dme-mir-4950- Best orthologs

dme-mir-4950	chr3R:3277173-3277265 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 3277226-3277247
   star strand at position 3277187-3277208
   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:3277158-3277280 +		1	TTTATACATT-T-GTT--------------TATAATGCA----CA------------------TAATAAATGCCAACCATTCATCATGAAATTATAAATAG-------------------T------------ATCA--------------TTTC---------------------------------------------------------------------------------------AAGAT--------GCATGGTAAGGCTTTAT-------TTTGTTTTGCAATCAAAGACATCTTTCTT
droSim1	chr3R:3321450-3321569 +	LASTZ	0	TTTATATATA-TTATT--------------TATTATGCT----------------------CAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTA-------------------T----------ATATT----------------ATA---------------------------------------------------------------------------------------TAAAT--------TCATGGTAAGGCTTCAT-------TTTTTAACGCAGTCTAAGACA----TCTT
droSec1	super_6:3368064-3368189 +	LASTZ	0	TTTATATATA-TTATT--------------TATTATGCT----------------------CAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTA-------------------T----------ATATTA--------------TTTC---------------------------------------------------------------------------------------TAGAT--------TCATGGTAAAGTTTCAT-------TTTGTAACGCAGTCTAAGACATCTTTCTC
droYak2	chr2L_random:3663454-3663574 -	LASTZ	0	TTTAGCCAAG-T-TAA--------------TTTGGT-------------------------AAAAACAAAAACCAGAAACCGGCTACACGATGAAACGCTA-------------------A----------ATGCCA--------------TTTT---------------------------------------------------------------------------------------AGCAG--------TC-AGGTAATTATATAT-------TTATTTTTAAATTTAAACCCATTTTTTAT
droEre2	scaffold_4784:2237866-2237984 -	LASTZ	0	TTTCCAAATT-T-GAA--------------TGCAGATTT----TTAGA-----------------CAATTGCTCCAGAAACATTT-----------AGAGG-------------------T----------ATGCCA--------------CTTC----------A-------------AAAT-------------ACGATA-------------------------------------------AT--------TGAAGGTTGAATTAT----------GGACTTTAGA-ACTTCAGCCTTCTTTTT
droEug1	scf7180000405460:7334-7455 +	LASTZ	0	TTTAACAAATGT---TTAT-----------TTAAATAAGACTATAAGA----------------------TACCCGTGACTGT------------------------------------------------------------------------TCTATACAATTAT---AAAATATTCATTTAATATAATAGTA---------------------------------------CCACTATAAGAT--------A---------------------------CGCTGGTATCT-AAAGATTGTACAT
droBia1	scf7180000302178:13133-13249 +	LASTZ	0	TTTATACAAT-T-TGT--------------TATATAGGA----AACA-TAAGTT-----------------------------------------------------------------------------TTACCACTTTT-------------------------------------AAAA-------------AAAATAGATAGTTTG------------------------GCGAGA-AAAAT--------GCTGAGAATAGCTTAAT-------TTTG--TA-CACATGAAAAAAATTTTGTT
droTak1	scf7180000413709:12828-12948 -	LASTZ	0	TTTATACTAA-T-AATAAAACAGATTAGTATAATTTTCT----------------------TTATAAGGAAATTAAACTTTTGTTAG----------------------------------------------------------------------------------------------------------------------------------------------------TGGAGTGAAAAT--------GCTTGATTTAATTTTGT-------TATCTTTTGCAATTTATTACATTTTTGTT
droEle1	scf7180000491080:2841398-2841515 -	LASTZ	0	AAAT-ATATC-GAATT--------------TAAAAAGAA----AAAG-TGAGTGCTAATAC---------------ATTTTTTTTATACAATTGGAAATAA-------------------A------------AACA--------------TTT-----------------------------------------------------------------------------------------AAAA--------AAAGAGCAGGGCTCAAC-------CGGGA-TTTGA-----ACCCGGGACCTCT
droRho1	scf7180000776225:2196-2314 +	LASTZ	0	TATATTAAGT-T-GTT--------------GAG---GCA----AA------------------TATTAAG-------------------------------TACGT-TGAA-AAGTACAAGAACTTGCAATTTATCATTATT----------------------------------------------------------------------------------------------------AAAAC--------AAAAGTTAACATTTTGT-------TTAATATAACAAGCAAGGAAAGCTAACTT
droFic1	scf7180000454048:281166-281287 -	LASTZ	0	TCCAGAGGTT-T--TC--------------TGTACTAGATACTTTAAT-----------------A-----AAAAAG----------------------------------------------------------------------------------------------------------------------------------TTTTTTAATATAAGTTATAAGTTCATCTT------AATGTACATTTT-G---AGGAAATATATAT-------TATTTATTAACAATAAAAAAGTTCTGGTT
droKik1	scf7180000302517:216660-216785 -	LASTZ	0	TTTATATTAT-A-AAT--------------TATAATGCC----------------------GAAAACAGACACTAAACAGATAACATAACATTTTACCTAT-------------------A------------CTTA---TTACCATAT---GTT-----------------------------------------------TACAGTTTGACAGTTATA---------------------------------------------GTTAT-----------ACATTCACAGCT----TTACATTTTCT
droAna3	scaffold_13340:2198726-2198841 +	LASTZ	0	TTAATAATTT-T-ATT--------------TATCGAACT----AA------------------TT---------AGGCTTTTCATA---------------CAGATTTAAG-CTTAATATTAAATT--------------------------A----------------------------------------------------------------------------------TAGAG------CACTGGCT-G---CGGTGGTATAT----------ATATTTTTCA-ATAAACACATTTTTATG
droBip1	scf7180000395023:6052-6160 -	LASTZ	0	TATATATATA-T-ATA--------------TATAATATA----TATA-TATATATAATATA---------------------------ATATATAATATAT-------------------A------------TATT---ATATTATAATATTTC---------------------------------------------------------------------------------------AGCAT--------ACATTTTAAA--TTTAT-------TTAGAAATGAG-------------ATTAA
dp4	chrXR_group6:912830-912970 -	LASTZ	0	TTTATACCAC-G-CAC--------------TAGATTGGGTTCTCCAGA-----------------T-----AACGAATGTTGT------------------------------------------------------------------------CCAGTAAAATCCC---AATCCATTCAAATGGATTATGTGAC---------------------------------------CAGTGTTAAGAT--------GCGTCGAGGGCAGTCAG-------CTTGTGTTGCTATCTCGCTCCCCTCCGCC
droPer1	super_3:249021-249147 +	LASTZ	0	TTTTAAATCTGT--TC-CC-----------TAAAATATACTTTT-----------------TGAACGAGAGAGTATATATGTATG----------------TATGC-CGAGCAACTTCTAGTACCCCC----------------------------------------------------------------------------------------------------------------------T-----AC---TCAATATGTTTTTTT-------TTGGCTTAGTAAAATAATACATCTATATC
droWil1	scaffold_180708:152570-152690 -	LASTZ	0	TTTATATATA-T-ATA--------------TATGATGTA----GATA-TATATTTTTTATA-------------------------------------------------------------------------------------------------------TTTA---AATTTTTTTAAA-------------GTGATTTTTGTCAAG------------------------GC---------------------TAGAAAAGCTTTATTTTTTGTTTTGT--TTTAGTTTATGCGATATTTCTT
droVir3	scaffold_135:841-956 -	LASTZ	0	TATATATATG-T-GAA--------------CATAACTTA----TATAATA-------------------------------------------------CA-------------------T----------ATGACA--------------TACTGCCAGACAAATAAACGTAACTATTTATGTTTGAAATCAAGA---------------------------------------T----------CACCAAAATAAATGA--TGATTTTAT-------TT----------------------TACAA
droMoj3	scaffold_6308:1934837-1934961 -	LASTZ	0	TTTATATATT-A-TAA--------------AAAAAATTA----CT----------------TAAATTAAAGCTTAGGAAATATTTGTA--TCCATAAAAAA-------------------T----------ATGATA--------------TATT---------------------------------------------------------------------------------------TTTAT--------GCATGGTAAATTTAATT-------TTTAATTTCTAATAAAAAAAATTATATAT
droGri2	scaffold_14906:7885716-7885837 +	LASTZ	0	ATTATTATTT-T-TTT--------------TTTATTTCA------------------------AGTTAATTTACAATTATCGAA-----------------CCGGT-TAAA-CTAAATTTTAGCTT--------------------------A----------------------------------------------------------------------------------TAGATATTTATT--------G---CTTAATTAACTGT-------TTTTTTTTGTT-GTTAAAACATTTTTTTT

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	TTTATACATTTGTTTATAATGCACATAATAAATGCCAACCATTCATCATGAAATTATAAATAGTATCATTTCAAGATGCATGGTAAGGCTTTATTTTGTTTTGCAATCAAAGACATCTTTCTT

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

TTTATATATA-TTATT--------------TATTATGCT----------------------CAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTA-------------------T----------ATATT----------------ATA---------------------------------------------------------------------------------------TAAAT--------TCATGGTAAGGCTTCAT-------TTTTTAACGCAGTCTAAGACA----TCTT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................................................TGCCAAGCATTCGTCGTGAAATTATAAA..................................................................................................................................................................................................................	28	1	1.00	0.00	0.00	0.00	1.00

droSec1

TTTATATATA-TTATT--------------TATTATGCT----------------------CAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTA-------------------T----------ATATTA--------------TTTC---------------------------------------------------------------------------------------TAGAT--------TCATGGTAAAGTTTCAT-------TTTGTAACGCAGTCTAAGACATCTTTCTC

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

TTTAGCCAAG-T-TAA--------------TTTGGT-------------------------AAAAACAAAAACCAGAAACCGGCTACACGATGAAACGCTA-------------------A----------ATGCCA--------------TTTT---------------------------------------------------------------------------------------AGCAG--------TC-AGGTAATTATATAT-------TTATTTTTAAATTTAAACCCATTTTTTAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................................................................................................................................................................................................................................................................................................GTTTTTTAT	18	8	0.13	0.00	0.00	0.00	0.00	0.13

droEre2

TTTCCAAATT-T-GAA--------------TGCAGATTT----TTAGA-----------------CAATTGCTCCAGAAACATTT-----------AGAGG-------------------T----------ATGCCA--------------CTTC----------A-------------AAAT-------------ACGATA-------------------------------------------AT--------TGAAGGTTGAATTAT----------GGACTTTAGA-ACTTCAGCCTTCTTTTT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.TTCTAAATT-T-GAA--------------TGCAGATTT----.........................................................................................................................................................................................................................................................................	22	45	0.04	0.00	0.00	0.00	0.04
......AATT-T-GAA--------------TGCAGATAT----TTAGA-----------------...................................................................................................................................................................................................................................................	22	16	0.06	0.06	0.00	0.00	0.00
......................................................................GCACCAGAAACATTT-----------AGAGG-------------------T----------.................................................................................................................................................................................	21	30	0.03	0.00	0.00	0.00	0.03
.....................................TT----TTAGA-----------------GAATTGCTCCAGAAACATTT-----------....................................................................................................................................................................................................................	27	37	0.03	0.00	0.00	0.00	0.03
...................................................................ATTGCGGCAGAAACATTT-----------AGAGG-------------------............................................................................................................................................................................................	23	22	0.05	0.00	0.00	0.00	0.05
......................................................................TCTTCAGAAACATTT-----------AGAGG-------------------T----------.................................................................................................................................................................................	21	10	0.10	0.00	0.00	0.00	0.10
............................................................................................................................................................................................................................................................................AT----------GGACTTTAGA-ACTTCCGTC........	21	9	0.11	0.11	0.00	0.00	0.00
..........................................................................CAGAAACATTT-----------AGAGG-------------------T----------ATGCCA--------------CTT..........................................................................................................................................................	26	31	0.03	0.00	0.00	0.00	0.03
......................................................................GCTTCAGAAACATTT-----------AGAG................................................................................................................................................................................................................	19	23	0.04	0.04	0.00	0.00	0.00
.........................................................................CCAGAAACATTT-----------AGAGG-------------------T----------ATG..............................................................................................................................................................................	21	30	0.03	0.00	0.00	0.00	0.03
...................................................................................................................................ATGACA--------------CTTC----------A-------------AAAT-------------CCGAT...........................................................................................................	20	33	0.03	0.00	0.00	0.00	0.03
.................................................................GAATTGCTCCAGAAACATTT-----------AGAG................................................................................................................................................................................................................	24	18	0.06	0.06	0.00	0.00	0.00
.........................................................................TCAGAAACATTT-----------AAAGG-------------------T----------.................................................................................................................................................................................	18	26	0.04	0.00	0.00	0.00	0.04
....................................................................TTGCGCCAGAAACATTT-----------AGAGG-------------------T----------.................................................................................................................................................................................	23	20	0.05	0.00	0.00	0.00	0.05
....................................TTT----TTAGA-----------------GAATTGCTCCAGA......................................................................................................................................................................................................................................	21	39	0.03	0.00	0.00	0.00	0.03
......................................................................GCACCAGAAAAATTT-----------AGAGG-------------------T----------.................................................................................................................................................................................	21	18	0.06	0.00	0.00	0.00	0.06
...........................................................................AGAAACATTT-----------AGAGG-------------------T----------ATGC.............................................................................................................................................................................	20	35	0.03	0.00	0.00	0.00	0.03
...........................................................................................................................................................................................................................................................................TAT----------GGACTTTAGA-ACTTTC...........	19	8	0.13	0.00	0.00	0.00	0.13
...................................................................ATTGCTCCAGAAACATTT-----------AGAGG-------------------T----------.................................................................................................................................................................................	24	21	0.05	0.05	0.00	0.00	0.00
......................................................................GCGCCAGAAACATTT-----------AGAGG-------------------T----------.................................................................................................................................................................................	21	20	0.05	0.00	0.00	0.00	0.05
.........................................................................................................................................................................................................................................................................GTTAT----------GGACTTTAGA-ACTTCAGC.........	23	21	0.05	0.00	0.00	0.00	0.05
...............................................A-----------------GAATTGCTCCAGAAACATTT-----------AGAG................................................................................................................................................................................................................	25	18	0.06	0.00	0.00	0.00	0.06
................................................................................CATTC-----------AGAGA-------------------T----------ATGCCA--------------CTTC----------A-------------AA...............................................................................................................................	24	21	0.05	0.05	0.00	0.00	0.00
...................................................................ATGGCACCAGAAACATTT-----------AGAGG-------------------T----------A................................................................................................................................................................................	25	18	0.06	0.00	0.00	0.00	0.06
...............A--------------TGCAGATGT----TTAGA-----------------GAATTGCT...........................................................................................................................................................................................................................................	23	25	0.04	0.00	0.00	0.00	0.04
....................................TTT----TTAGA-----------------GAATTGCTCC.........................................................................................................................................................................................................................................	18	42	0.02	0.00	0.00	0.00	0.02
...................................................................ATTGCTCAAGAAACATTT-----------AGAGG-------------------T----------AT...............................................................................................................................................................................	26	24	0.04	0.00	0.00	0.00	0.04
...................................................................ATTCCACCAGAAACATTT-----------AGAG................................................................................................................................................................................................................	22	21	0.05	0.00	0.00	0.00	0.05
.....................................................................TGCGCCAGAAACATTT-----------AGAGG-------------------T----------.................................................................................................................................................................................	22	20	0.05	0.00	0.00	0.00	0.05
...................................................................ATTGTGCCAGAAACATTT-----------AGA.................................................................................................................................................................................................................	21	28	0.04	0.00	0.00	0.00	0.04
...................................................................ATTGCGCCAGAAACATTT-----------AGAGG-------------------............................................................................................................................................................................................	23	20	0.05	0.05	0.00	0.00	0.00
......................................................................GCGCCAGAAACATTT-----------ATAGG-------------------T----------.................................................................................................................................................................................	21	22	0.05	0.05	0.00	0.00	0.00
............................................................................................................................................................................................................................................................................AT----------GGTCTTTAGA-ACTTCAGTC........	21	8	0.13	0.00	0.00	0.00	0.13
................................CAGATGT----TTAGA-----------------GAATTGCTC..........................................................................................................................................................................................................................................	21	25	0.04	0.00	0.00	0.00	0.04
....................................TGT----TTAGA-----------------GAATTGCTCCAG.......................................................................................................................................................................................................................................	20	43	0.02	0.00	0.02	0.00	0.00
...................................................................ATTGCTCCAGAAACATTT-----------AGAGG-------------------T----------AT...............................................................................................................................................................................	26	21	0.05	0.00	0.00	0.00	0.05
................................................................................CATTT-----------AGAGG-------------------T----------ATGCCA--------------CGTC----------...............................................................................................................................................	21	37	0.03	0.00	0.00	0.00	0.03
.................................................................GAATTGCTCCAGAAACATTT-----------AGAGG-------------------T----------.................................................................................................................................................................................	26	18	0.06	0.00	0.00	0.00	0.06
.........T-T-GAA--------------TGCAGATTT----TAAG.....................................................................................................................................................................................................................................................................	18	15	0.07	0.00	0.00	0.00	0.07
................................CAGATGT----TTAGA-----------------GAATTGCT...........................................................................................................................................................................................................................................	20	26	0.04	0.00	0.00	0.00	0.04
...................................................................ATTGCGCCAGAAACATTT-----------AGA.................................................................................................................................................................................................................	21	27	0.04	0.00	0.00	0.00	0.04
........................................................................GCCAGAAACATTT-----------AGAGG-------------------T----------.................................................................................................................................................................................	19	24	0.04	0.00	0.00	0.00	0.04
.......................................................................CTCCAGAAACATTT-----------AGAGG-------------------............................................................................................................................................................................................	19	24	0.04	0.00	0.00	0.00	0.04
..............AA--------------TGCAGATTT----TAAGA-----------------TAATT..............................................................................................................................................................................................................................................	21	20	0.05	0.00	0.00	0.00	0.05
...............A--------------TGCAGATTT----TTGGA-----------------GAATTG.............................................................................................................................................................................................................................................	21	49	0.02	0.02	0.00	0.00	0.00
........................................................................................................................................................................................................................................................................AGATAT----------GGACTTTAGA-AC...............	18	14	0.07	0.00	0.00	0.00	0.07
.................................................................................ATTT-----------AGAGG-------------------T----------ATGCCA--------------CTTC----------A-------------AA...............................................................................................................................	23	36	0.03	0.00	0.00	0.00	0.03
.....................................................................TGCTCCAGAAACATTT-----------AGAG................................................................................................................................................................................................................	20	21	0.05	0.00	0.00	0.00	0.05
.........................................................................................................................................................................................................................................................................GTTAT----------GGACCTTAGA-ACTTCA...........	21	12	0.08	0.00	0.00	0.00	0.08
...........................................................................................................................................................................................................................................................................TAT----------GGACCTTAGA-ACTTCA...........	19	12	0.08	0.00	0.00	0.00	0.08
......................................................................GCGCCATAAACATTT-----------AGAG................................................................................................................................................................................................................	19	25	0.04	0.00	0.00	0.00	0.04
.....................................................................TGCGCCAGAAACATTT-----------ATA.................................................................................................................................................................................................................	19	49	0.02	0.00	0.00	0.00	0.02
........................................................................TCCACAAACATTT-----------AGAGG-------------------T----------ATGC.............................................................................................................................................................................	23	12	0.08	0.00	0.00	0.00	0.08
....................................TTT----GTAGG-----------------CAATTGCTCCA........................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................TTGCGCCAGAAACATTT-----------AGAG................................................................................................................................................................................................................	21	22	0.05	0.00	0.00	0.00	0.05
.....................................AT----TTAGA-----------------GAATTGCTCCAGAA.....................................................................................................................................................................................................................................	21	42	0.02	0.00	0.00	0.00	0.02
..........................................................................................................................................................................................................................................................................TTAT----------GGAGTTTAGA-ACTT.............	18	19	0.05	0.00	0.00	0.00	0.05
..................................................................AATTGCGCCAGAAACATTT-----------AGAG................................................................................................................................................................................................................	23	22	0.05	0.00	0.00	0.00	0.05
.........T-T-GAA--------------TGCAGATGT----TTAGA-----------------...................................................................................................................................................................................................................................................	19	20	0.05	0.00	0.00	0.00	0.05
....................................................................TTGCTCCAGAAACATTT-----------AGAG................................................................................................................................................................................................................	21	21	0.05	0.00	0.00	0.00	0.05
......................................................................GCGCCAGAAACATTT-----------AGA.................................................................................................................................................................................................................	18	27	0.04	0.00	0.00	0.00	0.04
..........................................................................CAGAAACATTT-----------AGAGG-------------------T----------ATG..............................................................................................................................................................................	20	32	0.03	0.00	0.00	0.00	0.03
.....................................................................TGCGCCAGAAACATTT-----------AGAG................................................................................................................................................................................................................	20	22	0.05	0.00	0.00	0.00	0.05
.....................................................................TGCGCCAGAAACATTT-----------AGAGG-------------------............................................................................................................................................................................................	21	20	0.05	0.00	0.00	0.00	0.05
.....................................TT----TTAGA-----------------GAATTGCTTCAGAAAC...................................................................................................................................................................................................................................	23	40	0.03	0.00	0.00	0.00	0.03
............................................................................................................................................................................................................................................................................AT----------GGACCTTAGA-ACTTCAGTC........	21	9	0.11	0.11	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................GTTTAGA-ACTTCAGCCTT......	18	10	0.10	0.00	0.00	0.00	0.10
.................................................................................ATTT-----------AGAGG-------------------T----------ATGCCA--------------CTT..........................................................................................................................................................	19	40	0.03	0.00	0.00	0.00	0.03
.....................................................................TGCGCCAGAAACATTT-----------AGAGG-------------------T----------ATGCC............................................................................................................................................................................	27	20	0.05	0.00	0.00	0.00	0.05
......................................................................GATCCAGAAACATTT-----------AGAGG-------------------T----------ATGCCA--------------.............................................................................................................................................................	27	7	0.14	0.00	0.00	0.00	0.14
...................................................................ATTGAGCCAGAAACATTT-----------AGA.................................................................................................................................................................................................................	21	28	0.04	0.00	0.00	0.00	0.04
.............................................................................AAAAATTT-----------AGAGG-------------------T----------AAGCC............................................................................................................................................................................	19	31	0.03	0.00	0.00	0.00	0.03
...................................................................................TA-----------AGAGG-------------------T----------ATGCCA--------------CTTC----------A-------------AA...............................................................................................................................	21	36	0.03	0.00	0.00	0.00	0.03

droEug1

TTTAACAAATGT---TTAT-----------TTAAATAAGACTATAAGA----------------------TACCCGTGACTGT------------------------------------------------------------------------TCTATACAATTAT---AAAATATTCATTTAATATAATAGTA---------------------------------------CCACTATAAGAT--------A---------------------------CGCTGGTATCT-AAAGATTGTACAT

Size

Hit Count

Total Norm

droBia1

TTTATACAAT-T-TGT--------------TATATAGGA----AACA-TAAGTT-----------------------------------------------------------------------------TTACCACTTTT-------------------------------------AAAA-------------AAAATAGATAGTTTG------------------------GCGAGA-AAAAT--------GCTGAGAATAGCTTAAT-------TTTG--TA-CACATGAAAAAAATTTTGTT

Size

Hit Count

Total Norm

droTak1

TTTATACTAA-T-AATAAAACAGATTAGTATAATTTTCT----------------------TTATAAGGAAATTAAACTTTTGTTAG----------------------------------------------------------------------------------------------------------------------------------------------------TGGAGTGAAAAT--------GCTTGATTTAATTTTGT-------TATCTTTTGCAATTTATTACATTTTTGTT

Size

Hit Count

Total Norm

droEle1

AAAT-ATATC-GAATT--------------TAAAAAGAA----AAAG-TGAGTGCTAATAC---------------ATTTTTTTTATACAATTGGAAATAA-------------------A------------AACA--------------TTT-----------------------------------------------------------------------------------------AAAA--------AAAGAGCAGGGCTCAAC-------CGGGA-TTTGA-----ACCCGGGACCTCT

Size

Hit Count

Total Norm

droRho1

TATATTAAGT-T-GTT--------------GAG---GCA----AA------------------TATTAAG-------------------------------TACGT-TGAA-AAGTACAAGAACTTGCAATTTATCATTATT----------------------------------------------------------------------------------------------------AAAAC--------AAAAGTTAACATTTTGT-------TTAATATAACAAGCAAGGAAAGCTAACTT

Size

Hit Count

Total Norm

droFic1

TCCAGAGGTT-T--TC--------------TGTACTAGATACTTTAAT-----------------A-----AAAAAG----------------------------------------------------------------------------------------------------------------------------------TTTTTTAATATAAGTTATAAGTTCATCTT------AATGTACATTTT-G---AGGAAATATATAT-------TATTTATTAACAATAAAAAAGTTCTGGTT

Size

Hit Count

Total Norm

droKik1

TTTATATTAT-A-AAT--------------TATAATGCC----------------------GAAAACAGACACTAAACAGATAACATAACATTTTACCTAT-------------------A------------CTTA---TTACCATAT---GTT-----------------------------------------------TACAGTTTGACAGTTATA---------------------------------------------GTTAT-----------ACATTCACAGCT----TTACATTTTCT

Size

Hit Count

Total Norm

droAna3

TTAATAATTT-T-ATT--------------TATCGAACT----AA------------------TT---------AGGCTTTTCATA---------------CAGATTTAAG-CTTAATATTAAATT--------------------------A----------------------------------------------------------------------------------TAGAG------CACTGGCT-G---CGGTGGTATAT----------ATATTTTTCA-ATAAACACATTTTTATG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..........................................................................................................................................................................................................................................................................ATAT----------ATxTTTATCG-ATAAA............	18	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................................................................................................................................T-G---CxGTGGTATAT----------ATATGTTT....................	20	1	1.00	0.00	0.00	1.00	0.00

droBip1

TATATATATA-T-ATA--------------TATAATATA----TATA-TATATATAATATA---------------------------ATATATAATATAT-------------------A------------TATT---ATATTATAATATTTC---------------------------------------------------------------------------------------AGCAT--------ACATTTTAAA--TTTAT-------TTAGAAATGAG-------------ATTAA

Size

Hit Count

Total Norm

dp4

TTTATACCAC-G-CAC--------------TAGATTGGGTTCTCCAGA-----------------T-----AACGAATGTTGT------------------------------------------------------------------------CCAGTAAAATCCC---AATCCATTCAAATGGATTATGTGAC---------------------------------------CAGTGTTAAGAT--------GCGTCGAGGGCAGTCAG-------CTTGTGTTGCTATCTCGCTCCCCTCCGCC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TTTTAAATCTGT--TC-CC-----------TAAAATATACTTTT-----------------TGAACGAGAGAGTATATATGTATG----------------TATGC-CGAGCAACTTCTAGTACCCCC----------------------------------------------------------------------------------------------------------------------T-----AC---TCAATATGTTTTTTT-------TTGGCTTAGTAAAATAATACATCTATATC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
................................AAAGATAxTTTT-----------------TGAACGA................................................................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
.....................................................................AGAGTATATATGTATG----------------TGAG...........................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................................................................................................................................................................................................................................................ATTTTTTT-------TTGGCTGAGT...................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................GAGAxCGTATATATGGATG----------------T..............................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................................................................................................................................................................................................................................................GTTTTATT-------TTGGCTTAATA..................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................................................................................................................GTTTTATT-------TTGGCTTATTA..................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

TTTATATATA-T-ATA--------------TATGATGTA----GATA-TATATTTTTTATA-------------------------------------------------------------------------------------------------------TTTA---AATTTTTTTAAA-------------GTGATTTTTGTCAAG------------------------GC---------------------TAGAAAAGCTTTATTTTTTGTTTTGT--TTTAGTTTATGCGATATTTCTT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..................................ATGTA----GAGA-TAxATTTTTT..........................................................................................................................................................................................................................................................	18	3	4.00	0.00	3.00	1.00	0.00
..................................ATGTC----GATA-TAxATTTTTT..........................................................................................................................................................................................................................................................	18	1	8.00	0.00	7.00	1.00	0.00
.......................................................TTTATA-------------------------------------------------------------------------------------------------------TGTA---AATTTTTGTA...............................................................................................................................	20	3	2.00	0.00	1.67	0.00	0.33
........................................................TTATA-------------------------------------------------------------------------------------------------------TGTA---AATTTTTGTA...............................................................................................................................	19	4	0.75	0.00	0.75	0.00	0.00
.........................................................TATA-------------------------------------------------------------------------------------------------------TGTA---AATTTTTGTA...............................................................................................................................	18	6	0.33	0.00	0.33	0.00	0.00
....................................................................................................................................................................................AAA-------------GTGATTTTTGTAAAC------------------------.........................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................A----GTTA-TTTATTTTTTATA-------------------------------------------------------------------------------------------------------T...............................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................................................................ATTTTTTGTTTTGC--TTTATT................	20	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................................ATTTTCTATTTTGT--TTTAG.................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................................ATTCTTTTTTGTTTTGT--T.....................	18	14	0.07	0.00	0.07	0.00	0.00
...ATATATA-T-AGA--------------GATGATGTA----.........................................................................................................................................................................................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................TTTTTTGTTTTGA--TTTGGT................	19	3	0.33	0.00	0.33	0.00	0.00
..............................................................................................................................................................................................................................................................................TTTTTTTGTTTTGT--TTTGG.................	19	19	0.05	0.00	0.05	0.00	0.00
...........................................................................................................................................................................................................................................................................ATTATTTTTTGTTTTGT--GT....................	19	4	0.25	0.00	0.25	0.00	0.00
......TATA-T-ATA--------------TTCGATGTA----GA.......................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
................................................................................................................................................................................................................................................................................TTTTTGTATTGT--TTTATT................	18	7	0.14	0.00	0.14	0.00	0.00
..............................................................................................................................................................................................................................................................................TTTTTTTGTTTTGT--TTTTGTT...............	21	26	0.04	0.00	0.04	0.00	0.00
...........................................................................................................................................................................................................................................................................TTTAGTTTTGGTTTTGT--TT....................	19	5	0.20	0.00	0.20	0.00	0.00
...........................................................................................................................................................................................................................................................................TTTATATTTTGTTTTGT--T.....................	18	22	0.05	0.00	0.05	0.00	0.00
........................................................TTATA-------------------------------------------------------------------------------------------------------TGTA---AATTTTTGT................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00

droVir3

TATATATATG-T-GAA--------------CATAACTTA----TATAATA-------------------------------------------------CA-------------------T----------ATGACA--------------TACTGCCAGACAAATAAACGTAACTATTTATGTTTGAAATCAAGA---------------------------------------T----------CACCAAAATAAATGA--TGATTTTAT-------TT----------------------TACAA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.............................................................................................................................................................................................................................................................ATATATGA--TGATTTTCT-------T............................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
........TG-A-GAC--------------CATAACTTA----T........................................................................................................................................................................................................................................................................	16	2	0.50	0.00	0.50	0.00	0.00	0.00

droMoj3

TTTATATATT-A-TAA--------------AAAAAATTA----CT----------------TAAATTAAAGCTTAGGAAATATTTGTA--TCCATAAAAAA-------------------T----------ATGATA--------------TATT---------------------------------------------------------------------------------------TTTAT--------GCATGGTAAATTTAATT-------TTTAATTTCTAATAAAAAAAATTATATAT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

ATTATTATTT-T-TTT--------------TTTATTTCA------------------------AGTTAATTTACAATTATCGAA-----------------CCGGT-TAAA-CTAAATTTTAGCTT--------------------------A----------------------------------------------------------------------------------TAGATATTTATT--------G---CTTAATTAACTGT-------TTTTTTTTGTT-GTTAAAACATTTTTTTT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:17:27 EDT

dme-mir-4950

chr3R:3277173-3277265 +

Known_mirbase

intergenic

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