Locus 9452

Sequence ID dm3.chr3R
Location 6,779,547 – 6,779,640
Length 93
Max. P 0.877231
window12962 window12963

overview

Window 2

Location 6,779,547 – 6,779,640
Length 93
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 94.97
Shannon entropy 0.08751
G+C content 0.52845
Mean single sequence MFE -34.40
Consensus MFE -31.82
Energy contribution -31.50
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -1.81
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.877231
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6779547 93 + 27905053
UGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAACUACAUCUGCAGCUGCUUCUGUUAGCGG------
.....(((...((((.((...)).))))..)))..((..(((((((.(((.((((((....)))))).))).)))))))(((......)))))------ ( -31.00, z-score =  -1.50, R)
>droSim1.chr3R 12937574 93 - 27517382
UGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGG------
.((((((..((((((.((...)).))))..((...))..))..))))))((((..((((((((((......))))))))))..))))......------ ( -31.80, z-score =  -1.12, R)
>droSec1.super_0 5947463 93 - 21120651
UGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGUUCCCGUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGG------
.....(((...((((.((...)).))))..)))..((((..........((((..((((((((((......))))))))))..))))..))))------ ( -34.20, z-score =  -1.73, R)
>droYak2.chr3R 10817769 93 + 28832112
UGUUUGCCUUCGCCAUGCUACGCUUGGCUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGAUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGG------
.....(((...((((.((...)).))))..))).......((((.....(((((((((((((......)))))))))))))......))))..------ ( -34.50, z-score =  -1.80, R)
>droEre2.scaffold_4770 2918969 99 - 17746568
UGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGCUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUCAGCGGCUUACG
.((..(((...((((.(((......))).)))).......((((.....((((..((((((((((......))))))))))..)))))))))))..)). ( -40.50, z-score =  -2.88, R)
>consensus
UGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGG______
.....(((...((((.((...)).))))..)))..((..(((((((.(((.((((((....)))))).))).)))))))(((......)))))...... (-31.82 = -31.50 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,779,547 – 6,779,640
Length 93
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 94.97
Shannon entropy 0.08751
G+C content 0.52845
Mean single sequence MFE -31.64
Consensus MFE -28.46
Energy contribution -28.50
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.78
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.814277
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6779547 93 - 27905053
------CCGCUAACAGAAGCAGCUGCAGAUGUAGUUGCAACUGCAACUGCAUUUACAACCAAGGGAACCAAGCCAAGCGGAGCAUGGCGAAGGCAAACA
------(((((.......((....))((((((((((((....))))))))))))........((........)).)))))......((....))..... ( -29.90, z-score =  -1.78, R)
>droSim1.chr3R 12937574 93 + 27517382
------CCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCAAGGGAACCAAGCCAAGCGGAGCAUGGCGAAGGCAAACA
------(((((..(((..((((((((....))))))))..)))...................((........)).)))))......((....))..... ( -30.20, z-score =  -1.59, R)
>droSec1.super_0 5947463 93 + 21120651
------CCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCACGGGAACCAAGCCAAGCGGAGCAUGGCGAAGGCAAACA
------(((((..(((..((((((((....))))))))..)))...................((........)).)))))......((....))..... ( -30.30, z-score =  -1.65, R)
>droYak2.chr3R 10817769 93 - 28832112
------CCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAUCUGCAACUGCAUUUACAACCAAGGGAACCAAGCCAAGCGUAGCAUGGCGAAGGCAAACA
------..(((.......((((.(((((((((....))))))))).)))).....................((((.((...)).))))...)))..... ( -31.80, z-score =  -2.03, R)
>droEre2.scaffold_4770 2918969 99 + 17746568
CGUAAGCCGCUGACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCAAGGGAGCCAAGCCAAGCGGAGCAUGGCGAAGGCAAACA
.((((((.(.((.(((..((((((((....))))))))..))))).).))..))))..........(((..((((.((...)).))))...)))..... ( -36.00, z-score =  -1.85, R)
>consensus
______CCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCAAGGGAACCAAGCCAAGCGGAGCAUGGCGAAGGCAAACA
......(((((..(((..((((((((....))))))))..)))...................((........)).)))))......((....))..... (-28.46 = -28.50 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:04:41 2011