Locus 3954

Sequence ID 3R_DroMel_CAF1
Location 10,693,463 – 10,693,599
Length 136
Max. P 0.837375
window6337 window6338

overview

Window 7

Location 10,693,463 – 10,693,569
Length 106
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 92.58
Mean single sequence MFE -24.98
Consensus MFE -20.44
Energy contribution -20.56
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -1.64
Structure conservation index 0.82
SVM decision value 0.74
SVM RNA-class probability 0.837375
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10693463 106 + 27905053
GUUUGCAUUUAAUAUGGGCCUUAUAACAAUA--------GCCACUGUUGGCAUAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUUGCUAAGAACAAUAAAAAACAAAAGCCCAU
.............((((((......(((...--------((((((((((((...)))))).))))))...)))......(((...)))....................)))))) ( -28.10)
>DroSec_CAF1 34810 106 + 1
GUUUGCAUUUAAUAUGGGUCUUAUAACAAUA--------ACCACUGUUGGCAUAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUUGCUAAGAACAAUAAAAAACAAAAGGCCAU
................((((((...(((...--------((((((((((((...)))))).))))))...)))......(((...)))..................)))))).. ( -26.40)
>DroSim_CAF1 37264 106 + 1
GUUUGCAUUUAAUAUGGGUCUUAUAACAAUA--------GCCACUGUUGGCAUAGCCAGCUGGUGGUAGGUGUAUUAAGAGCAUUGCUAAGAACAAUAAAAAACAAAAGGCCAU
................((((((...(((...--------((((((((((((...)))))).))))))...)))......(((...)))..................)))))).. ( -26.80)
>DroEre_CAF1 32283 114 + 1
GUUUGCAUUUAAUAUGGGUCUUAUAACAAUAGCCGCAUAGCCACUGUUAGCACAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUGGCCAGGAACAAUAAAAAACAAAAGCCCAU
...(((.((((((((.(((..(......)..))).....(((((..(((((.......)))))..)).))))))))))).))).(((.....................)))... ( -23.40)
>DroYak_CAF1 27271 106 + 1
GUUUGCAUUUAAUAUAGGUCUUAUAACAAUA--------GCCACUGUUAGCAUAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUUGCCAUGAACAAUAAAAAACAAAAGCCCAU
((((((.((((((((..((......))....--------(((((..(((((.......)))))..)).))))))))))).))((((.......))))...)))).......... ( -20.20)
>consensus
GUUUGCAUUUAAUAUGGGUCUUAUAACAAUA________GCCACUGUUGGCAUAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUUGCUAAGAACAAUAAAAAACAAAAGCCCAU
...(((.(((((((((.((......))............((((((((((((...)))))).))))))...))))))))).)))............................... (-20.44 = -20.56 +   0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,693,494 – 10,693,599
Length 105
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 88.11
Mean single sequence MFE -27.52
Consensus MFE -21.22
Energy contribution -22.80
Covariance contribution 1.58
Combinations/Pair 1.07
Mean z-score -1.83
Structure conservation index 0.77
SVM decision value 0.61
SVM RNA-class probability 0.797472
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10693494 105 + 27905053
-----GCCACUGUUGGCAUAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUUGCUAAGAACAAUAAAAAACAAAAGCCCAUUUUGU-------GUGGGUAUUACUUGUGAAAACAAGG
-----((((((((((((...)))))).)))))).(((((.......))))).......................((((((.....-------))))))....(((((....))))). ( -32.50)
>DroSec_CAF1 34841 105 + 1
-----ACCACUGUUGGCAUAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUUGCUAAGAACAAUAAAAAACAAAAGGCCAUUUUGU-------GUGGGUAUUACUUGUGAAAACAAGG
-----((((((((((((...)))))).)))))).(((((.......))))).........((((....((((((.....))))))-------.....)))).(((((....))))). ( -28.10)
>DroSim_CAF1 37295 105 + 1
-----GCCACUGUUGGCAUAGCCAGCUGGUGGUAGGUGUAUUAAGAGCAUUGCUAAGAACAAUAAAAAACAAAAGGCCAUUUUGU-------GUGGGUAUUACUUGUGAAAACAAGG
-----((((((((((((...)))))).)))))).(((((.......))))).........((((....((((((.....))))))-------.....)))).(((((....))))). ( -28.40)
>DroEre_CAF1 32317 117 + 1
GCAUAGCCACUGUUAGCACAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUGGCCAGGAACAAUAAAAAACAAAAGCCCAUUUUGUGGAGAAUGUGCAUAUUACUUGCAAAAACAAGG
(((((.((..((((......(((((((..(((((....)))))..))).))))....)))).......((((((.....))))))))....)))))......((((......)))). ( -27.20)
>DroYak_CAF1 27302 112 + 1
-----GCCACUGUUAGCAUAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUUGCCAUGAACAAUAAAAAACAAAAGCCCAUUUUGUGGAGAAUGUGCAUAUUACUUGUAAAAACCGGG
-----(((((..(((((.......)))))..)).)))(((.((...(((((.(((..((.....................))..)))..)))))...)).))).............. ( -21.40)
>consensus
_____GCCACUGUUGGCAUAGCCAGCUGGUGGUAGGUGUAUUAAAAGCAUUGCUAAGAACAAUAAAAAACAAAAGCCCAUUUUGU_______GUGGGUAUUACUUGUGAAAACAAGG
.....((((((((((((...)))))).)))))).(((((.......)))))........((.......((((((.....))))))........)).......(((((....))))). (-21.22 = -22.80 +   1.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:22 2006