Locus 10227

Sequence ID dm3.chr3R
Location 12,275,026 – 12,275,179
Length 153
Max. P 0.995235
window14063 window14064

overview

Window 3

Location 12,275,026 – 12,275,179
Length 153
Sequences 5
Columns 153
Reading direction forward
Mean pairwise identity 76.00
Shannon entropy 0.43323
G+C content 0.39024
Mean single sequence MFE -39.87
Consensus MFE -14.41
Energy contribution -16.91
Covariance contribution 2.50
Combinations/Pair 1.27
Mean z-score -3.00
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.44
SVM RNA-class probability 0.940458
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12275026 153 + 27905053
CAGGGGCGGAUCUAGUUGUGGUUUGCAAGGAAUAUUCCCCUAAUGUUUUGGUAAUUAAACUUAGCUUCUGAAAGUAUCUUUUAAUUAUACUCUCAGUUGUCACCACAUUAAAAUAUUUAAACCUACUGAAAAACUAGCCUCCAGAUCCGCCCC
..(((((((((((...((((((..(((((((....))).((((.((((........))))))))...((((.(((((.........))))).)))))))).))))))..................(((......))).....))))))))))) ( -41.50, z-score =  -3.25, R)
>droEre2.scaffold_4770 11806071 118 + 17746568
--------------------------------CAGGGGCGGAUUGCAUGGG--AUUAGGAUGAGGUUAUGAAAGGAUCUUUAAAUUAUACCAACAGUUGUCACCCCAUUAAAA-AUGUAACCUCGCUGUAAAUUUUUCCUCCAGAUCCGCCCC
--------------------------------..((((((((((....(((--((((.(.(((((((((....((..............)).((....)).............-..))))))))).).)))....))))....)))))))))) ( -33.74, z-score =  -1.57, R)
>droYak2.chr3R 14692662 152 - 28832112
CAGGGGCGGAUCCAGAAGGGGUUUGCAAGGAAUAUUCCCCUAAUAUUUUGGUAAAGAAACAUAGACUAUGAAAGUAUCUUUUAAUUAUACCAAAAGUUGUCACCACAUUAAAA-AUGUAGCCCCGCAGAAAAAUUUGCCUCGAGAUCCGCCCC
..((((((((((..((.((((((.((((((........)))....((((((((.........(((.(((....))))))........))))))))..................-.)))))))))(((((....))))).))..)))))))))) ( -50.43, z-score =  -4.98, R)
>droSec1.super_12 251109 153 - 2123299
CAGGGGCGGAUCCAGAUGUGCUUUGCAAGGGAUAUUCCCCUAAUGUUUUAGUAAUUAAACUUAGCUUAUGAAAGUAUAUAUUAAUUAUACCAUCAGUUGUCACCACAUUAAAAUAUUUAAACCCACUGAAAAAUUAGCCUCCAGAUCCGUCCC
..((((((((((..((.(.(((.....((((......))))(((((((((((.........(((((.(((...(((((.......)))))))).))))).......)))))))))))..................))))))..)))))))))) ( -38.59, z-score =  -3.12, R)
>droSim1.chr3R 18329505 153 - 27517382
CAGGGGCGGAUCCAGAUGUGCUUUGCAAGGAAUAUUCCCCUAAUGUUUUGGUAAUUAAACUUAGCUUAUGAAAGUAUUUUUUAAUUAUACCAUCAGUUGUCACCACAUUAAAAUAUUAAAACCCACUGAAAAAUUAGCCUCCAGAUCCGUCCC
..((((((((((..((((((....(((((((....))).....((...(((((((((((....((((....))))....))))))..))))).)).))))...))))))................((((....))))......)))))))))) ( -35.10, z-score =  -2.06, R)
>consensus
CAGGGGCGGAUCCAGAUGUGCUUUGCAAGGAAUAUUCCCCUAAUGUUUUGGUAAUUAAACUUAGCUUAUGAAAGUAUCUUUUAAUUAUACCAUCAGUUGUCACCACAUUAAAAUAUUUAAACCCACUGAAAAAUUAGCCUCCAGAUCCGCCCC
..((((((((((..........((((...(((((((.....)))))))..))))......................................(((((...........................)))))..............)))))))))) (-14.41 = -16.91 +   2.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,275,026 – 12,275,179
Length 153
Sequences 5
Columns 153
Reading direction reverse
Mean pairwise identity 76.00
Shannon entropy 0.43323
G+C content 0.39024
Mean single sequence MFE -45.53
Consensus MFE -20.08
Energy contribution -23.20
Covariance contribution 3.12
Combinations/Pair 1.28
Mean z-score -3.39
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.78
SVM RNA-class probability 0.995235
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12275026 153 - 27905053
GGGGCGGAUCUGGAGGCUAGUUUUUCAGUAGGUUUAAAUAUUUUAAUGUGGUGACAACUGAGAGUAUAAUUAAAAGAUACUUUCAGAAGCUAAGUUUAAUUACCAAAACAUUAGGGGAAUAUUCCUUGCAAACCACAACUAGAUCCGCCCCUG
(((((((((((((..(((........))).(((((........(((((((((((...((((((((((.........))))))))))((((...))))..)))))...))))))(((((....)))))..)))))....))))))))))))).. ( -54.60, z-score =  -5.69, R)
>droEre2.scaffold_4770 11806071 118 - 17746568
GGGGCGGAUCUGGAGGAAAAAUUUACAGCGAGGUUACAU-UUUUAAUGGGGUGACAACUGUUGGUAUAAUUUAAAGAUCCUUUCAUAACCUCAUCCUAAU--CCCAUGCAAUCCGCCCCUG--------------------------------
(((((((((.(((((((.(((((..(((((..(((((.(-(......)).)))))...)))))....)))))...((.....)).........))))...--.)))....)))))))))..-------------------------------- ( -32.50, z-score =  -1.04, R)
>droYak2.chr3R 14692662 152 + 28832112
GGGGCGGAUCUCGAGGCAAAUUUUUCUGCGGGGCUACAU-UUUUAAUGUGGUGACAACUUUUGGUAUAAUUAAAAGAUACUUUCAUAGUCUAUGUUUCUUUACCAAAAUAUUAGGGGAAUAUUCCUUGCAAACCCCUUCUGGAUCCGCCCCUG
(((((((((((.((((((........)))((((((((((-.....)))))).......((((((((.......((((.((.............)).))))))))))))...(((((((...)))))))....))))))).))))))))))).. ( -50.63, z-score =  -3.90, R)
>droSec1.super_12 251109 153 + 2123299
GGGACGGAUCUGGAGGCUAAUUUUUCAGUGGGUUUAAAUAUUUUAAUGUGGUGACAACUGAUGGUAUAAUUAAUAUAUACUUUCAUAAGCUAAGUUUAAUUACUAAAACAUUAGGGGAAUAUCCCUUGCAAAGCACAUCUGGAUCCGCCCCUG
(((.((((((..((.(((........((((((((((............((....))..(((.((((((.......)))))).))))))))).(((......)))....))))(((((.....)))))....)))...))..)))))).))).. ( -45.80, z-score =  -3.35, R)
>droSim1.chr3R 18329505 153 + 27517382
GGGACGGAUCUGGAGGCUAAUUUUUCAGUGGGUUUUAAUAUUUUAAUGUGGUGACAACUGAUGGUAUAAUUAAAAAAUACUUUCAUAAGCUAAGUUUAAUUACCAAAACAUUAGGGGAAUAUUCCUUGCAAAGCACAUCUGGAUCCGCCCCUG
(((.((((((..((.(((......(((((..(((...((((....))))...))).)))))(((((..((((((.....(((....))).....)))))))))))......(((((((...)))))))...)))...))..)))))).))).. ( -44.10, z-score =  -2.97, R)
>consensus
GGGGCGGAUCUGGAGGCUAAUUUUUCAGUGGGUUUAAAUAUUUUAAUGUGGUGACAACUGAUGGUAUAAUUAAAAGAUACUUUCAUAAGCUAAGUUUAAUUACCAAAACAUUAGGGGAAUAUUCCUUGCAAACCACAUCUGGAUCCGCCCCUG
(((.((((((((((((((............((((((............((....))..(((.(((((.........))))).))))))))).)))))..............((((((.....))))))..........))))))))).))).. (-20.08 = -23.20 +   3.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:19:55 2011