Locus 13182

Sequence ID dm3.chrX
Location 4,819,249 – 4,819,378
Length 129
Max. P 0.999121
window18127 window18128

overview

Window 7

Location 4,819,249 – 4,819,378
Length 129
Sequences 3
Columns 130
Reading direction forward
Mean pairwise identity 88.72
Shannon entropy 0.15540
G+C content 0.57829
Mean single sequence MFE -59.23
Consensus MFE -52.12
Energy contribution -53.23
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -4.28
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.54
SVM RNA-class probability 0.998908
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4819249 129 + 22422827
AGUAUCCUGUAGUUGGACUCAAACAAGUCCCUCC-UUCCGCUCGACUGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCAGGAGCGAACUUG
.(..(((.......)))..)...(((((.(((((-(..((((..((.(.((((((((((((..((((..((((((...))))))..))))..)))))))))))).).))..))))..))))).).))))) ( -54.90, z-score =  -4.81, R)
>droSim1.chrX 3726451 130 + 17042790
AGCGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUG
...((((.......)))).....((((..(((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).)..)))) ( -63.10, z-score =  -4.10, R)
>droSec1.super_4 4251638 130 - 6179234
AGUGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUG
.(.((((.......)))).).....(((((((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).).)))). ( -59.70, z-score =  -3.94, R)
>consensus
AGUGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUG
.(.((((.......)))).)...(((((.(((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).).))))) (-52.12 = -53.23 +   1.12)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 4,819,249 – 4,819,378
Length 129
Sequences 3
Columns 130
Reading direction reverse
Mean pairwise identity 88.72
Shannon entropy 0.15540
G+C content 0.57829
Mean single sequence MFE -62.50
Consensus MFE -56.15
Energy contribution -55.93
Covariance contribution -0.21
Combinations/Pair 1.11
Mean z-score -4.78
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.66
SVM RNA-class probability 0.999121
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4819249 129 - 22422827
CAAGUUCGCUCCUGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCAGUCGAGCGGAA-GGAGGGACUUGUUUGAGUCCAACUACAGGAUACU
(((((((.(((((..(((((.((.((((((((((((((..(.(((.((((((...)))))).))).)..)))))))))))))).)).)))))..)-))))))))))).....((((.......))))... ( -64.70, z-score =  -6.55, R)
>droSim1.chrX 3726451 130 - 17042790
CAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACGCU
(((((((..((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))).))).)))).....((((.......))))... ( -62.40, z-score =  -3.68, R)
>droSec1.super_4 4251638 130 + 6179234
CAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACACU
(((((((..((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))).)))).))).....((((.......))))... ( -60.40, z-score =  -4.12, R)
>consensus
CAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACACU
((((.((.(((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).))).)))).)))))).....((((.......))))... (-56.15 = -55.93 +  -0.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:17 2011