Locus 5854

Sequence ID X_DroMel_CAF1
Location 15,115,337 – 15,115,481
Length 144
Max. P 0.901861
window9496 window9497 window9498 window9499

overview

Window 6

Location 15,115,337 – 15,115,442
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.39
Mean single sequence MFE -31.33
Consensus MFE -26.64
Energy contribution -27.32
Covariance contribution 0.69
Combinations/Pair 1.03
Mean z-score -1.66
Structure conservation index 0.85
SVM decision value 0.48
SVM RNA-class probability 0.752507
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15115337 105 + 22224390
AUUUGUUUGGGUUUCGGCCCGGCCU-GUGUGCAUCCACUUGUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUUCGCCGGCC--------------
........((((....))))(((((-(((((((......)).)))((..(((((((((((....)))))))))))..)))))......((((.....)))).))))-------------- ( -32.20)
>DroSec_CAF1 27054 106 + 1
AUUUGUUUGGGUUUCGGCCCGGCCCGGUGUGCAUCCACUUGUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUUCGCCGGUC--------------
......((((((....)))))).(((((((((......((((.(((...(((((((((((....)))))))))))))).)))).....))).......))))))..-------------- ( -29.61)
>DroEre_CAF1 34354 104 + 1
AUUUGUUUGGGUUUCGGCCCG-CCU-GUGUGCAUCCACUUGUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUCCGCCGGCC--------------
........((((....))))(-(((-(((((((......)).)))((..(((((((((((....)))))))))))..)))))......(((.......))).))).-------------- ( -28.20)
>DroYak_CAF1 34290 118 + 1
AUUUGUUUGGGUUUCGGCCCG-CCU-GUGUGCAUCCACUUGUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUUCGCCGGCCAACGGCCAAUGGCC
........((((....))))(-(((-(((((((......)).)))((..(((((((((((....)))))))))))..)))))......((((.....)))).((((...))))...))). ( -35.30)
>consensus
AUUUGUUUGGGUUUCGGCCCG_CCU_GUGUGCAUCCACUUGUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUUCGCCGGCC______________
........((((....))))((((..(((.(((......))))))((..(((((((((((....)))))))))))..)).........((((.....)))).)))).............. (-26.64 = -27.32 +   0.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,115,337 – 15,115,442
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.39
Mean single sequence MFE -31.20
Consensus MFE -25.04
Energy contribution -25.10
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.28
Structure conservation index 0.80
SVM decision value 1.02
SVM RNA-class probability 0.901861
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15115337 105 - 22224390
--------------GGCCGGCGAAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAACAAGUGGAUGCACAC-AGGCCGGGCCGAAACCCAAACAAAU
--------------(((((((((.....))))).....((((.((((.((((((((....)))))))).))..(((.......))).)))))).-.))))(((......)))........ ( -31.40)
>DroSec_CAF1 27054 106 - 1
--------------GACCGGCGAAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAACAAGUGGAUGCACACCGGGCCGGGCCGAAACCCAAACAAAU
--------------...((((((...((((((.(((((((.....))))))).).))))).)).....(((..(((......(((......))))))..))))))).............. ( -27.90)
>DroEre_CAF1 34354 104 - 1
--------------GGCCGGCGGAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAACAAGUGGAUGCACAC-AGG-CGGGCCGAAACCCAAACAAAU
--------------((((.((((...((.(((.......))))).((.((((((((....)))))))).))..)).......(((......)))-..)-).))))............... ( -29.60)
>DroYak_CAF1 34290 118 - 1
GGCCAUUGGCCGUUGGCCGGCGAAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAACAAGUGGAUGCACAC-AGG-CGGGCCGAAACCCAAACAAAU
((((...)))).((((((.((((...((((((.(((((((.....))))))).).))))).))...................(((......)))-..)-).))))))............. ( -35.90)
>consensus
______________GGCCGGCGAAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAACAAGUGGAUGCACAC_AGG_CGGGCCGAAACCCAAACAAAU
..............((((((((((...)))))).....((((.((((.((((((((....)))))))).))..(((.......))).))))))........))))............... (-25.04 = -25.10 +   0.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,115,376 – 15,115,481
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.11
Mean single sequence MFE -28.27
Consensus MFE -20.75
Energy contribution -20.62
Covariance contribution -0.13
Combinations/Pair 1.07
Mean z-score -1.92
Structure conservation index 0.73
SVM decision value 0.18
SVM RNA-class probability 0.623568
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15115376 105 + 22224390
GUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUUCGCCGGCC--------------AAUGUCACUCUGUGCAGCAUUU-UCCGGAAUUUUCGUGAU
(((((((..(((((((((((....)))))))))))..))..((((((.((((.....)))).((..--------------((((((((...)))..))))).-.))))))))...))))) ( -28.30)
>DroSec_CAF1 27094 105 + 1
GUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUUCGCCGGUC--------------AACGUCACUCUGUGCAGCAUUU-UCCGGAAUUUUCCUGAU
.....((..(((((((((((....)))))))))))..))......((((.(((.......((((..--------------((.(((((...)))..)).)).-.))))....))))))). ( -24.80)
>DroEre_CAF1 34392 106 + 1
GUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUCCGCCGGCC--------------AACGUCACUCUGUGCAGCAUUUUUUCGGAAUUUUCCUGAU
.....((..(((((((((((....)))))))))))..))......((((.(((..(((((...((.--------------.(((......)))...)).......)))))..))))))). ( -27.20)
>DroYak_CAF1 34328 119 + 1
GUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUUCGCCGGCCAACGGCCAAUGGCCAACGUCACUCUGUGCAGCAUUU-UCCGGAAUUUUCCUGAU
.....((..(((((((((((....)))))))))))..))......((((.(((..(((((..(((((........)))))...(.(((...)))).......-..)))))..))))))). ( -32.80)
>consensus
GUUACGGUUCAGUUUUUGACAUUCGUCAAAAAUUGUGUCACAAUUUCAGCGAACUUUUCGCCGGCC______________AACGUCACUCUGUGCAGCAUUU_UCCGGAAUUUUCCUGAU
.....((..(((((((((((....)))))))))))..))......((((.(((..(((((..(((..................)))....((.....))......)))))..))))))). (-20.75 = -20.62 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,115,376 – 15,115,481
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.11
Mean single sequence MFE -28.32
Consensus MFE -20.95
Energy contribution -20.82
Covariance contribution -0.13
Combinations/Pair 1.07
Mean z-score -1.73
Structure conservation index 0.74
SVM decision value 0.05
SVM RNA-class probability 0.559404
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15115376 105 - 22224390
AUCACGAAAAUUCCGGA-AAAUGCUGCACAGAGUGACAUU--------------GGCCGGCGAAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAAC
.((((((......(((.-.((((..((.....))..))))--------------..)))((((.....)))).....))))))..((.((((((((....)))))))).))......... ( -27.40)
>DroSec_CAF1 27094 105 - 1
AUCAGGAAAAUUCCGGA-AAAUGCUGCACAGAGUGACGUU--------------GACCGGCGAAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAAC
.((((.......((((.-.((((..((.....))..))))--------------..)))).((...((((((.(((((((.....))))))).).))))).)).....))))........ ( -26.20)
>DroEre_CAF1 34392 106 - 1
AUCAGGAAAAUUCCGAAAAAAUGCUGCACAGAGUGACGUU--------------GGCCGGCGGAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAAC
.(((((((..(((((....((((..((.....))..))))--------------......)))))..))).))))..........((.((((((((....)))))))).))......... ( -25.10)
>DroYak_CAF1 34328 119 - 1
AUCAGGAAAAUUCCGGA-AAAUGCUGCACAGAGUGACGUUGGCCAUUGGCCGUUGGCCGGCGAAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAAC
.((.(((....))).))-...(((.(..(((.(((.(((((((((........)))))))))......((((.......)))))))..((((((((....)))))))))))..).))).. ( -34.60)
>consensus
AUCAGGAAAAUUCCGGA_AAAUGCUGCACAGAGUGACGUU______________GGCCGGCGAAAAGUUCGCUGAAAUUGUGACACAAUUUUUGACGAAUGUCAAAAACUGAACCGUAAC
....(((....))).......(((.(..(((..(((((((.................(((((((...)))))))((((((.....))))))......)))))))....)))..).))).. (-20.95 = -20.82 +  -0.13)

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 11:57:58 2006