Locus 408

Sequence ID 3L_DroMel_CAF1
Location 1,193,290 – 1,193,381
Length 91
Max. P 0.738468
window596 window597

overview

Window 6

Location 1,193,290 – 1,193,381
Length 91
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 89.17
Mean single sequence MFE -27.85
Consensus MFE -19.10
Energy contribution -18.73
Covariance contribution -0.38
Combinations/Pair 1.10
Mean z-score -2.38
Structure conservation index 0.69
SVM decision value 0.44
SVM RNA-class probability 0.738468
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1193290 91 + 23771897
CUAAUGGCUGCACGCAACCCAG---CGAGUGGCCAACUUACUUUCAGCCAUAC-------CCGAAAAAGAAAUUUCU--------UUCUUCACGCGAUUUUGCGGUGGC
....((((..(.(((......)---)).)..))))...........(((((..-------..((((((((....)))--------)).))).((((....))))))))) ( -28.80)
>DroSec_CAF1 8931 91 + 1
CUAAUGGCUACACGCAACCCAG---CGAGUGGCCAACUUACUUUCAGCCGUAC-------CCGAAAAAGAAAUUUCU--------UUCUUCACGCGAUUUUGCGGUGGC
....(((((((.(((......)---)).)))))))...........((((...-------..((((((((....)))--------)).))).((((....)))).)))) ( -27.30)
>DroSim_CAF1 8326 94 + 1
CUAAUGGCUACACGCAACCCAGCGGCGAGUGGCCAACUUACUUUCAGCCGUAC-------CCGAAAAAGAAAUUUCU--------UUCUUCACGCGAUUUUGCGGUGGC
....(((((((.(((.........))).)))))))...........((((...-------..((((((((....)))--------)).))).((((....)))).)))) ( -26.20)
>DroYak_CAF1 8450 106 + 1
CUAAUGGCUACACGCAACCCAG---UGAGUGGCCAACUUACUUUCAGCCUUACUCUUCGCCCGAAAAAGAAAUUUCUUUCUUUCUUUCUUCACGCGAUUUUGCGGUGGC
......(((((.(((((...((---(((((.....)))))))..............((((..((((((((((........))))))).)))..))))..)))))))))) ( -29.10)
>consensus
CUAAUGGCUACACGCAACCCAG___CGAGUGGCCAACUUACUUUCAGCCGUAC_______CCGAAAAAGAAAUUUCU________UUCUUCACGCGAUUUUGCGGUGGC
....(((((((.((...........)).)))))))...........(((.............((((......))))................((((....))))..))) (-19.10 = -18.73 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 1,193,290 – 1,193,381
Length 91
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 89.17
Mean single sequence MFE -31.95
Consensus MFE -20.79
Energy contribution -20.60
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -2.22
Structure conservation index 0.65
SVM decision value 0.03
SVM RNA-class probability 0.550931
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1193290 91 - 23771897
GCCACCGCAAAAUCGCGUGAAGAA--------AGAAAUUUCUUUUUCGG-------GUAUGGCUGAAAGUAAGUUGGCCACUCG---CUGGGUUGCGUGCAGCCAUUAG
(((..(((......))).((((((--------(....)))))))....)-------))(((((((...((((.(..((.....)---)..).))))...)))))))... ( -32.80)
>DroSec_CAF1 8931 91 - 1
GCCACCGCAAAAUCGCGUGAAGAA--------AGAAAUUUCUUUUUCGG-------GUACGGCUGAAAGUAAGUUGGCCACUCG---CUGGGUUGCGUGUAGCCAUUAG
(((..(((......))).((((((--------(....)))))))....)-------))..(((((...((((.(..((.....)---)..).))))...)))))..... ( -30.00)
>DroSim_CAF1 8326 94 - 1
GCCACCGCAAAAUCGCGUGAAGAA--------AGAAAUUUCUUUUUCGG-------GUACGGCUGAAAGUAAGUUGGCCACUCGCCGCUGGGUUGCGUGUAGCCAUUAG
((.(((((((..(.(((.((((((--------(....)))))))..(((-------((..(((..(.......)..)))))))).))).)..))))).)).))...... ( -30.10)
>DroYak_CAF1 8450 106 - 1
GCCACCGCAAAAUCGCGUGAAGAAAGAAAGAAAGAAAUUUCUUUUUCGGGCGAAGAGUAAGGCUGAAAGUAAGUUGGCCACUCA---CUGGGUUGCGUGUAGCCAUUAG
((.(((((((..((((.(((.....((((((((....))))))))))).)))).((((..(((..(.......)..))))))).---.....))))).)).))...... ( -34.90)
>consensus
GCCACCGCAAAAUCGCGUGAAGAA________AGAAAUUUCUUUUUCGG_______GUACGGCUGAAAGUAAGUUGGCCACUCG___CUGGGUUGCGUGUAGCCAUUAG
.((.((((......))).)..............((((......))))))...........(((((...((((.(..(..........)..).))))...)))))..... (-20.79 = -20.60 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:07 2006