Locus 14315

Sequence ID dm3.chrX
Location 12,558,443 – 12,558,560
Length 117
Max. P 0.994539
window19704 window19705 window19706

overview

Window 4

Location 12,558,443 – 12,558,557
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 98.25
Shannon entropy 0.02417
G+C content 0.44152
Mean single sequence MFE -30.69
Consensus MFE -30.61
Energy contribution -30.39
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.78
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.71
SVM RNA-class probability 0.994539
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12558443 114 + 22422827
UAUUGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUACCCAACAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAACA
..(((..(((((((.....(((.....((((((.............)))))).(((....)))..)))...((((((........)))))).......)))))))....))).. ( -30.92, z-score =  -2.94, R)
>droSec1.super_21 312718 114 + 1102487
UAUUGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUAUCCAACAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAGCA
.......(((((((.....(((((...((((((.............))))))..((....)))).)))...((((((........)))))).......)))))))((....)). ( -30.72, z-score =  -2.43, R)
>droSim1.chrX 9607201 114 + 17042790
UAUUGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUAUCCAAAAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAACA
..(((..(((((((.....(((((...((((((.............))))))..((....)))).)))...((((((........)))))).......)))))))....))).. ( -30.42, z-score =  -2.97, R)
>consensus
UAUUGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUAUCCAACAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAACA
..(((..(((((((.....(((((...((((((.............))))))..((....)))).)))...((((((........)))))).......)))))))....))).. (-30.61 = -30.39 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,558,443 – 12,558,557
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 98.25
Shannon entropy 0.02417
G+C content 0.44152
Mean single sequence MFE -29.40
Consensus MFE -27.17
Energy contribution -27.50
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.525415
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12558443 114 - 22422827
UGUUGCUGCCCCGGCCUCAUGUCCUCAUGUGCGUUUUCAUGAGUUUAAGUGCCCUGUUGGGUAGUGAGUUUAGUUGAUAUGCUCACUUUAGCCUUUUUAUAGCCAGGUUCAAUA
(((((..(((..(((....((..((((((........))))))..))..(((((....)))))((((((.((.....)).))))))...............))).))).))))) ( -31.90, z-score =  -2.03, R)
>droSec1.super_21 312718 114 - 1102487
UGCUGCUGCCCCGGCCUCAUGUCCUCAUGUGCGUUUUCAUGAGUUUAAGUGCCCUGUUGGAUAGUGAGUUUAGUUGAUAUGCUCACUUUAGCCUUUUUAUAGCCAGGUUCAAUA
..((((((....(((((..((..((((((........))))))..)))).))).....((..(((((((.((.....)).)))))))....))......))).)))........ ( -27.70, z-score =  -0.62, R)
>droSim1.chrX 9607201 114 - 17042790
UGUUGCUGCCCCGGCCUCAUGUCCUCAUGUGCGUUUUCAUGAGUUUAAGUGCCCUUUUGGAUAGUGAGUUUAGUUGAUAUGCUCACUUUAGCCUUUUUAUAGCCAGGUUCAAUA
(((((..(((..(((....((..((((((........))))))..))...........((..(((((((.((.....)).)))))))....))........))).))).))))) ( -28.60, z-score =  -1.61, R)
>consensus
UGUUGCUGCCCCGGCCUCAUGUCCUCAUGUGCGUUUUCAUGAGUUUAAGUGCCCUGUUGGAUAGUGAGUUUAGUUGAUAUGCUCACUUUAGCCUUUUUAUAGCCAGGUUCAAUA
(((((..(((..(((....((..((((((........))))))..))((.((((....))..(((((((.((.....)).)))))))...)))).......))).))).))))) (-27.17 = -27.50 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,558,446 – 12,558,560
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 98.25
Shannon entropy 0.02417
G+C content 0.45029
Mean single sequence MFE -30.22
Consensus MFE -29.79
Energy contribution -29.79
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.74
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.59
SVM RNA-class probability 0.993168
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12558446 114 + 22422827
UGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUACCCAACAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAACAACA
....(((((((.....(((.....((((((.............)))))).(((....)))..)))...((((((........)))))).......)))))))............ ( -30.22, z-score =  -2.82, R)
>droSec1.super_21 312721 114 + 1102487
UGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUAUCCAACAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAGCAACA
....(((((((.....(((((...((((((.............))))))..((....)))).)))...((((((........)))))).......)))))))((....)).... ( -30.72, z-score =  -2.53, R)
>droSim1.chrX 9607204 114 + 17042790
UGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUAUCCAAAAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAACAACA
....(((((((.....(((((...((((((.............))))))..((....)))).)))...((((((........)))))).......)))))))............ ( -29.72, z-score =  -2.88, R)
>consensus
UGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUAUCCAACAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAACAACA
....(((((((.....(((((...((((((.............))))))..((....)))).)))...((((((........)))))).......)))))))............ (-29.79 = -29.79 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:37:52 2011