Locus 6736

Sequence ID 3L_DroMel_CAF1
Location 18,042,241 – 18,042,338
Length 97
Max. P 0.991109
window10951 window10952

overview

Window 1

Location 18,042,241 – 18,042,338
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 78.83
Mean single sequence MFE -22.18
Consensus MFE -13.84
Energy contribution -13.64
Covariance contribution -0.20
Combinations/Pair 1.21
Mean z-score -1.91
Structure conservation index 0.62
SVM decision value 0.68
SVM RNA-class probability 0.820765
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18042241 97 + 23771897
GCGGCAAGUGGAAAACCAGUUAAUGCCAUAGGAAGACUAACUGGAAGUUUUCCACCAACUAAAGCUAAAGGAAUGCUGAAAAUAUAUUGUGCAAUAC
(((.((((((((((((((((((...((...)).....)))))))...)))))))).......(((.........))).........))))))..... ( -22.40)
>DroSec_CAF1 157035 97 + 1
GCGGCAAGUGGAAAACCAGUUAAUGGCAUAGGAAGACUAACUAGAAGUUUUCCACCAACUAAAGCUAAAAGAAUGCUGCAAAUAUUUUGUGCAAUGC
(((((((((((....(((.....)))....((((((((.......)))))))).)).)))....(.....)..)))))).................. ( -22.00)
>DroSim_CAF1 168820 97 + 1
GCGGCAAGUGGAAAACCAGUUAAUGGCAUAGGAAGACUAACUAGAAGUUUUCCACCAACUAAACCUAAAUGAAUGCUGAAAAUUUAUUGUGCAAUUC
((((..(((((....(((.....)))....((((((((.......)))))))).)).)))...))..(((((((.......)))))))..))..... ( -20.30)
>DroEre_CAF1 157149 79 + 1
GCGGCAAGUGGAAAACCAGUUAAUGGCUUAGGAGGACCAACUGCAAGUUUUCCACCAGCUAAA-------AUAUA-----------UUUCGCAAUGC
..(((..(((((((((((((...(((((.....)).)))))))...)))))))))..)))...-------.....-----------........... ( -20.80)
>DroYak_CAF1 164261 86 + 1
GCGGCAAGUGGAAAACCAGUUAAUGGCAUACGAAGAUCAACUGAAGGUUUUCCACCAGCCAAAGGUAGAAGAAUG-----------CUCCGCAAUGC
(((((..((((((((((.((.....)).........((....)).))))))))))..)))...((.((.......-----------))))))..... ( -25.40)
>consensus
GCGGCAAGUGGAAAACCAGUUAAUGGCAUAGGAAGACUAACUGGAAGUUUUCCACCAACUAAAGCUAAAAGAAUGCUG_AAAU_U_UUGUGCAAUGC
(((..((.(((....))).))..(((....((((((((.......)))))))).)))................................)))..... (-13.84 = -13.64 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,042,241 – 18,042,338
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 78.83
Mean single sequence MFE -23.85
Consensus MFE -20.44
Energy contribution -19.56
Covariance contribution -0.88
Combinations/Pair 1.20
Mean z-score -2.39
Structure conservation index 0.86
SVM decision value 2.25
SVM RNA-class probability 0.991109
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18042241 97 - 23771897
GUAUUGCACAAUAUAUUUUCAGCAUUCCUUUAGCUUUAGUUGGUGGAAAACUUCCAGUUAGUCUUCCUAUGGCAUUAACUGGUUUUCCACUUGCCGC
.....((.............(((.........)))...((.(((((((((...(((((((((((......)).)))))))))))))))))).)).)) ( -24.20)
>DroSec_CAF1 157035 97 - 1
GCAUUGCACAAAAUAUUUGCAGCAUUCUUUUAGCUUUAGUUGGUGGAAAACUUCUAGUUAGUCUUCCUAUGCCAUUAACUGGUUUUCCACUUGCCGC
((..((((.........))))))...............((.(((((((((((...(((((((...........)))))))))))))))))).))... ( -21.90)
>DroSim_CAF1 168820 97 - 1
GAAUUGCACAAUAAAUUUUCAGCAUUCAUUUAGGUUUAGUUGGUGGAAAACUUCUAGUUAGUCUUCCUAUGCCAUUAACUGGUUUUCCACUUGCCGC
((((.((..............)))))).....(((......(((((((((((...(((((((...........)))))))))))))))))).))).. ( -22.34)
>DroEre_CAF1 157149 79 - 1
GCAUUGCGAAA-----------UAUAU-------UUUAGCUGGUGGAAAACUUGCAGUUGGUCCUCCUAAGCCAUUAACUGGUUUUCCACUUGCCGC
.....((((((-----------.....-------))).((.(((((((((((......((((........))))......))))))))))).))))) ( -22.70)
>DroYak_CAF1 164261 86 - 1
GCAUUGCGGAG-----------CAUUCUUCUACCUUUGGCUGGUGGAAAACCUUCAGUUGAUCUUCGUAUGCCAUUAACUGGUUUUCCACUUGCCGC
.....((((((-----------....)))).......(((.(((((((((((...(((((((...........)))))))))))))))))).))))) ( -28.10)
>consensus
GCAUUGCACAA_A_AUUU_CAGCAUUCUUUUAGCUUUAGUUGGUGGAAAACUUCCAGUUAGUCUUCCUAUGCCAUUAACUGGUUUUCCACUUGCCGC
......................................((.((((((((((...((((((((...........)))))))))))))))))).))... (-20.44 = -19.56 +  -0.88)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:44 2006