Locus 84

Sequence ID 2R_DroMel_CAF1
Location 1,336,751 – 1,336,902
Length 151
Max. P 0.931091
window173 window174

overview

Window 3

Location 1,336,751 – 1,336,862
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.72
Mean single sequence MFE -31.74
Consensus MFE -23.44
Energy contribution -24.96
Covariance contribution 1.52
Combinations/Pair 1.19
Mean z-score -2.31
Structure conservation index 0.74
SVM decision value 1.21
SVM RNA-class probability 0.931091
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1336751 111 + 20766785
AGUUCU-GUGUUUUACACCCCGGCGGACAAACUCAC--------ACAUUAAUUGAUUUAAUGCCUGGAACACUAGGCAAACAUCGAGCUUUGUUUGGAGCUCCCAAAAUACACAGGACAA
.(((((-((((.........(..(((((((((((..--------.((.....))......(((((((....)))))))......))).))))))))..)..........))))))))).. ( -32.81)
>DroSec_CAF1 55271 112 + 1
AGUUCUGGUGUUUUACACCCCGGCGGACAAACUCAC--------ACAUUAAUUGAUUUAAUGCCUGGAACACUAGGCAAACAGCGAGCCUUGUUUGGAGCUCCCAAAAUACACAGGGCAA
.(((((((((((((......(..(((((((.(((.(--------.((.....))......(((((((....)))))))....).)))..)))))))..).....))))))).)))))).. ( -31.00)
>DroSim_CAF1 33470 112 + 1
AGUUCUGGUGUUUUACACCCCGGCGGACAAACUCAC--------ACAUUAAUUGAUUUAAUGCCCGGAACACUAGGCAAACAGCGAGCCUUGUUUGGAGCUCCCAAAAUACACAGGGCAA
....((((((((.......((((.(((.....))..--------.((((((.....)))))))))))))))))))((.....))..(((((((((((.....)))).....))))))).. ( -29.51)
>DroEre_CAF1 36680 120 + 1
AGUUCUGUCGCUCUACCUCCCGGCGGACGAACUCACACUUACACCCAUUAAUUGAUUUAAUGCCUGGAACAGCAGGCAAAUGCCGAGCUUUGUUUGGAGCUCCCAAAAUACACAGGACAA
.(((((((.((((....(((.(((((..................))(((((.....)))))))).)))......(((....)))))))....(((((.....)))))....))))))).. ( -32.67)
>DroYak_CAF1 23905 108 + 1
AGUUCUGGUGCUUUAUGUCCAGACGGAUAAGCUCAC--------GCAUUAAUUGAUUUAAUGCCUAGAACACUAGGCAAAUACCGAGCUUUG----AGUCUCCGAAAAUACACAGGACAA
.(((((((((.(((......((((....((((((..--------..(((((.....)))))((((((....)))))).......))))))..----.))))...))).))).)))))).. ( -32.70)
>consensus
AGUUCUGGUGUUUUACACCCCGGCGGACAAACUCAC________ACAUUAAUUGAUUUAAUGCCUGGAACACUAGGCAAACACCGAGCUUUGUUUGGAGCUCCCAAAAUACACAGGACAA
.(((((((((((((......(..(((((((((((............(((((.....)))))((((((....)))))).......))).))))))))..).....))))))).)))))).. (-23.44 = -24.96 +   1.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,336,786 – 1,336,902
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.28
Mean single sequence MFE -30.98
Consensus MFE -22.80
Energy contribution -24.44
Covariance contribution 1.64
Combinations/Pair 1.10
Mean z-score -1.82
Structure conservation index 0.74
SVM decision value 0.47
SVM RNA-class probability 0.749357
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1336786 116 + 20766785
----ACAUUAAUUGAUUUAAUGCCUGGAACACUAGGCAAACAUCGAGCUUUGUUUGGAGCUCCCAAAAUACACAGGACAAGCGGAGCAUUAGCGGAUAGUCAAAUAGUGGAAAUCGAGCU
----.(((((.((((((...(((((((....)))))))........((((((((((....(((...........)))))))))))))..........)))))).)))))........... ( -30.90)
>DroSec_CAF1 55307 106 + 1
----ACAUUAAUUGAUUUAAUGCCUGGAACACUAGGCAAACAGCGAGCCUUGUUUGGAGCUCCCAAAAUACACAGGGCAAGCGGAGCAUUAGCGGAUAGUCAAAUAGUGG----------
----.(((((.((((((...(((((((....)))))))....((..(((((((((((.....)))).....)))))))..))...((....))....)))))).))))).---------- ( -34.90)
>DroSim_CAF1 33506 106 + 1
----ACAUUAAUUGAUUUAAUGCCCGGAACACUAGGCAAACAGCGAGCCUUGUUUGGAGCUCCCAAAAUACACAGGGCAAGCGGAGCAUUAGCGGAUAGUCAAAUAGUGG----------
----.(((((.(((((((((((((((.........((.....))..(((((((((((.....)))).....)))))))...))).))))))......)))))).))))).---------- ( -32.20)
>DroEre_CAF1 36720 120 + 1
ACACCCAUUAAUUGAUUUAAUGCCUGGAACAGCAGGCAAAUGCCGAGCUUUGUUUGGAGCUCCCAAAAUACACAGGACAAGCGGAACAUGGACGGAUAGUCAAGUAGUGGAAAUCGAGCU
....((((((.((((((...((((((.....((.(((....)))(((((((....)))))))..................))....)).)).))...)))))).)))))).......... ( -31.70)
>DroYak_CAF1 23941 112 + 1
----GCAUUAAUUGAUUUAAUGCCUAGAACACUAGGCAAAUACCGAGCUUUG----AGUCUCCGAAAAUACACAGGACAAGCGGAACAUUAGCGGAUAGUCAAGUUGUGGAAAGGCAGCU
----((..............(((((((....)))))))....((((((((.(----(.(.((((..(((.....(......).....)))..)))).).))))))).)))....)).... ( -25.20)
>consensus
____ACAUUAAUUGAUUUAAUGCCUGGAACACUAGGCAAACACCGAGCUUUGUUUGGAGCUCCCAAAAUACACAGGACAAGCGGAGCAUUAGCGGAUAGUCAAAUAGUGGAAA___AGCU
.....(((((.((((((...(((((((....)))))))........((((((((((....(((...........)))))))))))))..........)))))).)))))........... (-22.80 = -24.44 +   1.64)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:20 2006