Locus 3605

Sequence ID dm3.chr2R
Location 6,648,066 – 6,648,240
Length 174
Max. P 0.997920
window4946 window4947

overview

Window 6

Location 6,648,066 – 6,648,240
Length 174
Sequences 3
Columns 188
Reading direction forward
Mean pairwise identity 87.52
Shannon entropy 0.16607
G+C content 0.44465
Mean single sequence MFE -61.61
Consensus MFE -49.56
Energy contribution -51.12
Covariance contribution 1.56
Combinations/Pair 1.04
Mean z-score -3.92
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.21
SVM RNA-class probability 0.997920
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6648066 174 + 21146708
GUGUAUGCUUAAGCGGCUAAUUAGACUCGCGACCCUCCAACAAAACCGGAGGCAUACAUAUAUGACCACUUGGCUCGGGGUUAAGCCUGGCCAAGUGGUCA--------UACGUGCAACUAUACAAGUGCUCCCAUAUGUAGCCAUAUUCAUAUAUAU------AAAUUAUAUGAAGACACCCAGGUU
((((..((....))(((....(((...((((..(((((.........)))))........((((((((((((((.((((......))))))))))))))))--------))))))...)))((((.(((....))).)))))))...((((((((...------....)))))))).))))....... ( -61.70, z-score =  -4.43, R)
>droYak2.chr2R 18629045 175 - 21139217
GUGUGUGUGUAAGCGGCUAAUUAGACUCGCGACCCUCCAACAAAACCGGAGGCAU------AUGACCACUUGGCUCGGGGUUAAGCCUGGCCAAGUGGCCAAGUGGCCAUACGUGCAACUAUACGUGUGCUCC-AUAUGCAGUCAUAUUCAUAUAUAU------AAAUUAUAUAAAGACACACAGGUC
.(((((((.(..((((((....)).).)))(((.((((.........))))((((------(((.(((((((((.((((......)))))))))))))......(((.(((((((......)))))))))).)-)))))).))).......((((((.------....)))))).).))))))).... ( -63.50, z-score =  -3.53, R)
>droSec1.super_1 4228023 175 + 14215200
GUGUGUGUGUAAGCGGCUAAUUAGACUCGCGACCCUCCAACAAAACCGGAGGCAU----AUAUGACCACUUGGCUCGGGGUUAAGCCUGGACAAGUGGUCA--------UACGUGCAACUAUACAAGUGCUCC-AUAAGUAGUCAUAUUCAUAUAUAUGUAUAUAAAUUAUAUGAAGACACACAGGUU
.(.(((((((....(((((.(((....(((....((((.........))))(((.----.((((((((((((..(((((......))))).))))))))))--------))..)))..........)))....-.))).)))))...((((((((.............)))))))).))))))).).. ( -59.62, z-score =  -3.82, R)
>consensus
GUGUGUGUGUAAGCGGCUAAUUAGACUCGCGACCCUCCAACAAAACCGGAGGCAU____AUAUGACCACUUGGCUCGGGGUUAAGCCUGGCCAAGUGGUCA________UACGUGCAACUAUACAAGUGCUCC_AUAUGUAGUCAUAUUCAUAUAUAU______AAAUUAUAUGAAGACACACAGGUU
.(((((((......((((...(((...((((..(((((.........)))))..........((((((((((((.((((......))))))))))))))))..........))))...))).......((........))))))...((((((((.............)))))))).))))))).... (-49.56 = -51.12 +   1.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,648,066 – 6,648,240
Length 174
Sequences 3
Columns 188
Reading direction reverse
Mean pairwise identity 87.52
Shannon entropy 0.16607
G+C content 0.44465
Mean single sequence MFE -61.17
Consensus MFE -49.40
Energy contribution -49.52
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -3.43
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.79
SVM RNA-class probability 0.995365
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6648066 174 - 21146708
AACCUGGGUGUCUUCAUAUAAUUU------AUAUAUAUGAAUAUGGCUACAUAUGGGAGCACUUGUAUAGUUGCACGUA--------UGACCACUUGGCCAGGCUUAACCCCGAGCCAAGUGGUCAUAUAUGUAUGCCUCCGGUUUUGUUGGAGGGUCGCGAGUCUAAUUAGCCGCUUAAGCAUACAC
.......((((.((((((((....------...))))))))...(((((...((...((.((((((.....((((..((--------((((((((((((..((.......))..))))))))))))))..))))..(((((((.....)))))))...)))))))).)))))))((....))..)))) ( -62.00, z-score =  -3.09, R)
>droYak2.chr2R 18629045 175 + 21139217
GACCUGUGUGUCUUUAUAUAAUUU------AUAUAUAUGAAUAUGACUGCAUAU-GGAGCACACGUAUAGUUGCACGUAUGGCCACUUGGCCACUUGGCCAGGCUUAACCCCGAGCCAAGUGGUCAU------AUGCCUCCGGUUUUGUUGGAGGGUCGCGAGUCUAAUUAGCCGCUUACACACACAC
.....(((((.((((((((.(.((------((((......)))))).)..))))-)))))))))(((.(((.((.(((((((((((((((((....)))).(((((......)))))))))))))))------)))(((((((.....)))))))(.(....).)......)).))))))........ ( -65.60, z-score =  -3.96, R)
>droSec1.super_1 4228023 175 - 14215200
AACCUGUGUGUCUUCAUAUAAUUUAUAUACAUAUAUAUGAAUAUGACUACUUAU-GGAGCACUUGUAUAGUUGCACGUA--------UGACCACUUGUCCAGGCUUAACCCCGAGCCAAGUGGUCAUAU----AUGCCUCCGGUUUUGUUGGAGGGUCGCGAGUCUAAUUAGCCGCUUACACACACAC
....((((((((((((((....((((((.(((....))).)))))).....)))-)))).....(((.(((.((..(((--------(((((((((.....(((((......)))))))))))))))))----...(((((((.....)))))))(.(....).)......)).))))))))))))). ( -55.90, z-score =  -3.25, R)
>consensus
AACCUGUGUGUCUUCAUAUAAUUU______AUAUAUAUGAAUAUGACUACAUAU_GGAGCACUUGUAUAGUUGCACGUA________UGACCACUUGGCCAGGCUUAACCCCGAGCCAAGUGGUCAUAU____AUGCCUCCGGUUUUGUUGGAGGGUCGCGAGUCUAAUUAGCCGCUUACACACACAC
....(((((((.((((((((.............))))))))...............((((.((..((.(.((((((...........((((((((((((..((.......))..))))))))))))..........(((((((.....))))))))).)))).).))...))..))))..))))))). (-49.40 = -49.52 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:13:21 2011