Locus 2468

Sequence ID 3R_DroMel_CAF1
Location 6,800,411 – 6,800,570
Length 159
Max. P 0.953179
window4041 window4042 window4043

overview

Window 1

Location 6,800,411 – 6,800,530
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 98.55
Mean single sequence MFE -34.32
Consensus MFE -31.07
Energy contribution -30.93
Covariance contribution -0.14
Combinations/Pair 1.03
Mean z-score -1.04
Structure conservation index 0.91
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6800411 119 + 27905053
CUGGCCAGGGGACAACCUGGCGUAUGCGCAACUUUAAUAACAUGAGCAGCAGCUGCAAAAGUUUCGCCUGUCAGG-GGGAGCAAGUUUAAUGCAGCAUGUAAAUAUUGUCAUGACACACG
...((((((......))))))...................(((((.(((((((((((((.(((((.((.....))-.)))))...))...)))))).)))......)))))))....... ( -34.70)
>DroSec_CAF1 59029 119 + 1
CUGGCCAGGGGACAACCUGGCGUAUGCGCAACUUUAAUAACAUGAGCAGCAGCUGCAAAAGUUUCGCCUGUCAAG-GGGAGCAAGUUUAAUGCAGCAUGUAAAUAUUGUCAUGACACACG
...((((((......))))))...................(((((.(((((((((((((.(((((.(((....))-))))))...))...)))))).)))......)))))))....... ( -34.30)
>DroSim_CAF1 64164 119 + 1
CAGGCCAGGGGACAACCUGGCGUAUGCGCAACUUUAAUAACAUGAGCAGCAGCUGCAAAAGUUUCGCCUGUCAAG-GGGAGCAAGUUUAAUGCAGCAUGUAAAUAUUGUCAUGACACACG
...((((((......))))))...................(((((.(((((((((((((.(((((.(((....))-))))))...))...)))))).)))......)))))))....... ( -34.30)
>DroEre_CAF1 44291 119 + 1
CUGGCCAGGGGACAACCUGGCGUAUGCGCAACUUUAAUAACAUGAGCAGCAGCUGCAAAAGUUUCGCCUGUCAAG-GGGAGCAAGUUUAAUGCAGCAUGUAAAUAUUGUCAUGACACACG
...((((((......))))))...................(((((.(((((((((((((.(((((.(((....))-))))))...))...)))))).)))......)))))))....... ( -34.30)
>DroYak_CAF1 57158 119 + 1
CUGGCCAGGGGACAACCUGGCGUAUGCGCAACUUUAAUAACAUGAGCAGCAGCUGCAAAAGUUUCGCCUGUCAUG-GGGAGCAAGUUUAAUGCAGCAUGUAAAUAUUGUCAUGACACACG
...((((((......))))))((..(((.((((((.......(((((....))).)))))))).))).(((((((-(.(((((.(((......))).))).....)).)))))))).)). ( -33.61)
>DroAna_CAF1 16833 120 + 1
CUGGCCAGGGGACAACCUGGCGUAUGCGCAACUUUAAUAACAUGAGCAGCAGCUGCAAAAGUUUUGCCUGUCAGGAGGGAGCAAGUUUAAUGCAGCAUGUAAAUAUUGUCAUGACACACG
...((((((......))))))...................(((((.(((((((((((.....(((((((.(....).)).))))).....)))))).)))......)))))))....... ( -34.70)
>consensus
CUGGCCAGGGGACAACCUGGCGUAUGCGCAACUUUAAUAACAUGAGCAGCAGCUGCAAAAGUUUCGCCUGUCAAG_GGGAGCAAGUUUAAUGCAGCAUGUAAAUAUUGUCAUGACACACG
...((((((......))))))...................(((((.((((((((((((((.((.(.(((.......))).).)).)))..)))))).)))......)))))))....... (-31.07 = -30.93 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,800,411 – 6,800,530
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 98.55
Mean single sequence MFE -32.48
Consensus MFE -32.49
Energy contribution -32.35
Covariance contribution -0.14
Combinations/Pair 1.04
Mean z-score -1.03
Structure conservation index 1.00
SVM decision value 1.43
SVM RNA-class probability 0.953179
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6800411 119 - 27905053
CGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CCUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUGUUAUUAAAGUUGCGCAUACGCCAGGUUGUCCCCUGGCCAG
.((((((.................((((((......(((((...-.......)))))......)))))).((.(((...........))).))))))))((((((......))))))... ( -32.40)
>DroSec_CAF1 59029 119 - 1
CGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CUUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUGUUAUUAAAGUUGCGCAUACGCCAGGUUGUCCCCUGGCCAG
.((((((.................((((((......(((((...-.......)))))......)))))).((.(((...........))).))))))))((((((......))))))... ( -32.40)
>DroSim_CAF1 64164 119 - 1
CGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CUUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUGUUAUUAAAGUUGCGCAUACGCCAGGUUGUCCCCUGGCCUG
.((((((.................((((((......(((((...-.......)))))......)))))).((.(((...........))).))))))))((((((......))))))... ( -32.40)
>DroEre_CAF1 44291 119 - 1
CGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CUUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUGUUAUUAAAGUUGCGCAUACGCCAGGUUGUCCCCUGGCCAG
.((((((.................((((((......(((((...-.......)))))......)))))).((.(((...........))).))))))))((((((......))))))... ( -32.40)
>DroYak_CAF1 57158 119 - 1
CGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CAUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUGUUAUUAAAGUUGCGCAUACGCCAGGUUGUCCCCUGGCCAG
(((.(((((((....(((....)))..(((.......)))....-))))))).)))........((((((...((....))......))))))......((((((......))))))... ( -32.70)
>DroAna_CAF1 16833 120 - 1
CGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCCUCCUGACAGGCAAAACUUUUGCAGCUGCUGCUCAUGUUAUUAAAGUUGCGCAUACGCCAGGUUGUCCCCUGGCCAG
.((((((.................((((((......(((((...........)))))......)))))).((.(((...........))).))))))))((((((......))))))... ( -32.60)
>consensus
CGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC_CUUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUGUUAUUAAAGUUGCGCAUACGCCAGGUUGUCCCCUGGCCAG
.((((((.................((((((......(((((...........)))))......)))))).((.(((...........))).))))))))((((((......))))))... (-32.49 = -32.35 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,800,451 – 6,800,570
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 97.99
Mean single sequence MFE -33.18
Consensus MFE -30.27
Energy contribution -30.43
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.14
Structure conservation index 0.91
SVM decision value 0.31
SVM RNA-class probability 0.684809
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6800451 119 - 27905053
GUCCUCAAGAGCCUGUCAACAAAGGGCCAGUGAAAGUUUUCGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CCUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUG
........((((((((((.....(((..(((..((((((..(((((.((((..........)))).))))).)))))))))..)-)))))))))).........((((...))))))... ( -32.00)
>DroSec_CAF1 59069 119 - 1
GUCCUCGAGAGCCUGUCAACAAAGGGCCAGUGAAAGUUUUCGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CUUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUG
......(((.((((((((....((((..(((..((((((..(((((.((((..........)))).))))).))))))))).))-)))))))))).........((....))..)))... ( -33.40)
>DroSim_CAF1 64204 119 - 1
GUCCUCGAGAGCCUGUCAACAAAGGGCCAGUGAAAGUUUUCGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CUUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUG
......(((.((((((((....((((..(((..((((((..(((((.((((..........)))).))))).))))))))).))-)))))))))).........((....))..)))... ( -33.40)
>DroEre_CAF1 44331 119 - 1
GUCCUCGAGAGCCUGUCAACAAAGGGCCAGUGAAAGUUUUCGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CUUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUG
......(((.((((((((....((((..(((..((((((..(((((.((((..........)))).))))).))))))))).))-)))))))))).........((....))..)))... ( -33.40)
>DroYak_CAF1 57198 119 - 1
GUCCUCGAGAGCCUGUCAACAAAGGGCCAGUGAAAGUUUUCGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC-CAUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUG
......((((((((........))(((..(..(((((((.(((.(((((((....(((....)))..(((.......)))....-))))))).))))))))))..).)))))).)))... ( -33.60)
>DroAna_CAF1 16873 120 - 1
GUCCUCGUGAGCCUGUCAACAAAGGACCAGUGAAAGUUUUCGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCCUCCUGACAGGCAAAACUUUUGCAGCUGCUGCUCAUG
.....(((((((((((((....(((....(((((.(((.(((((...))))).))).))))).....(((.......)))..)))..)))))))).........((((...))))))))) ( -33.30)
>consensus
GUCCUCGAGAGCCUGUCAACAAAGGGCCAGUGAAAGUUUUCGUGUGUCAUGACAAUAUUUACAUGCUGCAUUAAACUUGCUCCC_CUUGACAGGCGAAACUUUUGCAGCUGCUGCUCAUG
........((((((((((.....(((..(((..((((((..(((((.((((..........)))).))))).))))))))))))...)))))))).........((((...))))))... (-30.27 = -30.43 +   0.17)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:06 2006