Locus 8671

Sequence ID dm3.chr3R
Location 591,655 – 591,747
Length 92
Max. P 0.996423
window11902 window11903

overview

Window 2

Location 591,655 – 591,747
Length 92
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 69.62
Shannon entropy 0.45930
G+C content 0.53551
Mean single sequence MFE -35.75
Consensus MFE -27.04
Energy contribution -27.10
Covariance contribution 0.06
Combinations/Pair 1.40
Mean z-score -2.35
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.93
SVM RNA-class probability 0.996423
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 591655 92 + 27905053
--------UUCGCCGUAUUUGGACACGAAGUUCGAGGCACCUUGCCCGUGGAAAUUGGGCAGAAUUAAUAGGUCCUCGACUUUCCACUCGAAAGUCGCAG---------
--------...((.......((((.....))))((((.((((((((((.......))))))........))))))))(((((((.....)))))))))..--------- ( -31.30, z-score =  -2.34, R)
>droSim1.chr3R 633440 94 + 27517382
------UUUGCGCCGUACUUGGACACGAAGUUCAAGGCACCUUACCCGUGGAAAUUGGGCGAGGUUAAUAGGUCCUCGACUUUCGACUCCAAAGUCGCAG---------
------..((((((((.(((((((.....)))))))))((((..((((.......))))..)))).....)))....((((((.......))))))))).--------- ( -30.90, z-score =  -1.70, R)
>droSec1.super_6 692323 94 + 4358794
------UUCGCACCGUACUUGGACACGAAGUUCAAGGCACCUUGCCCGUGGAAAUUGGGCGAGGUUAAUAGGUCCUCGACUUUCGACUCGAAAGUCGCAG---------
------...(((((((.(((((((.....)))))))))((((((((((.......)))))))))).....)))....((((((((...))))))))))..--------- ( -40.10, z-score =  -4.18, R)
>droAna3.scaffold_13340 22808202 109 + 23697760
CUCUCGAGUUCGCCGUACUUGGACGUCAAGUUCGAAGCACUUGGUCAAUGCAAAUGAGGCAAACUGGAGAGGUCCUCGACUCCGGGCCCCGGGCCUGGGUUCAUCCCAU
(((((.((((.(((....((((((.....)))))).(((.((....)))))......))).)))).)))))......((..(((((((...)))))))..))....... ( -40.70, z-score =  -1.19, R)
>consensus
______UUUGCGCCGUACUUGGACACGAAGUUCAAGGCACCUUGCCCGUGGAAAUUGGGCAAAGUUAAUAGGUCCUCGACUUUCGACUCCAAAGUCGCAG_________
...........(((((.(((((((.....)))))))))((((((((((.......)))))))))).....)))...((((((((.....))))))))............ (-27.04 = -27.10 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 591,655 – 591,747
Length 92
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 69.62
Shannon entropy 0.45930
G+C content 0.53551
Mean single sequence MFE -34.98
Consensus MFE -18.76
Energy contribution -17.95
Covariance contribution -0.81
Combinations/Pair 1.50
Mean z-score -2.27
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.89
SVM RNA-class probability 0.973477
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 591655 92 - 27905053
---------CUGCGACUUUCGAGUGGAAAGUCGAGGACCUAUUAAUUCUGCCCAAUUUCCACGGGCAAGGUGCCUCGAACUUCGUGUCCAAAUACGGCGAA--------
---------.((((((((((.....)))))))((((((((........(((((.........))))))))).))))......(((((....))))))))..-------- ( -31.30, z-score =  -2.27, R)
>droSim1.chr3R 633440 94 - 27517382
---------CUGCGACUUUGGAGUCGAAAGUCGAGGACCUAUUAACCUCGCCCAAUUUCCACGGGUAAGGUGCCUUGAACUUCGUGUCCAAGUACGGCGCAAA------
---------.((((..((((((..((((..((((((........((((..(((.........)))..)))).))))))..))))..)))))).....))))..------ ( -34.60, z-score =  -2.85, R)
>droSec1.super_6 692323 94 - 4358794
---------CUGCGACUUUCGAGUCGAAAGUCGAGGACCUAUUAACCUCGCCCAAUUUCCACGGGCAAGGUGCCUUGAACUUCGUGUCCAAGUACGGUGCGAA------
---------...(((((((((...))))))))).(.(((.....((((.((((.........)))).))))..((((.((.....)).))))...))).)...------ ( -32.20, z-score =  -2.03, R)
>droAna3.scaffold_13340 22808202 109 - 23697760
AUGGGAUGAACCCAGGCCCGGGGCCCGGAGUCGAGGACCUCUCCAGUUUGCCUCAUUUGCAUUGACCAAGUGCUUCGAACUUGACGUCCAAGUACGGCGAACUCGAGAG
.((((.....))))(((((((...)))).)))......(((((.((((((((......(((((.....)))))...(.(((((.....))))).))))))))).))))) ( -41.80, z-score =  -1.94, R)
>consensus
_________CUGCGACUUUCGAGUCGAAAGUCGAGGACCUAUUAACCUCGCCCAAUUUCCACGGGCAAGGUGCCUCGAACUUCGUGUCCAAGUACGGCGAAAA______
.............((((....))))(((..((((((........((((.((((.........)))).)))).))))))..)))(((.((......)))))......... (-18.76 = -17.95 +  -0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:49:55 2011