAAAGTAAT------AATATGAAAGCGACCGGCC------C-A-C------CCCTCGC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GTGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCACAGTGGGT-------AGTGGGTA
droEre2	scaffold_4820:3199292-3199428 +	LASTZ	5	TAAAGTAAT------AATATGAAAGCGACCGGCC------C-A-C------CCCTTTC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GGGGGCG-------T-----------AG------------CACGGAATTCGGGGGCGTGGCACAGTGGCTAGTGGATAGTGGGTA
droEug1	scf7180000409787:744124-744277 +	LASTZ	0	TAAAGTAAT------AATATGAAAGCGACCGGCC------C-AGC------CCCTCTCTACGCC---------------------C------CCTTTTTATCC-------TTCGTCTACTGTTTCATCGCAGCACTC-------A-GGGGTGATAGGATAGGGGTTAGGGGTGAGGCT-GGGGCG-------G-----------T------------CCAAGGAATTCGGGGGCGTGGC-----------------GTTGGTA
droBia1	scf7180000302075:1908428-1908558 +	LASTZ	0	TAAAGTAAT------AATATGAAAGCAACCAGCC------C-T-C------CGCCAC---CGCC---------------------C------CCTCTTTATCC-------TTCGTCTAGTGTTTCATCGCAGGACTT-------T-G-------------------------------GG---TT-------TGTGCGCGGCGGGA-----------CCGAGGAATTCGGGGGCGTGGC--------T-------GGTTGGTA
droTak1	scf7180000415700:411921-412062 -	LASTZ	0	TAAAGTAAT------AATATGAAAGCGACCCTG----------------------GAC--CG-C---------------------CCCC---TTTCCTTATCC-------TTCGTCTACTGTTTCATCGCAGGACTT-------T-TGGGACGTAGGATAAGGG--AG-GCGAAGGCG-GGGGCA-------G-----------G------------ACAAGGAATTCGGGGGCGTGGC-----------------GTTGGTA
droEle1	scf7180000491261:1411208-1411334 -	LASTZ	0	TAAAGTAAT------AATATGAAAGCGACCAGCC------CCATA------C--------CG-C---------------------CTCCAACCGATTTTATCC-------TTCGTCTACTGTTTC-----AGGACTT-------TT---------------------GGGAT----CAGGGGGCG-------G-----------G------------CCAAGGAATTCGGGGGCGTGGCAGC--------------GTTGGTA
droRho1	scf7180000780007:218817-218951 +	LASTZ	0	TAAAGTAAT------AATATGAAAGCGACCACCC------CCAT-------CTC-G-C--CG-C-------------CGACCCGCCTCCATCCGATTTTATCC-------TTCGTCTACTGTTTC-----AGGACTT-------TT---------------------GGGAT----CAGGGGGCG-------G-----------G------------CCAAGGAACTCGGGGGCGTGGC-----------------GTTGGTA
droFic1	scf7180000454073:3512300-3512430 +	LASTZ	0	TAAAGTAAT------AATATGAAAGCGACCGGCC------C-T-C------CGAC-TC--CG-C---------------------C------TCCTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGACCC-------TGG----------AAAA------GGGGC----CGGGGGAGG-------G-----------G------------TCAAGGAATTCGGGGGCGTGGC-----------------GTGGGTA
droKik1	scf7180000302276:805592-805716 -	LASTZ	0	TAAAGTAAT------AATATGAAAGCGGCCAGCA------C-CTC------CTCCTC-----------------------------------GTCCTTGTTCC-------TGGGTCCTCTGTTTCAGGGCAGGACTCCGT--C-T----------------------------------CTGGCT-------G-----------AG------------GGGAAGATTCGGGGGCGTGGCGG---TGCT-------AGCTTCTA
droAna3	scaffold_13340:19733656-19733776 +	LASTZ	0	TAAAGTAAT------AATATAAAAGCGACCAGCC------C-CTA------CTTCTA---CTCC----------ACCCAACCAGCCTC---CCGATCCTGGGC-------AGCGTTGGTTGTTTCAGA-----------------------------------------------------GGCG-------G-----------C------------TTGAGGAACTCGGGGGCGTGCC-----------------GCTCCTA
droBip1	scf7180000396413:2657212-2657312 -	LASTZ	0	TAAAGTAAT------AATATAACAGCGGCCAGCC------C-CAG------CTCCACC-------------------CATCCAGCCTC---CCGATCCTGGCC-------AGCGCTTGCTGTTACAG-------------------------------------------------------------------------------------------------AGGCGGAGGCGTGGC-----------------GCTTCTA
dp4	chr3:722533-722667 -	LASTZ	0	TAAAGAGAT------AATGACAAAGCAACCCATT------A-AAAGCCATCCCTTGACAACACT---------------------C------CTCTCTCATCC-------CCT--TCATATTCCCATCTCCGAA----------A-A-------------------------------ATGAGCG-------A-----------AG------------AACGGAGAGCAACGTTTTAATAAATTTGTA-------AACAGATT
droPer1	super_26:1114277-1114391 -	LASTZ	0	GACGGTGGC------CTTCCA-------CTTCCT------C-TTC------CGCCGCC--AC-C-------------ACACCCCCTTC---CCAC-----TGCCAAGCA-CGC-----TCTTTTTATCGCAAT------------------------------------------------TGTTGTCGGCGG-------------------------------------ATTTTCGGCTTACATGCG-------AGGAGCTA
droWil1	scaffold_181096:10088805-10088934 +	LASTZ	0	CAAAATGTCCTTGATGACTGG-CATTCACACACA------C-A-C------ACACACA--CA-CACACATTTAAACACATCCATATGT---AC-------ATCCATGTATACATTTATCTAATA----------------------------------------------------CA-GATGCA-------G-----------AG------------CT---------------CGGAACTTCAAGT-------ATAAGGCA
droVir3	scaffold_13049:15807-15938 +	LASTZ	0	TATG-TGGC------AGTAGAAATTTCTCCCATAAATATAT-GTA------CCCTTTC--CG-T---------------------C------TTTATGTTTGT-------TTGGTTGAATGGATCGAACTACAAATC-------T-A-------------------------------GAGATTA-------G-----------AA------------ATTGGAAATCCGTATTCTAGTAA----TGT-------ATCCAGAA
droMoj3	scaffold_6500:17797597-17797712 +	LASTZ	0	CACACACAC------A--------------CACA------C-AGA------CTTTGGC--TA-C---------------------A------AAATGTTAACT-------TGAGTTTGAAATTTTCCAG-GGAATAT-------G-A-------------------------------GTGAGAG-------G-----------CG------------AGCGAAAGCAGTGAACAGAGTGAACAATGT-------ATAAAGTA
droGri2	scaffold_14853:8203259-8203387 +	LASTZ	0	CAAATTAAC------AACAAGAATTCTTTCCAGC------T-CCC------TCTCT----CTCT---------------------C------TCTCTCTCTCT-------CTAACTCCGTCTCTCATTTCCGAGAGA---GAGCT-A-------------------------------GTTACAT-------T-----------GCTGAGAGAGAAGTGAAGA-GA------GCCGAGC-----------------TTTGTTA

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	TAAAGTAATAATATGAAAGCGACC----CACCCATTCCCCTTCCGCCCATATTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGTGGGCGGAGCACGGAATTCGGGGGCGTGGCGCACT-------GGGTAGCGGGTA
droSim1	TAAAGTAATAATATGAAAGCGACC----CACCCATTCGCCGCCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGGGGGCGGAGCACGGAATTCGGGGGCGTGGCGCTCT-------GGGTAGCGGGTA
droSec1	TAAAGTAATAATATGAAAGCGACC----CACCCATTCGCCGCCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGGGGGCGGAGCACGGAATTCGGGGGCGTGGCGCACT-------GGGTAGCGGGTA
droYak2	TAAAGTAATAATATGAAAGCGACC----GGCCCACCCCTCG-CCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGTGGGCGGAGCACGGAATTCGGGGGCGTGGCACAGT-------GGGTAGTGGGTA
droEre2	TAAAGTAATAATATGAAAGCGACCGGCCCACCCCTT-----TCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGGGGGCGTAGCACGGAATTCGGGGGCGTGGCACAGTGGCTAGTGGATAGTGGGTA

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

TAAAGTAAT------AATATGAAAGCGACCCACC------C-ATT------CGCCGCC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GGGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCGCTCTGGGT-------AGCGGGTA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

TAAAGTAAT------AATATGAAAGCGACCCACC------C-ATT------CGCCGCC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GGGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCGCACTGGGT-------AGCGGGTA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................................................................................................................................................................................................CGTGGCGCAATTGGT-------AGC.....	18	1	134.00	5.00	4.00	125.00
..........................................................................................................................................................................................................................................GTGGCGCAGTTGGT-------AGCG....	18	1	46.00	0.00	9.00	37.00
.........................................................................................................................................................................................................................................CGTGGCGCAATTGGT-------AGCG....	19	1	38.00	0.00	0.00	38.00
..........................................................................................................................................................................................................................................GTGGCGCAATTGGT-------AGCG....	18	1	17.00	0.00	1.00	16.00
..........................................................................................................................................................................................................................................GTGGCGCAATGGAT-------AGCG....	18	1	15.00	0.00	1.00	14.00
..........................................................................................................................................................................................................................................GTGGCGCAATGGGT-------AACG....	18	1	9.00	0.00	0.00	9.00
..........................................................................................................................................................................................................................................GTGGCGCACTGGAT-------AACG....	18	1	4.00	0.00	0.00	4.00
..........................................................................................................................................................................................................................................GTGGCGCAATCGGT-------AGCG....	18	1	3.00	1.00	0.00	2.00
.........................................................................................................................................................................................................................................CGTGGCGCAGTTGGT-------AGC.....	18	1	3.00	0.00	1.00	2.00
.........................................................................................................................................................................................................................................CGTGGCGCATTGGTT-------AGCG....	19	1	2.00	0.00	0.00	2.00
.........................................................................................................................................................................................................................................CGTGGCGCATTGGTT-------AGC.....	18	1	2.00	0.00	1.00	1.00
.........................................................................................................................................................................................................................................CGTGGCGCAGTCGGT-------AGC.....	18	1	1.00	0.00	1.00	0.00
.................................................................................................................................CAGGATTT-------A-A-------------------------------GGGGGCG-------G-----------AG------------CA...........................................	22	1	1.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................................GTGGCGCAGTGGGT-------GGCG....	18	1	1.00	0.00	0.00	1.00
.........................................................................................................................................................................................................................................CGTGGCGCACxAGGT-------AGCG....	18	1	1.00	0.00	0.00	1.00
........................................................................................................................................................................................................................................GCGTGGCGTACTCGGT-------AGCG....	20	1	1.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................................GTGGCGCACTGGAT-------ACCG....	18	1	1.00	0.00	0.00	1.00
........................................................................................................................................................................................................................................CCGTGGCGCACTTGGT-------AGC.....	19	1	1.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................................GTGGCGCACTTGGT-------AGCG....	18	1	1.00	0.00	0.00	1.00
.........................................................................................................................................................................................................................................CGTGGCGCACxCGGT-------AGCG....	18	1	1.00	0.00	0.00	1.00
.........................................................................................................................................................................................................................................TGTGGCGCAATGGGT-------AGCG....	19	1	1.00	0.00	0.00	1.00
..........................................................................................................................................................................................................................................GTGGCGTACTCGGT-------AGCG....	18	1	1.00	0.00	0.00	1.00

droYak2

TAAAGTAAT------AATATGAAAGCGACCGGCC------C-A-C------CCCTCGC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GTGGGCG-------G-----------AG------------CACGGAATTCGGGGGCGTGGCACAGTGGGT-------AGTGGGTA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................................................................................................................................................................................................................................TGGCAGAGTGGGT-------AGTGGGG.	20	2	1.50	0.00	0.00	0.00	1.50	0.00
.......................................................................................................................................................................................................................................GGCGTAGCACAGTxGGT-------AGT.....	19	2	0.50	0.00	0.00	0.00	0.50	0.00
...............................................................................................................................................................................................................................AATTCxGGGGCGTGGCA.......................	16	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................................................TGGCAGTGTGGGT-------AGTGGGT.	20	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................................................TGGCACAGCCGGT-------AGTGGG..	19	2	0.50	0.00	0.00	0.00	0.50	0.00
................................CC------C-A-C------CCCGGGC--CG-C---------------------C------C..........................................................................................................................................................................	17	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................................................TGGCAGAGTGGGT-------AGTGGGT.	20	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................................................TGGCACTGTGGGT-------AGTGGGTT	21	2	0.50	0.00	0.00	0.00	0.50	0.00
..............................................................................................................................................................................................................................CAATTCxGGGGCGTGGCA.......................	17	3	0.33	0.00	0.00	0.00	0.33	0.00
...........................................................................................................................................................................................................................................TGGCAGTGTGGGT-------AGTGGG..	19	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................................................TGGCAGAGTGGGT-------AGTTGGT.	20	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................................................TGGCACCGTGGGT-------AGTTGGT.	20	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................................................TGGCAGAGTGGGT-------AGTGGGTT	21	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................................................TGGCAGAGTGGGT-------AGCGGG..	19	2	0.50	0.00	0.00	0.00	0.50	0.00

droEre2

TAAAGTAAT------AATATGAAAGCGACCGGCC------C-A-C------CCCTTTC--CG-C---------------------C------CACTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGATTT-------A-A-------------------------------GGGGGCG-------T-----------AG------------CACGGAATTCGGGGGCGTGGCACAGTGGCTAGTGGATAGTGGGTA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

TAAAGTAAT------AATATGAAAGCGACCGGCC------C-AGC------CCCTCTCTACGCC---------------------C------CCTTTTTATCC-------TTCGTCTACTGTTTCATCGCAGCACTC-------A-GGGGTGATAGGATAGGGGTTAGGGGTGAGGCT-GGGGCG-------G-----------T------------CCAAGGAATTCGGGGGCGTGGC-----------------GTTGGTA

Size

Hit Count

Total Norm

droBia1

TAAAGTAAT------AATATGAAAGCAACCAGCC------C-T-C------CGCCAC---CGCC---------------------C------CCTCTTTATCC-------TTCGTCTAGTGTTTCATCGCAGGACTT-------T-G-------------------------------GG---TT-------TGTGCGCGGCGGGA-----------CCGAGGAATTCGGGGGCGTGGC--------T-------GGTTGGTA

Size

Hit Count

Total Norm

droTak1

TAAAGTAAT------AATATGAAAGCGACCCTG----------------------GAC--CG-C---------------------CCCC---TTTCCTTATCC-------TTCGTCTACTGTTTCATCGCAGGACTT-------T-TGGGACGTAGGATAAGGG--AG-GCGAAGGCG-GGGGCA-------G-----------G------------ACAAGGAATTCGGGGGCGTGGC-----------------GTTGGTA

Size

Hit Count

Total Norm

droEle1

TAAAGTAAT------AATATGAAAGCGACCAGCC------CCATA------C--------CG-C---------------------CTCCAACCGATTTTATCC-------TTCGTCTACTGTTTC-----AGGACTT-------TT---------------------GGGAT----CAGGGGGCG-------G-----------G------------CCAAGGAATTCGGGGGCGTGGCAGC--------------GTTGGTA

Size

Hit Count

Total Norm

droRho1

TAAAGTAAT------AATATGAAAGCGACCACCC------CCAT-------CTC-G-C--CG-C-------------CGACCCGCCTCCATCCGATTTTATCC-------TTCGTCTACTGTTTC-----AGGACTT-------TT---------------------GGGAT----CAGGGGGCG-------G-----------G------------CCAAGGAACTCGGGGGCGTGGC-----------------GTTGGTA

Size

Hit Count

Total Norm

droFic1

TAAAGTAAT------AATATGAAAGCGACCGGCC------C-T-C------CGAC-TC--CG-C---------------------C------TCCTTTTATCC-------TTCGTCTACTGTTTCATCGCAGGACCC-------TGG----------AAAA------GGGGC----CGGGGGAGG-------G-----------G------------TCAAGGAATTCGGGGGCGTGGC-----------------GTGGGTA

Size

Hit Count

Total Norm

droKik1

TAAAGTAAT------AATATGAAAGCGGCCAGCA------C-CTC------CTCCTC-----------------------------------GTCCTTGTTCC-------TGGGTCCTCTGTTTCAGGGCAGGACTCCGT--C-T----------------------------------CTGGCT-------G-----------AG------------GGGAAGATTCGGGGGCGTGGCGG---TGCT-------AGCTTCTA

Size

Hit Count

Total Norm

droAna3

TAAAGTAAT------AATATAAAAGCGACCAGCC------C-CTA------CTTCTA---CTCC----------ACCCAACCAGCCTC---CCGATCCTGGGC-------AGCGTTGGTTGTTTCAGA-----------------------------------------------------GGCG-------G-----------C------------TTGAGGAACTCGGGGGCGTGCC-----------------GCTCCTA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..........................................CTA------CTTCTT---CTCC----------ACCCATC......................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................CTGGGA-------AGCGTGGGTTG..............................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
.................................................................................CATCCTC---ACGATCCTGGGC-------.........................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.....................AAAGTGACCAGCC------C-CTC------C...................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................GA-----------------------------------------------------GGCG-------G-----------C------------GTGCGGAAC.....................................	17	1	1.00	0.00	0.00	1.00	0.00

droBip1

TAAAGTAAT------AATATAACAGCGGCCAGCC------C-CAG------CTCCACC-------------------CATCCAGCCTC---CCGATCCTGGCC-------AGCGCTTGCTGTTACAG-------------------------------------------------------------------------------------------------AGGCGGAGGCGTGGC-----------------GCTTCTA

Size

Hit Count

Total Norm

dp4

TAAAGAGAT------AATGACAAAGCAACCCATT------A-AAAGCCATCCCTTGACAACACT---------------------C------CTCTCTCATCC-------CCT--TCATATTCCCATCTCCGAA----------A-A-------------------------------ATGAGCG-------A-----------AG------------AACGGAGAGCAACGTTTTAATAAATTTGTA-------AACAGATT

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GACGGTGGC------CTTCCA-------CTTCCT------C-TTC------CGCCGCC--AC-C-------------ACACCCCCTTC---CCAC-----TGCCAAGCA-CGC-----TCTTTTTATCGCAAT------------------------------------------------TGTTGTCGGCGG-------------------------------------ATTTTCGGCTTACATGCG-------AGGAGCTA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................A-------CTTCCA------C-TTG------CGCCGCC--...........................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

CAAAATGTCCTTGATGACTGG-CATTCACACACA------C-A-C------ACACACA--CA-CACACATTTAAACACATCCATATGT---AC-------ATCCATGTATACATTTATCTAATA----------------------------------------------------CA-GATGCA-------G-----------AG------------CT---------------CGGAACTTCAAGT-------ATAAGGCA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........................................C-A-C------ACACACA--CA-CATACAGT................................................................................................................................................................................................	20	19	0.11	0.05	0.05	0.00	0.00
.......................TTCCACACACA------C-A-C------ACACACA--...........................................................................................................................................................................................................	21	32	0.03	0.00	0.03	0.00	0.00
............................CACACA------C-A-C------ACACACA--CA-CAC.....................................................................................................................................................................................................	21	45	0.02	0.00	0.00	0.02	0.00
...............................ACA------C-A-C------ACAAACA--CA-CACACCT.................................................................................................................................................................................................	22	8	0.13	0.00	0.13	0.00	0.00
...............................ACA------C-A-G------ACACACA--CA-CACACA..................................................................................................................................................................................................	21	51	0.02	0.00	0.00	0.02	0.00
................................CA------C-A-C------ACACACA--CA-CACAC...................................................................................................................................................................................................	19	64	0.02	0.00	0.02	0.00	0.00
.............................ACACA------C-A-C------ACACACG--CA-CACTC...................................................................................................................................................................................................	22	51	0.02	0.00	0.02	0.00	0.00
..............................CACA------C-A-C------ACACACA--CA-CACAC...................................................................................................................................................................................................	21	45	0.02	0.00	0.00	0.02	0.00
...............................ATA------C-A-T------ACACACA--CA-CACACAT.................................................................................................................................................................................................	22	19	0.05	0.00	0.05	0.00	0.00
.........................TCACACACG------C-G-C------ACACACA--C..........................................................................................................................................................................................................	20	4	0.25	0.00	0.00	0.00	0.25
................................CA------C-A-C------ACACACA--CC-CACACAGT................................................................................................................................................................................................	22	8	0.13	0.00	0.00	0.13	0.00
..............................CACA------C-A-C------ACACACA--CA-CACACA..................................................................................................................................................................................................	22	40	0.03	0.00	0.03	0.00	0.00
..........................CACACACA------C-A-C------ACACACA--CA-CA......................................................................................................................................................................................................	22	40	0.03	0.00	0.03	0.00	0.00
.......................ATTCACACGCA------C-A-C------ACACGCA--...........................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................CACA------C-A-C------ACTCACA--CA-TACACAT.................................................................................................................................................................................................	23	7	0.14	0.14	0.00	0.00	0.00
..............................CACA------C-A-C------TCACACC--CA-CACAC...................................................................................................................................................................................................	21	51	0.02	0.02	0.00	0.00	0.00
......................CACTCACACACA------C-A-C------ACACACA--TA-CACA....................................................................................................................................................................................................	28	19	0.05	0.00	0.05	0.00	0.00
............................................C------ACACACA--CA-CACATAGT................................................................................................................................................................................................	18	42	0.02	0.00	0.02	0.00	0.00
..........................................A-C------ACAGACG--CA-CACACAT.................................................................................................................................................................................................	18	22	0.05	0.00	0.05	0.00	0.00
..........................CACACACT------C-A-C------ACCCACA--CA-C.......................................................................................................................................................................................................	21	51	0.02	0.02	0.00	0.00	0.00
..........................CACACATA------C-A-C------ACACACA--TA-CACACA..................................................................................................................................................................................................	26	25	0.04	0.00	0.04	0.00	0.00
.........................TTACACCCA------C-A-C------ACACACA--...........................................................................................................................................................................................................	19	24	0.04	0.00	0.04	0.00	0.00
.......................ATGCACGCACA------C-A-C------ACACACA--...........................................................................................................................................................................................................	21	15	0.07	0.00	0.07	0.00	0.00
..............................CACA------C-A-C------TCACACC--CA-CACACA..................................................................................................................................................................................................	22	45	0.02	0.00	0.00	0.02	0.00
........................................C-A-C------ACACACA--CA-CACACATCTG..............................................................................................................................................................................................	22	7	0.14	0.00	0.00	0.00	0.14
...........................ACACACA------C-A-C------ACACGCA--CA-CTC.....................................................................................................................................................................................................	22	51	0.02	0.00	0.02	0.00	0.00
.............................ACACA------G-A-C------ACACACA--CA-CACA....................................................................................................................................................................................................	21	51	0.02	0.00	0.00	0.02	0.00
...........................ACACACA------C-A-C------ACACACA--CA-CACA....................................................................................................................................................................................................	23	36	0.03	0.00	0.03	0.00	0.00
.................................A------C-A-C------ACACACA--CA-CACATGT.................................................................................................................................................................................................	20	37	0.03	0.00	0.03	0.00	0.00
......................TATGCACACACA------C-A-C------ACACACA--...........................................................................................................................................................................................................	22	26	0.04	0.00	0.00	0.04	0.00
.................................A------C-A-C------ACACACA--CA-CACACATTGT..............................................................................................................................................................................................	23	6	0.17	0.17	0.00	0.00	0.00
..........................CACACACT------C-A-C------ACCCACA--CA-CA......................................................................................................................................................................................................	22	45	0.02	0.00	0.00	0.02	0.00
.........................TTCCACACA------C-A-C------ACACACA--CA-........................................................................................................................................................................................................	21	32	0.03	0.00	0.03	0.00	0.00
..........................................A-C------ACACACA--CA-CACACATGT...............................................................................................................................................................................................	20	37	0.03	0.00	0.03	0.00	0.00
..........................CACACACA------C-A-C------ACACACA--CA-C.......................................................................................................................................................................................................	21	45	0.02	0.00	0.00	0.02	0.00
...........................ACACAGA------C-A-C------ACACACA--CA-CA......................................................................................................................................................................................................	21	51	0.02	0.00	0.00	0.02	0.00
...................................................ACACACA--CA-CACACATTTGT.............................................................................................................................................................................................	20	13	0.08	0.00	0.08	0.00	0.00
........................................C-A-C------ACACACA--CA-GACACAGT................................................................................................................................................................................................	20	15	0.07	0.00	0.07	0.00	0.00
.........................TCACACACA------C-A-C------ATATACA--C..........................................................................................................................................................................................................	20	12	0.08	0.00	0.08	0.00	0.00
...........................AGACACA------C-A-C------ACACACA--CA-AACA....................................................................................................................................................................................................	23	51	0.02	0.00	0.00	0.02	0.00
...................................................ACACACA--CA-CACACATTGT..............................................................................................................................................................................................	19	14	0.07	0.00	0.07	0.00	0.00
..........................................A-C------ACACACA--TA-CACACATTTAAA............................................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
............................CACACA------C-T-C------ACACCCA--CA-CAC.....................................................................................................................................................................................................	21	51	0.02	0.02	0.00	0.00	0.00
............................CACACA------C-T-C------ACACCCA--CA-CACA....................................................................................................................................................................................................	22	45	0.02	0.00	0.00	0.02	0.00
.............................ACAAG------C-A-C------ACACACA--CA-CACACA..................................................................................................................................................................................................	23	51	0.02	0.00	0.00	0.02	0.00
................................CT------C-A-C------ACACACA--CA-AACACAT.................................................................................................................................................................................................	21	10	0.10	0.00	0.10	0.00	0.00
...........................ACACACA------C-A-C------ACAAACA--CA-CACACAGT................................................................................................................................................................................................	27	5	0.20	0.20	0.00	0.00	0.00
........................................C-A-C------ACACACA--CA-CAGAGAT.................................................................................................................................................................................................	19	43	0.02	0.00	0.02	0.00	0.00
.............................ACACA------C-A-C------ACACACA--CA-CACACA..................................................................................................................................................................................................	23	36	0.03	0.00	0.03	0.00	0.00
......................................................CACA--CA-CACACATCTATACACA........................................................................................................................................................................................	22	3	0.33	0.00	0.33	0.00	0.00
........................................C-A-C------ACACACA--CA-CACACATTGT..............................................................................................................................................................................................	22	7	0.14	0.14	0.00	0.00	0.00
.............................AGACA------C-A-C------ACACACA--CA-CAAACA..................................................................................................................................................................................................	23	51	0.02	0.00	0.00	0.02	0.00
...........................ACAAGCA------C-A-C------ACACACA--CA-CACA....................................................................................................................................................................................................	23	51	0.02	0.00	0.00	0.02	0.00
............................................C------ACACACA--CA-CACACATTGT..............................................................................................................................................................................................	20	11	0.09	0.09	0.00	0.00	0.00
.................................A------C-A-C------ACACACA--CA-CACACAGT................................................................................................................................................................................................	21	10	0.10	0.00	0.10	0.00	0.00
............................CACACA------C-A-C------ACACACA--CA-CACA....................................................................................................................................................................................................	22	40	0.03	0.00	0.03	0.00	0.00

droVir3

TATG-TGGC------AGTAGAAATTTCTCCCATAAATATAT-GTA------CCCTTTC--CG-T---------------------C------TTTATGTTTGT-------TTGGTTGAATGGATCGAACTACAAATC-------T-A-------------------------------GAGATTA-------G-----------AA------------ATTGGAAATCCGTATTCTAGTAA----TGT-------ATCCAGAA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....................................................................................................................GAATGGATCGAACGACTA.................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00	0.00

droMoj3

CACACACAC------A--------------CACA------C-AGA------CTTTGGC--TA-C---------------------A------AAATGTTAACT-------TGAGTTTGAAATTTTCCAG-GGAATAT-------G-A-------------------------------GTGAGAG-------G-----------CG------------AGCGAAAGCAGTGAACAGAGTGAACAATGT-------ATAAAGTA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...................................................................................................................................................................................................................................................AATGT-------ATAATGTA	19	2	0.50	0.50	0.00	0.00	0.00
.ACACACAC------A--------------CACA------C-AGA------CGTA................................................................................................................................................................................................................	21	33	0.03	0.03	0.00	0.00	0.00
................................................................................................................................................G-A-------------------------------GTxAGCG-------G-----------CG------------AGCGAAA......................................	18	1	1.00	1.00	0.00	0.00	0.00

droGri2

CAAATTAAC------AACAAGAATTCTTTCCAGC------T-CCC------TCTCT----CTCT---------------------C------TCTCTCTCTCT-------CTAACTCCGTCTCTCATTTCCGAGAGA---GAGCT-A-------------------------------GTTACAT-------T-----------GCTGAGAGAGAAGTGAAGA-GA------GCCGAGC-----------------TTTGTTA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:38:00 EDT

dme-mir-4947

chr3R:24834474-24834574 -

Known_mirbase

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