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

View all possible LASTZ hits (20-flies)

sblock147283

chr3R:11757153-11757237 +

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

CDS

Legend:

   mature strand at position 11757203-11757225
   star strand at position 11757170-11757191
   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:11757138-11757252 + 1 CGCCAGCTTTGCGGCCAGAGCTGCAATGGCGCTTGTCCGGAAGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGCCTTCAGCTCCTCACGCGCCGCTGCC
droSim1 chr3R:9721216-9721330 - LASTZ 4 CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC
droSec1 super_0:10201448-10201562 - LASTZ 3 CGCCAGCTGTGCGGCCAAAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTTATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC
droYak2 chr3R:14680051-14680165 - LASTZ 4 CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCAGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTGCAGCTCCTCACGCGCCGCTGCC
droEre2 scaffold_4770:11278284-11278398 + LASTZ 3 CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTACAGCTCCTCACGCGCCGCTGCC
droEug1 scf7180000409797:1781742-1781856 - LASTZ 4 CGGCAGCTGTGCGGCCAGAGTTGTAATGGCGCCTGTCCAGAAGTGGAGCGTGTGATGCTCGCCGATGGCTGCCGCATCTCGGACAAAGGACTCCAGCTTCTAACTCGCCGTTGTC
droBia1 scf7180000302136:1362905-1363019 + LASTZ 4 CGGCAGCTGTGCGGGCAAAGTTGCAACGGAGCCTGTCCGGAAGTGGAGCGCGTAATGCTGGCCGATGGCTGCCGCATCTCGGATAAGGGTCTCCAGCTCCTCACCCGTCGCTGCC
droTak1 scf7180000415242:370457-370571 - LASTZ 4 CGGCAGCTGTGCGGCCAGAGTTGCAATGGCGCCTGTCCGGAAGTAGAGCGCGTCATGCTTTCTGATGGCTGTCGCATCTCGGACAAGGGCCTCCAGCTGCTCACCCGCCGATGTC
droEle1 scf7180000491080:1541800-1541914 + LASTZ 4 CGTCAGCTGTGCGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTGGAGCGCGTGATGCTCGCCGATGGCTGCCGCCTTTCGGACAAGGGCCTCCAGCTGCTGACGCGTCGCTGCC
droRho1 scf7180000758667:164702-164816 + LASTZ 4 CGGCAGCTTTGTGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTCGAGCGCGTAATGCTCGCCGATGGCTGCCGCATCTCGGATAAGGGTCTGCAGCTGCTCACGCGTCGCTGCC
droFic1 scf7180000452523:1135130-1135244 + LASTZ 4 CGGCAGTTGTGTGGCCAGAGTTGCAATGGCGCCTGTCCGGAAGTGGAGCGCGTGATGCTCGCCGATGGCTGCCGCATCTCAGACAAGGGCCTCCAGTTGCTCACCCGTCGCTGCC
droKik1 scf7180000302639:921690-921804 - LASTZ 4 CGGCAGCTGTGCGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTGGAGCGTGTCATGCTTGGCGACGGCTGCCGCATCACGGACAAGGGACTCCAGCTGCTCACGCGTCGCTGCC
droAna3 scaffold_13340:16358935-16359049 + LASTZ 3 CGGCAATTGTGCGGCCAGAGCTGCAACGGCGCATGCCCAGAGGTGGAAAGAGTTATGCTGGCCGATGGGTGCCGAATCTCTGATAAAGGCCTGCAATTGCTGACCCGCCGATGCC
droBip1 scf7180000396708:3686195-3686309 - LASTZ 4 CGGCAATTGTGCGGCCAGAGCTGCAATGGAGCCTGTCCGGAGGTGGAACGGGTGATGCTGGCCGATGGCTGCCGCATCTCAGACAAAGGCCTCCAATTGCTGACCCGCCGATGCC
dp4 chr2:20443804-20443918 + LASTZ 3 CGGCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC
droPer1 super_3:3191078-3191192 + LASTZ 3 CGTCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC
droWil1 scaffold_181089:5116759-5116873 - LASTZ 3 CGGCAATTATGCGGTCAAAGTTGTAACGGTTCTTGCCCGGAGGTAGAACGGGTGATGCTCGCTGACGGTTGTCGCATCTCGGACAAGGGCTTGCAAATGTTAGCCCGGCGTTGTC
droVir3 scaffold_13047:2419453-2419567 + LASTZ 4 CGCCAGCTGTGCGGACAGAGCTGCAATGGCGCCTGCCCGGAGGTGGAACGCGTTATGCTCGCCGATGGCTGTCGCATTTCAGACAAAGGTCTGCAGTTGCTCACGCGTCGCTGTC
droMoj3 scaffold_6540:15231982-15232096 - LASTZ 4 CGCCAGCTGTGCGGACAGAGCTGCAACGGCGCCTGCCCAGAGGTTGAGCGCGTCATGCTTGCCGATGGCTGTCGCATCTCAGACAAGGGTCTGCAGCTGCTGACGCGTCGCTGTC
droGri2 scaffold_15074:5996241-5996355 + LASTZ 4 CGGCAGTTGTGCGGCCAGAGTTGCAATGGTGCCTGCCCCGAGGTGGAACGCGTGATGCTCGCCGATGGCTGTCGCATCTCGGACAAGGGTCTGCAGTTGCTCACCCGTCGGTGTC

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 CGCCAGCTTTGCGGCCAGAGCTGCAATGGCGCTTGTCCGGAAGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGCCTTCAGCTCCTCACGCGCCGCTGCC
droSim1 CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC
droSec1 CGCCAGCTGTGCGGCCAAAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTTATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC
droYak2 CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCAGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTGCAGCTCCTCACGCGCCGCTGCC
droEre2 CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTACAGCTCCTCACGCGCCGCTGCC
droEug1 CGGCAGCTGTGCGGCCAGAGTTGTAATGGCGCCTGTCCAGAAGTGGAGCGTGTGATGCTCGCCGATGGCTGCCGCATCTCGGACAAAGGACTCCAGCTTCTAACTCGCCGTTGTC
droBia1 CGGCAGCTGTGCGGGCAAAGTTGCAACGGAGCCTGTCCGGAAGTGGAGCGCGTAATGCTGGCCGATGGCTGCCGCATCTCGGATAAGGGTCTCCAGCTCCTCACCCGTCGCTGCC
droTak1 CGGCAGCTGTGCGGCCAGAGTTGCAATGGCGCCTGTCCGGAAGTAGAGCGCGTCATGCTTTCTGATGGCTGTCGCATCTCGGACAAGGGCCTCCAGCTGCTCACCCGCCGATGTC
droEle1 CGTCAGCTGTGCGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTGGAGCGCGTGATGCTCGCCGATGGCTGCCGCCTTTCGGACAAGGGCCTCCAGCTGCTGACGCGTCGCTGCC
droRho1 CGGCAGCTTTGTGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTCGAGCGCGTAATGCTCGCCGATGGCTGCCGCATCTCGGATAAGGGTCTGCAGCTGCTCACGCGTCGCTGCC
droFic1 CGGCAGTTGTGTGGCCAGAGTTGCAATGGCGCCTGTCCGGAAGTGGAGCGCGTGATGCTCGCCGATGGCTGCCGCATCTCAGACAAGGGCCTCCAGTTGCTCACCCGTCGCTGCC
droKik1 CGGCAGCTGTGCGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTGGAGCGTGTCATGCTTGGCGACGGCTGCCGCATCACGGACAAGGGACTCCAGCTGCTCACGCGTCGCTGCC
droAna3 CGGCAATTGTGCGGCCAGAGCTGCAACGGCGCATGCCCAGAGGTGGAAAGAGTTATGCTGGCCGATGGGTGCCGAATCTCTGATAAAGGCCTGCAATTGCTGACCCGCCGATGCC
droBip1 CGGCAATTGTGCGGCCAGAGCTGCAATGGAGCCTGTCCGGAGGTGGAACGGGTGATGCTGGCCGATGGCTGCCGCATCTCAGACAAAGGCCTCCAATTGCTGACCCGCCGATGCC
dp4 CGGCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC
droPer1 CGTCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC
droWil1 CGGCAATTATGCGGTCAAAGTTGTAACGGTTCTTGCCCGGAGGTAGAACGGGTGATGCTCGCTGACGGTTGTCGCATCTCGGACAAGGGCTTGCAAATGTTAGCCCGGCGTTGTC
droVir3 CGCCAGCTGTGCGGACAGAGCTGCAATGGCGCCTGCCCGGAGGTGGAACGCGTTATGCTCGCCGATGGCTGTCGCATTTCAGACAAAGGTCTGCAGTTGCTCACGCGTCGCTGTC
droMoj3 CGCCAGCTGTGCGGACAGAGCTGCAACGGCGCCTGCCCAGAGGTTGAGCGCGTCATGCTTGCCGATGGCTGTCGCATCTCAGACAAGGGTCTGCAGCTGCTGACGCGTCGCTGTC
droGri2 CGGCAGTTGTGCGGCCAGAGTTGCAATGGTGCCTGCCCCGAGGTGGAACGCGTGATGCTCGCCGATGGCTGTCGCATCTCGGACAAGGGTCTGCAGTTGCTCACCCGTCGGTGTC

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
CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCCSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
...............................................................................CGGACAAGGGTCGTCAGCT.................1911.000.000.000.001.00
.................................................................................GACAATGGACTTCAGCTC................1811.000.000.000.001.00
AGCCAGCTGTGCGGACAG.................................................................................................1811.000.000.000.001.00
droSec1
CGCCAGCTGTGCGGCCAAAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTTATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCCSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
.....................................................TATGGTCGTCGATGGCTGCC..........................................2011.000.001.000.00
..................AGCTGCAATGGCGCCTGTC..............................................................................1911.000.000.001.00
.....................AGCAATGCCGCCTGTCCGG...........................................................................1911.000.001.000.00
droYak2
CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCAGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTGCAGCTCCTCACGCGCCGCTGCCSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTACAGCTCCTCACGCGCCGCTGCCSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
..............................CCCTATCCGGAGGTGGAG...................................................................1813.000.000.000.003.00
..............................CCCTATCCGGAGGTGGAGC..................................................................1912.000.000.000.002.00
droEug1
CGGCAGCTGTGCGGCCAGAGTTGTAATGGCGCCTGTCCAGAAGTGGAGCGTGTGATGCTCGCCGATGGCTGCCGCATCTCGGACAAAGGACTCCAGCTTCTAACTCGCCGTTGTCSizeHit CountTotal Norm
droBia1
CGGCAGCTGTGCGGGCAAAGTTGCAACGGAGCCTGTCCGGAAGTGGAGCGCGTAATGCTGGCCGATGGCTGCCGCATCTCGGATAAGGGTCTCCAGCTCCTCACCCGTCGCTGCCSizeHit CountTotal Norm
droTak1
CGGCAGCTGTGCGGCCAGAGTTGCAATGGCGCCTGTCCGGAAGTAGAGCGCGTCATGCTTTCTGATGGCTGTCGCATCTCGGACAAGGGCCTCCAGCTGCTCACCCGCCGATGTCSizeHit CountTotal Norm
droEle1
CGTCAGCTGTGCGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTGGAGCGCGTGATGCTCGCCGATGGCTGCCGCCTTTCGGACAAGGGCCTCCAGCTGCTGACGCGTCGCTGCCSizeHit CountTotal Norm
droRho1
CGGCAGCTTTGTGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTCGAGCGCGTAATGCTCGCCGATGGCTGCCGCATCTCGGATAAGGGTCTGCAGCTGCTCACGCGTCGCTGCCSizeHit CountTotal Norm
droFic1
CGGCAGTTGTGTGGCCAGAGTTGCAATGGCGCCTGTCCGGAAGTGGAGCGCGTGATGCTCGCCGATGGCTGCCGCATCTCAGACAAGGGCCTCCAGTTGCTCACCCGTCGCTGCCSizeHit CountTotal Norm
droKik1
CGGCAGCTGTGCGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTGGAGCGTGTCATGCTTGGCGACGGCTGCCGCATCACGGACAAGGGACTCCAGCTGCTCACGCGTCGCTGCCSizeHit CountTotal Norm
droAna3
CGGCAATTGTGCGGCCAGAGCTGCAACGGCGCATGCCCAGAGGTGGAAAGAGTTATGCTGGCCGATGGGTGCCGAATCTCTGATAAAGGCCTGCAATTGCTGACCCGCCGATGCCSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
...........CGGCCTGAGCTGCAACGCC.....................................................................................1911.000.000.001.000.00
droBip1
CGGCAATTGTGCGGCCAGAGCTGCAATGGAGCCTGTCCGGAGGTGGAACGGGTGATGCTGGCCGATGGCTGCCGCATCTCAGACAAAGGCCTCCAATTGCTGACCCGCCGATGCCSizeHit CountTotal Norm
dp4
CGGCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCCSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
.................................................................................GACAAGGGCTTCCAGCTG................1811.000.001.000.000.00
....AGCTGTGCGGCGAGTGCT.............................................................................................1811.000.001.000.000.00
droPer1
CGTCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCCSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
...........CGGCCTGAGCTGCAATGCC.....................................................................................19110.000.000.000.000.0010.00
................................CTATCCGGAGGTGGAGCT.................................................................1811.000.000.000.000.001.00
...........................................TGGAGCGAGTGATGGTGGC.....................................................1911.000.000.001.000.000.00
droWil1
CGGCAATTATGCGGTCAAAGTTGTAACGGTTCTTGCCCGGAGGTAGAACGGGTGATGCTCGCTGACGGTTGTCGCATCTCGGACAAGGGCTTGCAAATGTTAGCCCGGCGTTGTCSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
..................................................................................................................C2490.110.000.110.000.00
.......................................GAGGGCGAACGGGTGATG..........................................................1811.001.000.000.000.00
......................................................................GTCGCATCTCGGACAAGGGC.........................2011.000.000.001.000.00
droVir3
CGCCAGCTGTGCGGACAGAGCTGCAATGGCGCCTGCCCGGAGGTGGAACGCGTTATGCTCGCCGATGGCTGTCGCATTTCAGACAAAGGTCTGCAGTTGCTCACGCGTCGCTGTCSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
CGCCAGCTGTGCGGACAGAGCTGCAACGGCGCCTGCCCAGAGGTTGAGCGCGTCATGCTTGCCGATGGCTGTCGCATCTCAGACAAGGGTCTGCAGCTGCTGACGCGTCGCTGTCSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
.............GACAGAGCGGGAACGGCG....................................................................................1811.001.000.000.000.00
...........................GGCGCCTGCCCAGAGGTTGAGC..................................................................2211.001.000.000.000.00
..........................................GTTGAGCGCGTCATGCTTGCCGATGGC..............................................2711.001.000.000.000.00
............................................................................................GCAGCCGCAGACGCGTCGCT...2011.001.000.000.000.00
droGri2
CGGCAGTTGTGCGGCCAGAGTTGCAATGGTGCCTGCCCCGAGGTGGAACGCGTGATGCTCGCCGATGGCTGTCGCATCTCGGACAAGGGTCTGCAGTTGCTCACCCGTCGGTGTCSizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:18:02 EDT