Locus 4907

Sequence ID 3R_DroMel_CAF1
Location 12,887,749 – 12,887,854
Length 105
Max. P 0.848544
window8031 window8032

overview

Window 1

Location 12,887,749 – 12,887,854
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 89.29
Mean single sequence MFE -30.76
Consensus MFE -29.50
Energy contribution -29.70
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.96
SVM decision value 0.78
SVM RNA-class probability 0.848544
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12887749 105 + 27905053
GGGAACACAAUUCCAGGAAUUGUAACGACGAGUGGUCCCGCGACCGGUGCUUUGGUCUUUGGACAUCGCAGUUCCAUUGGCUCUCCGACUCCGACCGAUUCCGCC
.((((((((((((...)))))))...(.(((...((((...((((((....))))))...)))).)))).)))))(((((.((.........)))))))...... ( -31.40)
>DroSec_CAF1 5527 84 + 1
GGGAACACAAUUCCAGGAAUUGUAACGACGAGUGGUCCCGCGACCGGUGCUUUGGUCUUUGGACAUCGCGGUUCCAUUGGCUCU---------------------
.((((((((((((...)))))))..((.(((...((((...((((((....))))))...)))).)))))))))).........--------------------- ( -30.60)
>DroSim_CAF1 4584 84 + 1
GGGAACACAAUUCCAGGAAUUGUAACGACGAGUGGUCCCGCGACCGGUGCUUUGGUCUUUGGACAUCGCGGUUCCAUUGGCUUU---------------------
.((((((((((((...)))))))..((.(((...((((...((((((....))))))...)))).)))))))))).........--------------------- ( -30.60)
>DroEre_CAF1 3934 86 + 1
GGGAACACAAUUCCAGGAAUUGUAACGACGAGUGGUCCCGCGACCGGUGCUUUGGUCUUUGGACAUCGCGGUUCCAUUGGCUCUU-------------------U
.((((((((((((...)))))))..((.(((...((((...((((((....))))))...)))).))))))))))..........-------------------. ( -30.60)
>DroYak_CAF1 5562 86 + 1
GGGAACACAAUUCCAGGAAUUGUAACGACGAGUGGUCCCGCGACCGGUGCUUUGGUCUUUGGACAUCGCGGUUCCAUUGGCUCUU-------------------U
.((((((((((((...)))))))..((.(((...((((...((((((....))))))...)))).))))))))))..........-------------------. ( -30.60)
>consensus
GGGAACACAAUUCCAGGAAUUGUAACGACGAGUGGUCCCGCGACCGGUGCUUUGGUCUUUGGACAUCGCGGUUCCAUUGGCUCU_____________________
.((((((((((((...)))))))..((.(((...((((...((((((....))))))...)))).)))))))))).............................. (-29.50 = -29.70 +   0.20)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 2

Location 12,887,749 – 12,887,854
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 89.29
Mean single sequence MFE -27.66
Consensus MFE -26.20
Energy contribution -26.04
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.30
Structure conservation index 0.95
SVM decision value 0.45
SVM RNA-class probability 0.742560
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12887749 105 - 27905053
GGCGGAAUCGGUCGGAGUCGGAGAGCCAAUGGAACUGCGAUGUCCAAAGACCAAAGCACCGGUCGCGGGACCACUCGUCGUUACAAUUCCUGGAAUUGUGUUCCC
(((((....(((((((((((.((..((...))..)).)))).)))...((((........))))....))))..)))))..((((((((...))))))))..... ( -33.10)
>DroSec_CAF1 5527 84 - 1
---------------------AGAGCCAAUGGAACCGCGAUGUCCAAAGACCAAAGCACCGGUCGCGGGACCACUCGUCGUUACAAUUCCUGGAAUUGUGUUCCC
---------------------.........((((((((((.((((...((((........))))...))))...))).))..(((((((...)))))))))))). ( -26.30)
>DroSim_CAF1 4584 84 - 1
---------------------AAAGCCAAUGGAACCGCGAUGUCCAAAGACCAAAGCACCGGUCGCGGGACCACUCGUCGUUACAAUUCCUGGAAUUGUGUUCCC
---------------------.........((((((((((.((((...((((........))))...))))...))).))..(((((((...)))))))))))). ( -26.30)
>DroEre_CAF1 3934 86 - 1
A-------------------AAGAGCCAAUGGAACCGCGAUGUCCAAAGACCAAAGCACCGGUCGCGGGACCACUCGUCGUUACAAUUCCUGGAAUUGUGUUCCC
.-------------------..........((((((((((.((((...((((........))))...))))...))).))..(((((((...)))))))))))). ( -26.30)
>DroYak_CAF1 5562 86 - 1
A-------------------AAGAGCCAAUGGAACCGCGAUGUCCAAAGACCAAAGCACCGGUCGCGGGACCACUCGUCGUUACAAUUCCUGGAAUUGUGUUCCC
.-------------------..........((((((((((.((((...((((........))))...))))...))).))..(((((((...)))))))))))). ( -26.30)
>consensus
_____________________AGAGCCAAUGGAACCGCGAUGUCCAAAGACCAAAGCACCGGUCGCGGGACCACUCGUCGUUACAAUUCCUGGAAUUGUGUUCCC
..............................((((((((((.((((...((((........))))...))))...))).))..(((((((...)))))))))))). (-26.20 = -26.04 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:44 2006