Locus 2121

Sequence ID 3L_DroMel_CAF1
Location 5,808,756 – 5,808,865
Length 109
Max. P 0.999943
window3299 window3300 window3301

overview

Window 9

Location 5,808,756 – 5,808,846
Length 90
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 89.96
Mean single sequence MFE -17.42
Consensus MFE -13.27
Energy contribution -13.51
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -1.57
Structure conservation index 0.76
SVM decision value 0.11
SVM RNA-class probability 0.587789
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5808756 90 - 23771897
AAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAACAGCUAACAGCGGCAACAAGUGGCCAGGUAGUC-----GC
....((((((........))))))((((....((.(((((.................((.....))(....)..))))).))..))))-----.. ( -17.80)
>DroSec_CAF1 16694 90 - 1
AAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAACAGCUAACAGCGGCAACAAGUGGCCAAGUAGUC-----GC
....((((((........))))))((((...(((((((((.................((.....))(....)..)))).)))))))))-----.. ( -18.00)
>DroEre_CAF1 16902 83 - 1
AAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAA-------CAGCGGCAACAAGUGGCCAGGUAGUC-----GC
....((((((........))))))((((....((.(((((..((...........-------..))(....)..))))).))..))))-----.. ( -16.42)
>DroYak_CAF1 17528 90 - 1
AAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAACAGCUAACAGCGGCAACAAGUGGUCAGGUAGUC-----GC
....((((((........))))))((((...(((((((((.................((.....))(....)..)))).)))))))))-----.. ( -17.70)
>DroAna_CAF1 17010 91 - 1
AAAUAUUUUCACACAGACGAAAAUGAUUUCAAGUUGCCACCAGCGGGCAUAAUAACAG----AAGCAGCAACAAGUGGCCAGGUAGUCUGCAGGC
.............(((((((((....)))).....(((((..((..((..........----..)).)).....)))))......)))))..... ( -17.20)
>consensus
AAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAACAGCUAACAGCGGCAACAAGUGGCCAGGUAGUC_____GC
...(((((((........)))))))......(((((((((..((....................))(....)..)))).)))))........... (-13.27 = -13.51 +   0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,808,773 – 5,808,865
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 88.65
Mean single sequence MFE -23.03
Consensus MFE -18.50
Energy contribution -18.94
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.54
Structure conservation index 0.80
SVM decision value 0.29
SVM RNA-class probability 0.670166
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5808773 92 + 23771897
UGUUGCCGCUGUUAGCUGUUAUUAUGGUUGCUGGUGGCAAGUUGAAAUCAUUUUCGUGUGUGUGAAAAUAUUUUGCGGCAGAAUAGCAACAU
((((((.((..(((((.............)))))..))..(((((((..(((((((......)))))))..))).))))......)))))). ( -25.52)
>DroSec_CAF1 16711 92 + 1
UGUUGCCGCUGUUAGCUGUUAUUAUGGUUGCUGGUGGCAAGUUGAAAUCAUUUUCGUGUGUGUGAAAAUAUUUUGCGGCAGAAUAGCAACAU
((((((.((..(((((.............)))))..))..(((((((..(((((((......)))))))..))).))))......)))))). ( -25.52)
>DroEre_CAF1 16919 85 + 1
UGUUGCCGCUG-------UUAUUAUGGUUGCUGGUGGCAAGUUGAAAUCAUUUUCGUGUGUGUGAAAAUAUUUUGCGGCAGAAUAGUAACAA
..(((((((((-------((((((.......))))))))....(((((.(((((((......)))))))))))))))))))........... ( -20.80)
>DroYak_CAF1 17545 92 + 1
UGUUGCCGCUGUUAGCUGUUAUUAUGGUUGCUGGUGGCAAGUUGAAAUCAUUUUCGUGUGUGUGAAAAUAUUUUGCGGCAGAAUAGUAACAA
..((((((((..(((((((....)))))))..))))))))(((((((..(((((((......)))))))..))).))))............. ( -24.40)
>DroAna_CAF1 17032 88 + 1
UGUUGCUGCUU----CUGUUAUUAUGCCCGCUGGUGGCAACUUGAAAUCAUUUUCGUCUGUGUGAAAAUAUUUUGCGGCAUCUCGCUACCAU
...((((((..----.........(((((....).))))....(((((.(((((((......))))))))))))))))))............ ( -18.90)
>consensus
UGUUGCCGCUGUUAGCUGUUAUUAUGGUUGCUGGUGGCAAGUUGAAAUCAUUUUCGUGUGUGUGAAAAUAUUUUGCGGCAGAAUAGUAACAU
..(((((((.......((((((((.......))))))))....(((((.(((((((......)))))))))))))))))))........... (-18.50 = -18.94 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,808,773 – 5,808,865
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 88.65
Mean single sequence MFE -17.46
Consensus MFE -16.78
Energy contribution -16.66
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -2.89
Structure conservation index 0.96
SVM decision value 4.73
SVM RNA-class probability 0.999943
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5808773 92 - 23771897
AUGUUGCUAUUCUGCCGCAAAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAACAGCUAACAGCGGCAACA
............((((((....(((((((........)))))))........((((.....))))..................))))))... ( -17.90)
>DroSec_CAF1 16711 92 - 1
AUGUUGCUAUUCUGCCGCAAAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAACAGCUAACAGCGGCAACA
............((((((....(((((((........)))))))........((((.....))))..................))))))... ( -17.90)
>DroEre_CAF1 16919 85 - 1
UUGUUACUAUUCUGCCGCAAAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAA-------CAGCGGCAACA
............((((((....(((((((........)))))))........((((.....)))).........-------..))))))... ( -17.90)
>DroYak_CAF1 17545 92 - 1
UUGUUACUAUUCUGCCGCAAAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAACAGCUAACAGCGGCAACA
............((((((....(((((((........)))))))........((((.....))))..................))))))... ( -17.90)
>DroAna_CAF1 17032 88 - 1
AUGGUAGCGAGAUGCCGCAAAAUAUUUUCACACAGACGAAAAUGAUUUCAAGUUGCCACCAGCGGGCAUAAUAACAG----AAGCAGCAACA
.((((((((......)))....(((((((........))))))).........)))))...((..((..........----..)).)).... ( -15.70)
>consensus
AUGUUACUAUUCUGCCGCAAAAUAUUUUCACACACACGAAAAUGAUUUCAACUUGCCACCAGCAACCAUAAUAACAGCUAACAGCGGCAACA
............((((((....(((((((........)))))))........((((.....))))..................))))))... (-16.78 = -16.66 +  -0.12)

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 10:24:53 2006