Locus 6632

Sequence ID dm3.chr3L
Location 8,417,454 – 8,417,631
Length 177
Max. P 0.997089
window9131 window9132 window9133 window9134 window9135

overview

Window 1

Location 8,417,454 – 8,417,564
Length 110
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 94.55
Shannon entropy 0.07513
G+C content 0.43030
Mean single sequence MFE -28.44
Consensus MFE -22.15
Energy contribution -21.93
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.34
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.715919
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 8417454 110 + 24543557
GGGGAGAGUUCGCGCCUCUGCAGGAAAAAUACGUACAUACAAAGUAUAUCCUCAAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUCCAACACAAGUCGCAUUUAAG
(.((((.((....)))))).).(((((.((.(((.((((((((((((.((((....)))).....))))))))))))))).))...)))))................... ( -28.00, z-score =  -2.95, R)
>droSec1.super_0 713512 110 + 21120651
GGGGAGAGUUCGCGCCUCUGCAGGAAAAAUACGUACAUACAGAGUACAUCCCCGAAAGGAAACAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCCCAUUUAAG
.(((((((.......)))((((((.......(((.(((((((((((.....((....)).......))))))))))))))......)))))).......))))....... ( -30.12, z-score =  -2.76, R)
>droSim1.chr3L 7876533 110 + 22553184
GGGGAGAGUUCGCGCCUCUGCAGGAAAAAUACGUACAUACAGAGUACUUCCCUGAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAG
((((...(....).))))(((...........((.(((((((((((.(((.((....))...))).)))))))))))))(((......)))..........)))...... ( -27.20, z-score =  -1.31, R)
>consensus
GGGGAGAGUUCGCGCCUCUGCAGGAAAAAUACGUACAUACAGAGUACAUCCCCGAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAG
(..(..((((.(((((((.....))...........((((((((((..(((......)))......)))))))))))))))...))))..)..)................ (-22.15 = -21.93 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,417,454 – 8,417,564
Length 110
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 94.55
Shannon entropy 0.07513
G+C content 0.43030
Mean single sequence MFE -35.93
Consensus MFE -27.51
Energy contribution -27.41
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -4.36
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.04
SVM RNA-class probability 0.997089
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 8417454 110 - 24543557
CUUAAAUGCGACUUGUGUUGGAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUUGAGGAUAUACUUUGUAUGUACGUAUUUUUCCUGCAGAGGCGCGAACUCUCCCC
......((((.(((.(((.(((((..((((((.((((((((((((.(((((......))))).))))))))))))..))))))))))).))).))))))).......... ( -40.30, z-score =  -6.59, R)
>droSec1.super_0 713512 110 - 21120651
CUUAAAUGGGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUGUUUCCUUUCGGGGAUGUACUCUGUAUGUACGUAUUUUUCCUGCAGAGGCGCGAACUCUCCCC
.......((((.((((((((((....((((((.((((((.(((((..((..((....))..))))))).))))))..)))))).....))))...))))))....)))). ( -34.10, z-score =  -2.91, R)
>droSim1.chr3L 7876533 110 - 22553184
CUUAAAUGCGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUCAGGGAAGUACUCUGUAUGUACGUAUUUUUCCUGCAGAGGCGCGAACUCUCCCC
......((((((....))))))......(((((((((((.(((((((((((......))))))))))).)))))....(((.......)))...)))))).......... ( -33.40, z-score =  -3.58, R)
>consensus
CUUAAAUGCGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUCGGGGAUGUACUCUGUAUGUACGUAUUUUUCCUGCAGAGGCGCGAACUCUCCCC
......((((.(((.(((........((((((.((((((.(((((.....((((....)))).))))).))))))..))))))......))).))))))).......... (-27.51 = -27.41 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,417,489 – 8,417,600
Length 111
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 90.27
Shannon entropy 0.13237
G+C content 0.35410
Mean single sequence MFE -25.40
Consensus MFE -19.87
Energy contribution -19.77
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -3.32
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.35
SVM RNA-class probability 0.989037
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 8417489 111 + 24543557
CAUACAAAGUAUAUCCUCAAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUCCAACACAAGUCGCAUUUAAGGCGAUAGUUGAUCGAUCAUCUAAGACUUAAAAUUAA
((((((((((((.((((....)))).....)))))))))))).((.(((((((..........(((((.......))))))))))))))...................... ( -25.60, z-score =  -3.72, R)
>droSec1.super_0 713547 107 + 21120651
CAUACAGAGUACAUCCCCGAAAGGAAACAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCCCAUUUAAGGCGAUAGUUGAUC----AUCAAAGACUUUAAAUUAA
(((((((((((.....((....)).......)))))))))))..(((......))).....(((((((......)).(((.....)))----......)))))........ ( -23.80, z-score =  -3.06, R)
>droSim1.chr3L 7876568 107 + 22553184
CAUACAGAGUACUUCCCUGAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAGGCGAUAGUCGAUC----AUCUAAGACUUUAAAUUAA
(((((((((((.(((.((....))...))).)))))))))))..(((......))).......(((((.......)))))((((....----......))))......... ( -26.80, z-score =  -3.16, R)
>consensus
CAUACAGAGUACAUCCCCGAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAGGCGAUAGUUGAUC____AUCUAAGACUUUAAAUUAA
(((((((((((..(((......)))......)))))))))))..(((......))).....(((((........(((....)))(((.....)))...)))))........ (-19.87 = -19.77 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,417,489 – 8,417,600
Length 111
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 90.27
Shannon entropy 0.13237
G+C content 0.35410
Mean single sequence MFE -26.97
Consensus MFE -20.24
Energy contribution -20.47
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -2.78
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.39
SVM RNA-class probability 0.935066
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 8417489 111 - 24543557
UUAAUUUUAAGUCUUAGAUGAUCGAUCAACUAUCGCCUUAAAUGCGACUUGUGUUGGAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUUGAGGAUAUACUUUGUAUG
((((((((..(((......)))....((((..((((.......)))).....)))))))))))).....((((((((((((.(((((......))))).)))))))))))) ( -26.90, z-score =  -3.05, R)
>droSec1.super_0 713547 107 - 21120651
UUAAUUUAAAGUCUUUGAU----GAUCAACUAUCGCCUUAAAUGGGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUGUUUCCUUUCGGGGAUGUACUCUGUAUG
..(((...(((((...(((----(......)))).((......)))))))..)))(((......)))..((((((.(((((..((..((....))..))))))).)))))) ( -24.40, z-score =  -1.61, R)
>droSim1.chr3L 7876568 107 - 22553184
UUAAUUUAAAGUCUUAGAU----GAUCGACUAUCGCCUUAAAUGCGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUCAGGGAAGUACUCUGUAUG
.........((((......----....))))..(((.((((.((((((....))))))..)))).))).((((((.(((((((((((......))))))))))).)))))) ( -29.60, z-score =  -3.69, R)
>consensus
UUAAUUUAAAGUCUUAGAU____GAUCAACUAUCGCCUUAAAUGCGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUCGGGGAUGUACUCUGUAUG
.................................(((.((((.((((((....))))))..)))).))).((((((.(((((.....((((....)))).))))).)))))) (-20.24 = -20.47 +   0.23)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,417,524 – 8,417,631
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 90.85
Shannon entropy 0.12638
G+C content 0.33209
Mean single sequence MFE -21.70
Consensus MFE -18.83
Energy contribution -18.50
Covariance contribution -0.33
Combinations/Pair 1.11
Mean z-score -1.46
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.554438
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 8417524 107 + 24543557
UUGUAUGGCGCAUCAAUUUCCAACACAAGUCGCAUUUAAGGCGAUAGUUGAUCGAUCAUCUAAGACUUAAAAUUAAGUUGAUGUAUAUGAUACAAGAAAUAGUGCCU
......(((((....(((((((((....(((((.......))))).))))((((((((((...((((((....)))))))))).)).))))....))))).))))). ( -24.30, z-score =  -1.79, R)
>droSec1.super_0 713582 103 + 21120651
UUGUAUGGCGCAUCAAUUUGCAACACAAGUCCCAUUUAAGGCGAUAGUUGAUC----AUCAAAGACUUUAAAUUAAAUUGAUGUAUAAGAUACGAAAAAUAAUGCCU
((((((.(..((((((((((......(((((((......)).(((.....)))----......))))).....))))))))))..)...))))))............ ( -18.50, z-score =  -0.91, R)
>droSim1.chr3L 7876603 103 + 22553184
UUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAGGCGAUAGUCGAUC----AUCUAAGACUUUAAAUUAAAUUGAUGUAUAAGAUACGAAAAAUAUUGCCU
......((((((((((((((........(((((.......)))))((((....----......))))......)))))))))))....((((.......))))))). ( -22.30, z-score =  -1.69, R)
>consensus
UUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAGGCGAUAGUUGAUC____AUCUAAGACUUUAAAUUAAAUUGAUGUAUAAGAUACGAAAAAUAAUGCCU
((((((.(..((((((((((......(((((........(((....)))(((.....)))...))))).....))))))))))..)...))))))............ (-18.83 = -18.50 +  -0.33)

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 Tue Apr 19 23:11:35 2011