Locus 3900

Sequence ID dm3.chr2R
Location 8,796,246 – 8,796,343
Length 97
Max. P 0.972743
window5344 window5345

overview

Window 4

Location 8,796,246 – 8,796,343
Length 97
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 74.49
Shannon entropy 0.46690
G+C content 0.58249
Mean single sequence MFE -28.25
Consensus MFE -18.51
Energy contribution -18.68
Covariance contribution 0.17
Combinations/Pair 1.32
Mean z-score -1.82
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.87
SVM RNA-class probability 0.972743
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8796246 97 + 21146708
GAAUGCUUCCAAAUCGCUGAUAAACAGCGAACAACUCGCGAGGUGUACAGCGGUGGGUGGGGCUGACUUGCCAAGGGGGGGGGGAAGGGGGGCAGUU
...(((((((..((((((((((....((((.....))))....))).))))))).((..((.....))..))...............)))))))... ( -35.10, z-score =  -2.44, R)
>droSim1.chr2R 7256663 91 + 19596830
GAAUGCUUCCAAAUCGCUGAUAAACAGCGAACAACUCGCGAGGUGAACAGCGGUGGGUGGGGCUGACUUGGCAGGGAUGGGGGAGGCGGAU------
...(((((((...((((((.....)))))).((.(((((.((((...((((..........)))))))).)).))).))..)))))))...------ ( -32.70, z-score =  -3.07, R)
>droSec1.super_1 6312194 91 + 14215200
GAAUGCUUCCAAAUCGCUGAUAAACAGCGAACAACUCGCGAGGUGAACAGCGGUGGGUGGGGCUGACUUGGCAGGGGUGGGGGAGGCGGAU------
...(((((((...((((((.....)))))).((.(((((.((((...((((..........)))))))).)).))).))..)))))))...------ ( -32.70, z-score =  -2.70, R)
>droYak2.chr2R 12964851 85 - 21139217
GAAUGCUUCCAAAUCGCUGAUAAACAGCGAACAACUCGCGAGGUGAGUAGCGGUGGGUGGGGUUCGCUUGCCACGGGGAGGGGAA------------
...(.(((((...((((((.....))))))...((((((...)))))).(.((..((((.....))))..)).)..))))).)..------------ ( -31.70, z-score =  -2.19, R)
>droEre2.scaffold_4845 5560793 76 - 22589142
GAAUGCUUCCAAAUCGCUGAUAAACAGCGAACAACUCGCGAGGUGAACAGCGGUGGGUGGGGU---------AGGGGGAGGGGAG------------
...(.(((((...((((((.....))))))((.(((((((..(....)..).))))))...))---------....))))).)..------------ ( -23.90, z-score =  -2.43, R)
>dp4.chr3 14819716 76 + 19779522
GAAUGCCUUCAAAUCGCUGAUAAACAGAGGAAGAGGUGUGCGGUGU---GCGGCAGGUGGGGA-------AUGGGGCUUGGGACGU-----------
....((((((..(((((((....(((..(.(.......).)..)))---.)))).)))...))-------...)))).........----------- ( -13.40, z-score =   1.93, R)
>consensus
GAAUGCUUCCAAAUCGCUGAUAAACAGCGAACAACUCGCGAGGUGAACAGCGGUGGGUGGGGCUGACUUGCCAGGGGGGGGGGAG____________
....(((.(((.(((((((....((.((((.....))))...))...)))))))...)))))).................................. (-18.51 = -18.68 +   0.17)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,796,246 – 8,796,343
Length 97
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 74.49
Shannon entropy 0.46690
G+C content 0.58249
Mean single sequence MFE -16.82
Consensus MFE -9.06
Energy contribution -9.56
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.30
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.534418
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8796246 97 - 21146708
AACUGCCCCCCUUCCCCCCCCCCUUGGCAAGUCAGCCCCACCCACCGCUGUACACCUCGCGAGUUGUUCGCUGUUUAUCAGCGAUUUGGAAGCAUUC
..........(((((..........(((......)))........(((((.(((....(((((...))))))))....)))))....)))))..... ( -20.80, z-score =  -1.61, R)
>droSim1.chr2R 7256663 91 - 19596830
------AUCCGCCUCCCCCAUCCCUGCCAAGUCAGCCCCACCCACCGCUGUUCACCUCGCGAGUUGUUCGCUGUUUAUCAGCGAUUUGGAAGCAUUC
------....((.(((...(((.(((..(((.((((...((..(((((..........))).)).))..)))))))..))).)))..))).)).... ( -18.70, z-score =  -1.57, R)
>droSec1.super_1 6312194 91 - 14215200
------AUCCGCCUCCCCCACCCCUGCCAAGUCAGCCCCACCCACCGCUGUUCACCUCGCGAGUUGUUCGCUGUUUAUCAGCGAUUUGGAAGCAUUC
------....((.(((........(((...((((((..........))))...))...)))......((((((.....))))))...))).)).... ( -18.50, z-score =  -1.48, R)
>droYak2.chr2R 12964851 85 + 21139217
------------UUCCCCUCCCCGUGGCAAGCGAACCCCACCCACCGCUACUCACCUCGCGAGUUGUUCGCUGUUUAUCAGCGAUUUGGAAGCAUUC
------------((((.((((..((((..((((............))))..))))...).)))....((((((.....))))))...))))...... ( -19.70, z-score =  -1.24, R)
>droEre2.scaffold_4845 5560793 76 + 22589142
------------CUCCCCUCCCCCU---------ACCCCACCCACCGCUGUUCACCUCGCGAGUUGUUCGCUGUUUAUCAGCGAUUUGGAAGCAUUC
------------.............---------............(((.(((((..(....)..))((((((.....))))))...)))))).... ( -14.10, z-score =  -1.68, R)
>dp4.chr3 14819716 76 - 19779522
-----------ACGUCCCAAGCCCCAU-------UCCCCACCUGCCGC---ACACCGCACACCUCUUCCUCUGUUUAUCAGCGAUUUGAAGGCAUUC
-----------................-------........((((((---.....))..........(.(((.....))).).......))))... (  -9.10, z-score =  -0.24, R)
>consensus
____________CUCCCCCACCCCUGCCAAGUCAGCCCCACCCACCGCUGUUCACCUCGCGAGUUGUUCGCUGUUUAUCAGCGAUUUGGAAGCAUUC
..........................................................((.......((((((.....)))))).......)).... ( -9.06 =  -9.56 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:18:56 2011