Locus 5658

Sequence ID dm3.chr3L
Location 314,465 – 314,589
Length 124
Max. P 0.907940
window7773 window7774

overview

Window 3

Location 314,465 – 314,589
Length 124
Sequences 3
Columns 133
Reading direction forward
Mean pairwise identity 64.91
Shannon entropy 0.48331
G+C content 0.35688
Mean single sequence MFE -29.83
Consensus MFE -15.80
Energy contribution -14.71
Covariance contribution -1.09
Combinations/Pair 1.45
Mean z-score -1.63
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.832356
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 314465 124 + 24543557
AAUCAAAAUAUAUACCGCACACG-CAUACACAUACAAUUGAUAUUUU------AGAGUGUCAAAUGUUGAAAAAUAUAAAUAUAUACUAAUGAUCAA-GUCAAAUAUGUAU-UGGAAUCAAAGAUGCAGAGAU
......................(-(((...((.(((.((((((((..------..)))))))).))))).........((((((((....((((...-))))..)))))))-)..........))))...... ( -16.60, z-score =   0.21, R)
>dp4.chrXR_group8 7802537 133 - 9212921
CAUUUAAAUAUAAAUCGCAGUCGAUUUGUAUUAGGAACUCGCGUUUGCCAAGAAAUAUGCCAAAUAAAUACUCUUCGGAUUGUUCAAGGACGAUGAAAGUCCAAAAAGUAUAUCGAGGGGGCGGGGGAGAGUU
......(((((((((((....)))))))))))...(((((.(.((((((.....((((((......((((.((....)).))))...((((.......)))).....))))))......)))))).).))))) ( -36.40, z-score =  -2.55, R)
>droPer1.super_32 65814 133 + 992631
CAUUUAAAUAUAAAUCGCAGUCGAUUUGUAUUAGGAACUCGCGUUUGCCAAGAAAUAUGCCAAAUAAAUACUCUUCGGAUUGUUCAAGGACGAUGAAAGUCCAAAAAGUAUAUCGAGGGGGCGGGGGAGAGUG
..((..(((((((((((....)))))))))))..))((((.(.((((((.....((((((......((((.((....)).))))...((((.......)))).....))))))......)))))).).)))). ( -36.50, z-score =  -2.56, R)
>consensus
CAUUUAAAUAUAAAUCGCAGUCGAUUUGUAUUAGGAACUCGCGUUUGCCAAGAAAUAUGCCAAAUAAAUACUCUUCGGAUUGUUCAAGGACGAUGAAAGUCCAAAAAGUAUAUCGAGGGGGCGGGGGAGAGUU
......(((((((((((....))))))))))).....(((((((.(........).))))..........((((((((.........((((.......))))..........))))))))......))).... (-15.80 = -14.71 +  -1.09)

alignment

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secondary structure

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dotplot

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Window 4

Location 314,465 – 314,589
Length 124
Sequences 3
Columns 133
Reading direction reverse
Mean pairwise identity 64.91
Shannon entropy 0.48331
G+C content 0.35688
Mean single sequence MFE -24.89
Consensus MFE -14.50
Energy contribution -14.07
Covariance contribution -0.43
Combinations/Pair 1.34
Mean z-score -1.62
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.20
SVM RNA-class probability 0.907940
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 314465 124 - 24543557
AUCUCUGCAUCUUUGAUUCCA-AUACAUAUUUGAC-UUGAUCAUUAGUAUAUAUUUAUAUUUUUCAACAUUUGACACUCU------AAAAUAUCAAUUGUAUGUGUAUG-CGUGUGCGGUAUAUAUUUUGAUU
....((((((...((......-((((((((.....-.(((.....((((((....))))))..)))(((.((((......------......)))).))))))))))).-)).)))))).............. ( -16.20, z-score =   1.14, R)
>dp4.chrXR_group8 7802537 133 + 9212921
AACUCUCCCCCGCCCCCUCGAUAUACUUUUUGGACUUUCAUCGUCCUUGAACAAUCCGAAGAGUAUUUAUUUGGCAUAUUUCUUGGCAAACGCGAGUUCCUAAUACAAAUCGACUGCGAUUUAUAUUUAAAUG
(((((......(((........((((((((((((..((((.......))))...))))))))))))......)))..........((....)))))))...((((.((((((....)))))).))))...... ( -29.54, z-score =  -3.11, R)
>droPer1.super_32 65814 133 - 992631
CACUCUCCCCCGCCCCCUCGAUAUACUUUUUGGACUUUCAUCGUCCUUGAACAAUCCGAAGAGUAUUUAUUUGGCAUAUUUCUUGGCAAACGCGAGUUCCUAAUACAAAUCGACUGCGAUUUAUAUUUAAAUG
.((((......(((........((((((((((((..((((.......))))...))))))))))))......)))..........((....))))))....((((.((((((....)))))).))))...... ( -28.94, z-score =  -2.88, R)
>consensus
AACUCUCCCCCGCCCCCUCGAUAUACUUUUUGGACUUUCAUCGUCCUUGAACAAUCCGAAGAGUAUUUAUUUGGCAUAUUUCUUGGCAAACGCGAGUUCCUAAUACAAAUCGACUGCGAUUUAUAUUUAAAUG
...........(((........((((((((((((..((((.......))))...))))))))))))......))).............(((....)))...((((.((((((....)))))).))))...... (-14.50 = -14.07 +  -0.43)

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 22:52:39 2011