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View alignment of MAF (12-files) vs LASTZ top hits (20-flies)

View all possible LASTZ hits (20-flies)

block806263

chr2R:11750900-11750969 -

Candidate
[View on UCSC Genome Browser {Cornell Mirror}]

intergenic

Legend:

   mature strand at position 11750906-11750926
   star strand at position 11750933-11750959
   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 chr2R:11750885-11750984 - 1 TACAATATAATATTATGTTCCAACGTGGGCGGA------------G--------CG-CTCTACACGCCACGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCAACAAAGAC---------GTTGGAT-------------AC-TT
droSim1 chr2R:10492788-10492882 - LASTZ 4 T-----ATAATATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGCGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCCACAAAGAC---------GTTGGAT-------------AC-TT
droSec1 super_1:9245417-9245511 - LASTZ 1 T-----ATAATATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGCGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCCACAAAGAC---------GTTGGAT-------------AC-TT
droYak2 chr2R:17232130-17232223 + LASTZ 4 A-----ATACTATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGATGGTGCGTGTTAGGTGC------------TCTGT---GCTCCG-GCGGA--------CAAGAC---------GTTGGAT-------------AC-TT
droEre2 scaffold_4845:14107458-14107544 + LASTZ 4 A-----ATAATATTGTATTCCAGCGTGGGCGGA------------G--------CG-TTCTGCACGCCGCGGATGCGTGCTAGGTG----------------------CTGCG-GCGGA--------CAAGAC---------GTTGGAT-------------AC-TT
droEug1 scf7180000409672:658894-658978 - LASTZ 4 A-----CT-----AATATTCCAGCGTGGGCGTA----------GAG--------CGCCTCTGCACGATGCTGGTGCGTGTTAAACG----------------------TTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droBia1 scf7180000302292:3898618-3898709 + LASTZ 4 C------------AAGATTCCAGCGTGGGCGGTGGTGGAGGTGGAG--------CA-CTCTGCACGCTGTGGGTGCGTGCTAAGCG----------------------CTCCG-CCGGG--------CGATCC---------GTTGGAT-------------AC-TT
droTak1 scf7180000415795:825736-825817 + LASTZ 4 C------------AAGATTCCAGCGTGGGCGGA-------GCAGAG--------CG-GTCTGCACGAAGTGGGTGCGTGTTAAACG----------------------CTCCG-CCGGA--------CA---C---------TTTGGAT-------------AC-TT
droEle1 scf7180000491107:745400-745492 - LASTZ 4 T---------TATAATATTCCGGCGTGGGTGGA------------G--------CA-TTCGGCACGCAGTGGGTGCGTGGTAGGCGTTTCG---------CTTC---GTTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droRho1 scf7180000779911:353759-353845 + LASTZ 4 T------------AATAACTCAGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGCGGGTGCGTGTTGAGCGT------------AGTAC---GTTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droFic1 scf7180000453809:251717-251796 - LASTZ 4 T------------GGTACTCCAGCGTGGGCGGA------------G--------CG-CTCTCCACGCAGTGGGAGCGTGCAAGGTG----------------------TTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droKik1 scf7180000302682:1952965-1953055 - LASTZ 4 --------------ATATTCCAGCGTGGGCGGA------------GTCTCTCTCCG-CTCTGCACGCTGCTGCTGCGTGTTGAGTG-------TCCG------C----GTCCG-CCGGA--------CAATTC----------TTGGAT-------------AC-TT
droAna3 scaffold_13266:12444035-12444112 + LASTZ 1 C---------------ATTCCGGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGCAGTTGCGTGCTTCTAC----------------------CACAG-CCGGA--------CAATCC---------CTTGGAT-------------ACACT
droBip1 scf7180000396547:44441-44521 - LASTZ 4 C---------------ATTCCGGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGTAGTTGCGTGCTTCTAC--------------------CGCCGCCGCCGGA--------CAATCC---------CTTGGAT-------------ACACT
dp4 chr3:19435499-19435615 + LASTZ 5 T-----------------TTCCGTGTGGGTGGT------------G--------CG---CTGCACGCAACAGCTGCGTGTTAT-CGTCCCGTGTCCGTATCTGTGCCGCCGCG-CCGGA--------CAAGCTCTACGGAGAGTCGGATATATACTACTCACAC-TT
droPer1 super_37:437404-437520 + LASTZ 5 T-----------------TTCCGTGTGGGTGGT------------G--------CG---CTGCACGCAACAGCTGCGTGTTAT-CGTCCCGTGTCCGTATCTGTGCCGCCGCG-CCGGA--------CAAGCTCTACGGAGAGTCGGATATATACTACTCGCAC-TT
droWil1 Unknown 0 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown 0 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown 0 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown 0 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------

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 TACAATATAATATTATGTTCCAACGTGGGCGGA------------G--------CG-CTCTACACGCCACGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCAACAAAGAC---------GTTGGAT-------------AC-TT
droSim1 T-----ATAATATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGCGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCCACAAAGAC---------GTTGGAT-------------AC-TT
droSec1 T-----ATAATATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGCGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCCACAAAGAC---------GTTGGAT-------------AC-TT
droYak2 A-----ATACTATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGATGGTGCGTGTTAGGTGC------------TCTGT---GCTCCG-GCGGA--------CAAGAC---------GTTGGAT-------------AC-TT
droEre2 A-----ATAATATTGTATTCCAGCGTGGGCGGA------------G--------CG-TTCTGCACGCCGCGGATGCGTGCTAGGTG----------------------CTGCG-GCGGA--------CAAGAC---------GTTGGAT-------------AC-TT
droEug1 A-----CT-----AATATTCCAGCGTGGGCGTA----------GAG--------CGCCTCTGCACGATGCTGGTGCGTGTTAAACG----------------------TTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droBia1 C------------AAGATTCCAGCGTGGGCGGTGGTGGAGGTGGAG--------CA-CTCTGCACGCTGTGGGTGCGTGCTAAGCG----------------------CTCCG-CCGGG--------CGATCC---------GTTGGAT-------------AC-TT
droTak1 C------------AAGATTCCAGCGTGGGCGGA-------GCAGAG--------CG-GTCTGCACGAAGTGGGTGCGTGTTAAACG----------------------CTCCG-CCGGA--------CA---C---------TTTGGAT-------------AC-TT
droEle1 T---------TATAATATTCCGGCGTGGGTGGA------------G--------CA-TTCGGCACGCAGTGGGTGCGTGGTAGGCGTTTCG---------CTTC---GTTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droRho1 T------------AATAACTCAGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGCGGGTGCGTGTTGAGCGT------------AGTAC---GTTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droFic1 T------------GGTACTCCAGCGTGGGCGGA------------G--------CG-CTCTCCACGCAGTGGGAGCGTGCAAGGTG----------------------TTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droKik1 --------------ATATTCCAGCGTGGGCGGA------------GTCTCTCTCCG-CTCTGCACGCTGCTGCTGCGTGTTGAGTG-------TCCG------C----GTCCG-CCGGA--------CAATTC----------TTGGAT-------------AC-TT
droAna3 C---------------ATTCCGGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGCAGTTGCGTGCTTCTAC----------------------CACAG-CCGGA--------CAATCC---------CTTGGAT-------------ACACT
droBip1 C---------------ATTCCGGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGTAGTTGCGTGCTTCTAC--------------------CGCCGCCGCCGGA--------CAATCC---------CTTGGAT-------------ACACT
dp4 T-----------------TTCCGTGTGGGTGGT------------G--------CG---CTGCACGCAACAGCTGCGTGTTAT-CGTCCCGTGTCCGTATCTGTGCCGCCGCG-CCGGA--------CAAGCTCTACGGAGAGTCGGATATATACTACTCACAC-TT
droPer1 T-----------------TTCCGTGTGGGTGGT------------G--------CG---CTGCACGCAACAGCTGCGTGTTAT-CGTCCCGTGTCCGTATCTGTGCCGCCGCG-CCGGA--------CAAGCTCTACGGAGAGTCGGATATATACTACTCGCAC-TT

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 None None None None
UNAFold Image None None None None

Small RNA-seq read pileup

Species Alignment
droSim1
T-----ATAATATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGCGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCCACAAAGAC---------GTTGGAT-------------AC-TTSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGCTC............................................2117.000.004.001.002.00
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGCTCC...........................................2217.000.005.002.000.00
................................................................................TAGGTG----------------------CTCCG-TCGGTGCTCC...........................................2113.000.003.000.000.00
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGCT.............................................2012.000.002.000.000.00
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGCC.............................................2012.000.001.001.000.00
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGC..............................................1912.000.001.001.000.00
...............................................................................TTAGGTG----------------------CTCCx-TCGGTGCTCCC..........................................2211.000.001.000.000.00
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGA..............................................1911.000.001.000.000.00
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGCTCCC..........................................2311.000.000.001.000.00
....................CAGCGTGGGCGGA------------G--------CG-CTCTGC........................................................................................................2211.000.000.001.000.00
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGCTT............................................2111.000.001.000.000.00
...............................................................................TTATGTG----------------------CTCCG-TCGGTGCTCCC..........................................2311.000.000.001.000.00
droSec1
T-----ATAATATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGCGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCCACAAAGAC---------GTTGGAT-------------AC-TTSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGCTC............................................2114.002.000.002.00
...............................................................................TTAGGTG----------------------CTCCG-TCGGTGCT.............................................2013.001.000.002.00
.................................................................................AGGTG----------------------CTCCG-TCGGTGCT.............................................1811.001.000.000.00
droYak2
A-----ATACTATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGATGGTGCGTGTTAGGTGC------------TCTGT---GCTCCG-GCGGA--------CAAGAC---------GTTGGAT-------------AC-TTSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
A-----ATAATATTGTATTCCAGCGTGGGCGGA------------G--------CG-TTCTGCACGCCGCGGATGCGTGCTAGGTG----------------------CTGCG-GCGGA--------CAAGAC---------GTTGGAT-------------AC-TTSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droEug1
A-----CT-----AATATTCCAGCGTGGGCGTA----------GAG--------CGCCTCTGCACGATGCTGGTGCGTGTTAAACG----------------------TTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TTSizeHit CountTotal Norm
droBia1
C------------AAGATTCCAGCGTGGGCGGTGGTGGAGGTGGAG--------CA-CTCTGCACGCTGTGGGTGCGTGCTAAGCG----------------------CTCCG-CCGGG--------CGATCC---------GTTGGAT-------------AC-TTSizeHit CountTotal Norm
droTak1
C------------AAGATTCCAGCGTGGGCGGA-------GCAGAG--------CG-GTCTGCACGAAGTGGGTGCGTGTTAAACG----------------------CTCCG-CCGGA--------CA---C---------TTTGGAT-------------AC-TTSizeHit CountTotal Norm
droEle1
T---------TATAATATTCCGGCGTGGGTGGA------------G--------CA-TTCGGCACGCAGTGGGTGCGTGGTAGGCGTTTCG---------CTTC---GTTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TTSizeHit CountTotal Norm
droRho1
T------------AATAACTCAGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGCGGGTGCGTGTTGAGCGT------------AGTAC---GTTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TTSizeHit CountTotal Norm
droFic1
T------------GGTACTCCAGCGTGGGCGGA------------G--------CG-CTCTCCACGCAGTGGGAGCGTGCAAGGTG----------------------TTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TTSizeHit CountTotal Norm
droKik1
--------------ATATTCCAGCGTGGGCGGA------------GTCTCTCTCCG-CTCTGCACGCTGCTGCTGCGTGTTGAGTG-------TCCG------C----GTCCG-CCGGA--------CAATTC----------TTGGAT-------------AC-TTSizeHit CountTotal Norm
droAna3
C---------------ATTCCGGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGCAGTTGCGTGCTTCTAC----------------------CACAG-CCGGA--------CAATCC---------CTTGGAT-------------ACACTSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
.......................CGAGGGCGGA------------G--------CA-CTGTGC........................................................................................................1911.000.000.001.000.00
................ATTCCGGCGTGGGCGGA------------G--------CA-CT............................................................................................................2211.000.001.000.000.00
.............................................................................TGCTTCTAC----------------------CACAG-CCGGA--------CA......................................2111.000.000.001.000.00
droBip1
C---------------ATTCCGGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGTAGTTGCGTGCTTCTAC--------------------CGCCGCCGCCGGA--------CAATCC---------CTTGGAT-------------ACACTSizeHit CountTotal Norm
dp4
T-----------------TTCCGTGTGGGTGGT------------G--------CG---CTGCACGCAACAGCTGCGTGTTAT-CGTCCCGTGTCCGTATCTGTGCCGCCGCG-CCGGA--------CAAGCTCTACGGAGAGTCGGATATATACTACTCACAC-TTSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
...........................GGTGGA------------G--------CG---CGGCACGCA...................................................................................................1811.001.000.000.000.00
droPer1
T-----------------TTCCGTGTGGGTGGT------------G--------CG---CTGCACGCAACAGCTGCGTGTTAT-CGTCCCGTGTCCGTATCTGTGCCGCCGCG-CCGGA--------CAAGCTCTACGGAGAGTCGGATATATACTACTCGCAC-TTSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
.............................................................GCACGCATCAGxTGCGTGT.......................................................................................1811.000.000.000.001.000.00
........................................................................CTGCGTGTTAT-CGTCCCG............................................................................1811.000.000.000.000.001.00
droWil1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
droVir3
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:15:55 EDT