Locus 13186

Sequence ID dm3.chrX
Location 4,820,350 – 4,820,469
Length 119
Max. P 0.999059
window18138 window18139

overview

Window 8

Location 4,820,350 – 4,820,469
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.44
Shannon entropy 0.14540
G+C content 0.57094
Mean single sequence MFE -57.23
Consensus MFE -50.95
Energy contribution -51.73
Covariance contribution 0.78
Combinations/Pair 1.07
Mean z-score -4.62
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.62
SVM RNA-class probability 0.999059
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4820350 119 + 22422827
AACAAGUCCCUCC-UUCCGCUCGACUGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCAGGAGCGAACUUGUUGGAGUCAAA
(((((((.(((((-(..((((..((.(.((((((((((((..((((..((((((...))))))..))))..)))))))))))).).))..))))..))))).).)))))))......... ( -54.90, z-score =  -5.20, R)
>droSim1.chrX 3726472 120 + 17042790
AACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUUGGAGUCAAA
((((((..(((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).)..))))))......... ( -60.40, z-score =  -4.63, R)
>droSec1.super_4 4252709 120 - 6179234
AACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUGUUGGAGUCAAA
(((((.((.((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).))..)))))......... ( -56.40, z-score =  -4.03, R)
>consensus
AACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUUGGAGUCAAA
(((((((.(((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).).)))))))......... (-50.95 = -51.73 +   0.78)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 4,820,350 – 4,820,469
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.44
Shannon entropy 0.14540
G+C content 0.57094
Mean single sequence MFE -60.13
Consensus MFE -53.56
Energy contribution -53.57
Covariance contribution 0.01
Combinations/Pair 1.09
Mean z-score -5.55
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.57
SVM RNA-class probability 0.998961
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4820350 119 - 22422827
UUUGACUCCAACAAGUUCGCUCCUGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCAGUCGAGCGGAA-GGAGGGACUUGUU
.........(((((((((.(((((..(((((.((.((((((((((((((..(.(((.((((((...)))))).))).)..)))))))))))))).)).)))))..)-))))))))))))) ( -63.80, z-score =  -7.21, R)
>droSim1.chrX 3726472 120 - 17042790
UUUGACUCCAACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUU
.........(((((((((..((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))).))).)))))) ( -59.30, z-score =  -4.71, R)
>droSec1.super_4 4252709 120 + 6179234
UUUGACUCCAACAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUU
.........(((((((((..((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))).)))).))))) ( -57.30, z-score =  -4.74, R)
>consensus
UUUGACUCCAACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUU
.........((((((.((.(((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).))).)))).)))))))) (-53.56 = -53.57 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:26 2011