Locus 13176

Sequence ID dm3.chrX
Location 4,817,572 – 4,817,730
Length 158
Max. P 0.999779
window18111 window18112

overview

Window 1

Location 4,817,572 – 4,817,730
Length 158
Sequences 3
Columns 159
Reading direction forward
Mean pairwise identity 67.92
Shannon entropy 0.45096
G+C content 0.56003
Mean single sequence MFE -65.87
Consensus MFE -54.82
Energy contribution -54.73
Covariance contribution -0.09
Combinations/Pair 1.22
Mean z-score -3.63
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.93
SVM RNA-class probability 0.999482
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4817572 158 + 22422827
AACAAGUCCCUCC-UUCCGCUCGACAGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCGGGAGCGAACUUGUUGGAGUCAAACUACAGGCUACCAGGGCGCUACAUUCAAUAAUUAACACA
(((((((.(((((-(..((((..((((.((((((((((((..((((..((((((...))))))..))))..)))))))))))).))))..))))..))))).).)))))))((((((........)))).))........................... ( -65.10, z-score =  -5.08, R)
>droSim1.chrX 13315941 148 - 17042790
AACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACGCUGGGGCCCUUGAGAACA-----------
......(((...(((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))(((((.((..(..(.((((.......)))).)..)))))))))))....----------- ( -67.90, z-score =  -2.90, R)
>droSec1.super_4 4251393 159 - 6179234
AACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUGUUGGAGUCAAACUUCAGGCUACCAGGGCGCCUCAUUCAACUAUUAACACU
.....((((((((((((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..)))))))))...))).....(((((((........)))).)))))))...................... ( -64.60, z-score =  -2.92, R)
>consensus
AACAAGUCCCUCCCUUCCGCUCGACCGACGCUGGAGAAUCAAAGCCGGCGGAAGUAACUUCCGGCGGUUAAGAUACUCCAGCGCCGGUGAAGCGGAAGGAGCGAACUUGUUGGAGUCAAACUACAGGCUACCAGGGCGCUUCAUUCAA__AUUAACAC_
((((((((.((((.(((((((..((((..((((((((.((..(((((.((((((...)))))).)))))..)).))))))))..))))..))))))))))).)).))))))((.(((.................))).))................... (-54.82 = -54.73 +  -0.09)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,817,572 – 4,817,730
Length 158
Sequences 3
Columns 159
Reading direction reverse
Mean pairwise identity 67.92
Shannon entropy 0.45096
G+C content 0.56003
Mean single sequence MFE -70.23
Consensus MFE -52.63
Energy contribution -54.20
Covariance contribution 1.57
Combinations/Pair 1.20
Mean z-score -4.29
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.37
SVM RNA-class probability 0.999779
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4817572 158 - 22422827
UGUGUUAAUUAUUGAAUGUAGCGCCCUGGUAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCCGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCUGUCGAGCGGAA-GGAGGGACUUGUU
.(((((((((....))).))))))..(((.((.(........).)))))((((((((.((((...(((((.(((((((((((((((((..(.(((.((((((...)))))).))).)..))))))))))))))))).)))))...-)))))))))))). ( -70.60, z-score =  -5.39, R)
>droSim1.chrX 13315941 148 + 17042790
-----------UGUUCUCAAGGGCCCCAGCGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUU
-----------.........(((..(((((........)))))..)))((((((..(((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).)..)))))) ( -70.30, z-score =  -4.04, R)
>droSec1.super_4 4251393 159 + 6179234
AGUGUUAAUAGUUGAAUGAGGCGCCCUGGUAGCCUGAAGUUUGACUCCAACAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUU
.........(((..(((.((((((....)).))))...)))..)))..(((((((((..((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))).)))).))))) ( -69.80, z-score =  -3.45, R)
>consensus
_GUGUUAAU__UUGAAUGAAGCGCCCUGGUAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCUUCCGCUUCACCGGCGCUGGAGAAUCUUAACCGCCGGAAGUAACUUCCGCCGGCUUAGAUACUCCAGCGUCGGUCGAGCGGAAGGGAGGGACUUGUU
....................((((....)).))...............(((((((((.((((((((((((.(((((.((((((((.((....(((.((((((...)))))).)))....)).)))))))).))))).)))))))))).))))))))))) (-52.63 = -54.20 +   1.57)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:05 2011