Locus 13177

Sequence ID dm3.chrX
Location 4,817,857 – 4,818,021
Length 164
Max. P 0.999856
window18113 window18114

overview

Window 3

Location 4,817,857 – 4,818,021
Length 164
Sequences 3
Columns 165
Reading direction forward
Mean pairwise identity 64.85
Shannon entropy 0.49928
G+C content 0.55169
Mean single sequence MFE -65.47
Consensus MFE -54.09
Energy contribution -54.33
Covariance contribution 0.24
Combinations/Pair 1.26
Mean z-score -3.69
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.06
SVM RNA-class probability 0.999594
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4817857 164 + 22422827
CAAGUCCCUCC-UUCCGCUCGACAGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCGGGAGCGAACUUGUUGGAGUCAAACUACAGGCUACCAGGGCGCUACAUUCAAUAAUUAACACACUAAUAAU
(((((.(((((-(..((((..((((.((((((((((((..((((..((((((...))))))..))))..)))))))))))).))))..))))..))))).).)))))((((((((........)))).))))................................. ( -63.90, z-score =  -4.97, R)
>droSim1.chrX 13316209 146 - 17042790
CAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACGCUGGGGCCCUUGAGAACA-------------------
....(((...(((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))(((((.((..(..(.((((.......)))).)..)))))))))))....------------------- ( -67.90, z-score =  -2.85, R)
>droSec1.super_4 4252445 165 - 6179234
CAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUGUUGGAGUCAAACUUCAGGCUACCAGGGCGCCUCAAUUAACUAUUAACACUACAAUAUU
...((((((((((((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..)))))))))...))).....(((((((........)))).))))))).............................. ( -64.60, z-score =  -3.25, R)
>consensus
CAAGUCCCUCCCUUCCGCUCGACCGACGCUGGAGAAUCAAAGCCGGCGGAAGUAACUUCCGGCGGUUAAGAUACUCCAGCGCCGGUGAAGCGGAAGGAGCGAACUUGUUGGAGUCAAACUACAGGCUACCAGGGCGCUUCAAUAAA__AUUAACAC___AAUA_U
...((((((((.(((((((..((((..((((((((.((..(((((.((((((...)))))).)))))..)).))))))))..))))..))))))))))).........(((((((........)))).))))))).............................. (-54.09 = -54.33 +   0.24)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,817,857 – 4,818,021
Length 164
Sequences 3
Columns 165
Reading direction reverse
Mean pairwise identity 64.85
Shannon entropy 0.49928
G+C content 0.55169
Mean single sequence MFE -69.30
Consensus MFE -50.23
Energy contribution -51.80
Covariance contribution 1.57
Combinations/Pair 1.21
Mean z-score -4.26
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.59
SVM RNA-class probability 0.999856
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4817857 164 - 22422827
AUUAUUAGUGUGUUAAUUAUUGAAUGUAGCGCCCUGGUAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCCGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCUGUCGAGCGGAA-GGAGGGACUUG
.(((((((.(((((((((....))).)))))).)))))))..................(((((((.((((...(((((.(((((((((((((((((..(.(((.((((((...)))))).))).)..))))))))))))))))).)))))...-))))))))))) ( -72.40, z-score =  -5.87, R)
>droSim1.chrX 13316209 146 + 17042790
-------------------UGUUCUCAAGGGCCCCAGCGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUG
-------------------.........(((..(((((........)))))..)))..((((..(((((.(((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))))).)..)))) ( -67.90, z-score =  -3.54, R)
>droSec1.super_4 4252445 165 + 6179234
AAUAUUGUAGUGUUAAUAGUUAAUUGAGGCGCCCUGGUAGCCUGAAGUUUGACUCCAACAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUG
..........((((...((((((((.((((((....)).)))).))..))))))..)))).((((..((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).)))))).)))).... ( -67.60, z-score =  -3.36, R)
>consensus
A_UAUU___GUGUUAAU__UUAAAUGAAGCGCCCUGGUAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCUUCCGCUUCACCGGCGCUGGAGAAUCUUAACCGCCGGAAGUAACUUCCGCCGGCUUAGAUACUCCAGCGUCGGUCGAGCGGAAGGGAGGGACUUG
............................((((....)).)).................(((((((.((((((((((((.(((((.((((((((.((....(((.((((((...)))))).)))....)).)))))))).))))).)))))))))).))))))))) (-50.23 = -51.80 +   1.57)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:07 2011