Locus 12355

Sequence ID dm3.chr3R
Location 27,533,771 – 27,533,866
Length 95
Max. P 0.999707
window16981 window16982

overview

Window 1

Location 27,533,771 – 27,533,866
Length 95
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 61.33
Shannon entropy 0.64802
G+C content 0.59407
Mean single sequence MFE -42.56
Consensus MFE -25.05
Energy contribution -25.21
Covariance contribution 0.16
Combinations/Pair 1.41
Mean z-score -1.66
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.77
SVM RNA-class probability 0.995160
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27533771 95 + 27905053
----------------------CUCCAGCGCCUCUCCAUGCCUGCGUGGCAGAAGAUCUGGUUGGUCAGCCAGGGAAAGCUUGAGGGGAGCGGGCCAGGGAUCCGCUAGAACAACAG
----------------------(((.(((.((((((((((....))))).)))....((((((....))))))))...))).)))...(((((((....).)))))).......... ( -35.00, z-score =   0.28, R)
>droSim1.chr3R 27148752 95 + 27517382
----------------------CUCCAGCGGCUCUCCAUGCCUGCGUGUCCGAAAAUCUGGUUGGUCAGCCAGGGAAAGCUUGAGGGGAGCGGGCAAGGGAUCCGCCAGAACAACAG
----------------------.((..((((.((.((.(((((((.(.(((.....(((((((....)))))))..........))).)))))))).)))).))))..))....... ( -36.76, z-score =  -0.75, R)
>droSec1.super_31 188200 95 + 568655
----------------------CUCCAGCGGCUCUCCAUGCCUGCGUGGCCGAAAAUCUGGUUGGUCAGUCAGGGAGAGCUUGAGGGGAGCGGGCAACGGAUCCGCCGGAACAACAG
----------------------.(((.((((.(((...(((((((.(((((((........))))))).(((((.....))))).....)))))))..))).)))).)))....... ( -38.30, z-score =  -0.80, R)
>droYak2.chr3R 28467141 105 + 28832112
------------UGCUCUGCUGCUCCAGCGGCUCUCCAUGCCCACUUGCCAGCAAAUCUGGCUCGGAAGCCAGGGAUUCCUGAUGGGGAGCGGGCAAGGGCUCCGCUGGAACAACAG
------------....(((.((.((((((((...(((.(((((.(((.(((.((..(((((((....)))))))......)).))).))).))))).)))..)))))))).)).))) ( -51.70, z-score =  -2.67, R)
>droAna3.scaffold_12911 1805300 117 - 5364042
CUUCUUGUGGAUAUUCUGGAAGGAUAGGCGGUUCCCUCUGCCUGCUCAUUAAGGAAUCCGAUCUAGGGAGUAAAUCGGAUUCCUCAUAAACAGGCAGAGGAUCCGCAGGGAUUUCAU
.(((((((((((((((.....)))))........((((((((((.......(((((((((((.((.....)).)))))))))))......)))))))))).))))))))))...... ( -51.02, z-score =  -4.35, R)
>consensus
______________________CUCCAGCGGCUCUCCAUGCCUGCGUGGCAGAAAAUCUGGUUGGUCAGCCAGGGAAAGCUUGAGGGGAGCGGGCAAGGGAUCCGCCGGAACAACAG
...........................((((.((.((.(((((((...........(((((((....)))))))...............))))))).)))).))))........... (-25.05 = -25.21 +   0.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 27,533,771 – 27,533,866
Length 95
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 61.33
Shannon entropy 0.64802
G+C content 0.59407
Mean single sequence MFE -42.54
Consensus MFE -22.12
Energy contribution -22.52
Covariance contribution 0.40
Combinations/Pair 1.44
Mean z-score -2.89
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.23
SVM RNA-class probability 0.999707
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27533771 95 - 27905053
CUGUUGUUCUAGCGGAUCCCUGGCCCGCUCCCCUCAAGCUUUCCCUGGCUGACCAACCAGAUCUUCUGCCACGCAGGCAUGGAGAGGCGCUGGAG----------------------
.......(((((((.....((((...(((.......)))......(((....))).)))).(((((((((.....)))).)))))..))))))).---------------------- ( -29.50, z-score =   0.81, R)
>droSim1.chr3R 27148752 95 - 27517382
CUGUUGUUCUGGCGGAUCCCUUGCCCGCUCCCCUCAAGCUUUCCCUGGCUGACCAACCAGAUUUUCGGACACGCAGGCAUGGAGAGCCGCUGGAG----------------------
.......((..((((.((((.((((.((.....(((.(((......))))))....((........))....)).)))).)).)).))))..)).---------------------- ( -32.50, z-score =  -0.64, R)
>droSec1.super_31 188200 95 - 568655
CUGUUGUUCCGGCGGAUCCGUUGCCCGCUCCCCUCAAGCUCUCCCUGACUGACCAACCAGAUUUUCGGCCACGCAGGCAUGGAGAGCCGCUGGAG----------------------
.......((((((((.(((((.(((.((...((......((.....))(((......)))......))....)).))))))))...)))))))).---------------------- ( -32.40, z-score =  -0.67, R)
>droYak2.chr3R 28467141 105 - 28832112
CUGUUGUUCCAGCGGAGCCCUUGCCCGCUCCCCAUCAGGAAUCCCUGGCUUCCGAGCCAGAUUUGCUGGCAAGUGGGCAUGGAGAGCCGCUGGAGCAGCAGAGCA------------
(((((((((((((((..(((.((((((((..(((.((((.....((((((....)))))).)))).)))..)))))))).)).)..)))))))))))))))....------------ ( -63.00, z-score =  -5.96, R)
>droAna3.scaffold_12911 1805300 117 + 5364042
AUGAAAUCCCUGCGGAUCCUCUGCCUGUUUAUGAGGAAUCCGAUUUACUCCCUAGAUCGGAUUCCUUAAUGAGCAGGCAGAGGGAACCGCCUAUCCUUCCAGAAUAUCCACAAGAAG
...........((((.(((((((((((((((((((((((((((((((.....))))))))))))))).))))))))))))))))..))))........................... ( -55.30, z-score =  -8.00, R)
>consensus
CUGUUGUUCCAGCGGAUCCCUUGCCCGCUCCCCUCAAGCUCUCCCUGGCUGACCAACCAGAUUUUCUGACACGCAGGCAUGGAGAGCCGCUGGAG______________________
.......((((((((.((((.((((.((....((.(((......((((........))))..))).))....)).)))).)).)).))))))))....................... (-22.12 = -22.52 +   0.40)

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 01:00:33 2011