Locus 4310

Sequence ID dm3.chr2R
Location 12,127,586 – 12,127,681
Length 95
Max. P 0.912803
window5909 window5910 window5911

overview

Window 9

Location 12,127,586 – 12,127,676
Length 90
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 77.78
Shannon entropy 0.30610
G+C content 0.45116
Mean single sequence MFE -26.37
Consensus MFE -15.76
Energy contribution -17.10
Covariance contribution 1.34
Combinations/Pair 1.17
Mean z-score -1.98
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.627160
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12127586 90 - 21146708
GUCAAUGAAAACCUCUCAGAAGAG---AGAGACGCUACUCCGCAGCCUUUAGCAGUUUCCAAGAACAUGGAG---GAGACUAUGCCCUCGAAUCCU
(((..(....).(((((....)))---)).)))....((((((........))....((((......)))))---))).................. ( -18.70, z-score =   0.18, R)
>droSim1.chr2R_random 2505451 96 - 2996586
GUCAAUGAAAACCUCUCAAAACAGUGUAAGGCUGCUACUCUGCAGCCUUUGGAAAGUUCCAAGAACAUGGAACUACAAGUAGAGGAGACUAUGCCU
(((..(....)((((((..........((((((((......)))))))).....(((((((......)))))))....).))))).)))....... ( -30.20, z-score =  -2.92, R)
>droSec1.super_1 9627071 96 - 14215200
GUCAAUGAAAACCUCUCAAAAGAGUGUAAGGCUGCUACUCUGCAGCCUUUGGAAAGUUCCAAGAACAUGGAACUACAAGUAAAGGAGACUAUGCCU
..........((((((....)))).))((((((((......)))))))).....(((((((......)))))))....(((.((....)).))).. ( -30.20, z-score =  -3.19, R)
>consensus
GUCAAUGAAAACCUCUCAAAAGAGUGUAAGGCUGCUACUCUGCAGCCUUUGGAAAGUUCCAAGAACAUGGAACUACAAGUAAAGGAGACUAUGCCU
............((((....))))...((((((((......)))))))).....(((((((......)))))))....(((.((....)).))).. (-15.76 = -17.10 +   1.34)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,127,591 – 12,127,681
Length 90
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 79.03
Shannon entropy 0.28621
G+C content 0.46000
Mean single sequence MFE -29.61
Consensus MFE -21.79
Energy contribution -22.80
Covariance contribution 1.01
Combinations/Pair 1.14
Mean z-score -1.82
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.819967
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12127591 90 + 21146708
UCGAGGGCAUAGUCUCCU------------CCAUGUUCUUGGAAACUGCUAAAGGCUGCGGAGUAGCGUCUCU---CUCUUCUGAGAGGUUUUCAUUGACCACUG
..(((((.......))))------------)...(((..(((((((........(((((...)))))..((((---(......))))))))))))..)))..... ( -25.10, z-score =  -0.13, R)
>droSim1.chr2R_random 2505452 100 + 2996586
-----GGCAUAGUCUCCUCUACUUGUAGUUCCAUGUUCUUGGAACUUUCCAAAGGCUGCAGAGUAGCAGCCUUACACUGUUUUGAGAGGUUUUCAUUGACCACUG
-----((((......(((((...((.(((((((......)))))))...))((((((((......))))))))...........))))).......)).)).... ( -32.52, z-score =  -2.65, R)
>droSec1.super_1 9627072 100 + 14215200
-----GGCAUAGUCUCCUUUACUUGUAGUUCCAUGUUCUUGGAACUUUCCAAAGGCUGCAGAGUAGCAGCCUUACACUCUUUUGAGAGGUUUUCAUUGACUACUG
-----....(((((......(((((((((((((......))))))).....((((((((......)))))))))).(((....))))))).......)))))... ( -31.22, z-score =  -2.68, R)
>consensus
_____GGCAUAGUCUCCU_UACUUGUAGUUCCAUGUUCUUGGAACUUUCCAAAGGCUGCAGAGUAGCAGCCUUACACUCUUUUGAGAGGUUUUCAUUGACCACUG
............((((...........((((((......))))))......((((((((......))))))))..........))))((((......)))).... (-21.79 = -22.80 +   1.01)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,127,591 – 12,127,681
Length 90
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 79.03
Shannon entropy 0.28621
G+C content 0.46000
Mean single sequence MFE -29.53
Consensus MFE -19.64
Energy contribution -21.53
Covariance contribution 1.89
Combinations/Pair 1.10
Mean z-score -2.31
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.912803
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12127591 90 - 21146708
CAGUGGUCAAUGAAAACCUCUCAGAAGAG---AGAGACGCUACUCCGCAGCCUUUAGCAGUUUCCAAGAACAUGG------------AGGAGACUAUGCCCUCGA
..((((((.........(((((......)---))))......((((((........)).((((....))))..))------------))..))))))........ ( -22.30, z-score =  -0.20, R)
>droSim1.chr2R_random 2505452 100 - 2996586
CAGUGGUCAAUGAAAACCUCUCAAAACAGUGUAAGGCUGCUACUCUGCAGCCUUUGGAAAGUUCCAAGAACAUGGAACUACAAGUAGAGGAGACUAUGCC-----
..((((((..(....)((((((..........((((((((......)))))))).....(((((((......)))))))....).))))).))))))...----- ( -34.00, z-score =  -3.27, R)
>droSec1.super_1 9627072 100 - 14215200
CAGUAGUCAAUGAAAACCUCUCAAAAGAGUGUAAGGCUGCUACUCUGCAGCCUUUGGAAAGUUCCAAGAACAUGGAACUACAAGUAAAGGAGACUAUGCC-----
..((((((.......((((((....)))).))((((((((......)))))))).....(((((((......)))))))............))))))...----- ( -32.30, z-score =  -3.47, R)
>consensus
CAGUGGUCAAUGAAAACCUCUCAAAAGAGUGUAAGGCUGCUACUCUGCAGCCUUUGGAAAGUUCCAAGAACAUGGAACUACAAGUA_AGGAGACUAUGCC_____
..((((((........................((((((((......)))))))).....(((((((......)))))))............))))))........ (-19.64 = -21.53 +   1.89)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:26:45 2011