Locus 13185

Sequence ID dm3.chrX
Location 4,820,048 – 4,820,207
Length 159
Max. P 0.998452
window18134 window18135 window18136 window18137

overview

Window 4

Location 4,820,048 – 4,820,167
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.27
Shannon entropy 0.16070
G+C content 0.58888
Mean single sequence MFE -45.99
Consensus MFE -39.01
Energy contribution -39.57
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.27
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944430
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4820048 119 + 22422827
AAGGGCCCCCCAGUAUCCUGUAGUUGGACUCAAACAAGUCCCUCC-UUCCGCUUGACUGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGU
..((((....((((.......((..(((((......)))))...)-)........))))..(((((((((((..((((..((((((...))))))..))))..))))))))))))))).. ( -45.06, z-score =  -3.48, R)
>droSim1.chrX 3726708 118 + 17042790
AAGGGCCCC--AGCGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGU
.(((((...--...)))))((((..(((((......))))).......))))...((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..)))) ( -46.50, z-score =  -1.55, R)
>droSec1.super_4 4252413 118 - 6179234
AAGGGCCCC--AGUGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGU
.(((((...--...)))))((((..(((((......))))).......))))...((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..)))) ( -46.40, z-score =  -1.79, R)
>consensus
AAGGGCCCC__AGUGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGU
...(((........(((..((((..(((((......))))).......))))..)))....((.((((..((..(((((.((((((...)))))).)))))..))..)))).)))))... (-39.01 = -39.57 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,820,048 – 4,820,167
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.27
Shannon entropy 0.16070
G+C content 0.58888
Mean single sequence MFE -51.87
Consensus MFE -45.65
Energy contribution -44.77
Covariance contribution -0.88
Combinations/Pair 1.13
Mean z-score -2.26
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.71
SVM RNA-class probability 0.962579
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4820048 119 - 22422827
ACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCAGUCAAGCGGAA-GGAGGGACUUGUUUGAGUCCAACUACAGGAUACUGGGGGGCCCUU
...((((((((((((((..(.(((.((((((...)))))).))).)..))))))))))))))..........((-((..((((((....))))))..(..(((....)))..)...)))) ( -50.90, z-score =  -3.31, R)
>droSim1.chrX 3726708 118 - 17042790
ACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACGCU--GGGGCCCUU
.(((((((((((((..(((..(((.((((((...)))))).)))((((..(((((.(((....)))))))))))).)))..))))(((((...)))))..)))..))))--))....... ( -53.10, z-score =  -1.73, R)
>droSec1.super_4 4252413 118 + 6179234
ACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACACU--GGGGCCCUU
(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).......(((((..((((((....))))))..(..(((....))--)..)))))) ( -51.60, z-score =  -1.75, R)
>consensus
ACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACACU__GGGGCCCUU
(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).)))))...........(((((.(((...((.((((.......)))).))..))).))))) (-45.65 = -44.77 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,820,088 – 4,820,207
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.22
Shannon entropy 0.17601
G+C content 0.58485
Mean single sequence MFE -55.87
Consensus MFE -45.30
Energy contribution -46.97
Covariance contribution 1.67
Combinations/Pair 1.05
Mean z-score -3.91
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.27
SVM RNA-class probability 0.998148
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4820088 119 + 22422827
-CCUCCUUCCGCUUGACUGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCAGGAGCGAACUUGUUGGAGUCAAACUACAGGC
-.(((((..(((((.((.(.((((((((((((..((((..((((((...))))))..))))..)))))))))))).).)).)))))..)))))....(((((.(........).))))). ( -53.20, z-score =  -4.60, R)
>droSim1.chrX 3726746 120 + 17042790
CCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUUGGAGUCAAACUACAGGC
....(((((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))).....((((((.(........).)))))) ( -57.50, z-score =  -3.54, R)
>droSec1.super_4 4252451 120 - 6179234
CCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUGUUGGAGUCAAACUUCAGGC
.((((((((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..)))))))))...)))....((((((.....)))))).. ( -56.90, z-score =  -3.57, R)
>consensus
CCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUUGGAGUCAAACUACAGGC
....(((((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))).....((((((.(........).)))))) (-45.30 = -46.97 +   1.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,820,088 – 4,820,207
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.22
Shannon entropy 0.17601
G+C content 0.58485
Mean single sequence MFE -53.40
Consensus MFE -47.73
Energy contribution -46.30
Covariance contribution -1.43
Combinations/Pair 1.19
Mean z-score -3.76
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.36
SVM RNA-class probability 0.998452
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4820088 119 - 22422827
GCCUGUAGUUUGACUCCAACAAGUUCGCUCCUGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCAGUCAAGCGGAAGGAGG-
...........((((......))))..(((((..(((((.((.((((((((((((((..(.(((.((((((...)))))).))).)..)))))))))))))).)).)))))..))))).- ( -52.60, z-score =  -4.49, R)
>droSim1.chrX 3726746 120 - 17042790
GCCUGUAGUUUGACUCCAACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGG
.(((((((((((.......)))))).))((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).))))))))) ( -55.80, z-score =  -3.73, R)
>droSec1.super_4 4252451 120 + 6179234
GCCUGAAGUUUGACUCCAACAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGG
((..((...(((....)))...))..))((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).))))))... ( -51.80, z-score =  -3.06, R)
>consensus
GCCUGUAGUUUGACUCCAACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGG
((..((...(((....)))...))..))((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).))))))... (-47.73 = -46.30 +  -1.43)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:24 2011