Locus 9175

Sequence ID 3R_DroMel_CAF1
Location 24,474,743 – 24,474,881
Length 138
Max. P 0.985838
window14677 window14678

overview

Window 7

Location 24,474,743 – 24,474,853
Length 110
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 94.84
Mean single sequence MFE -43.02
Consensus MFE -38.72
Energy contribution -38.76
Covariance contribution 0.04
Combinations/Pair 1.08
Mean z-score -1.76
Structure conservation index 0.90
SVM decision value 2.02
SVM RNA-class probability 0.985838
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24474743 110 + 27905053
CGCUUUAAAGCAAUCCGCAACCGAACAGGAAAAGUUUGCUGGGCCAAGUUCGCGCCCAGCGCCCAAGUGGUGGGUGGC-GGUUGCAUGGGCAUGUUGCAACUAGCAGCGCA
.((((....((((.((((..((.....))........((((((((......).)))))))(((((.....))))).))-))))))..))))..(((((.....)))))... ( -44.60)
>DroSec_CAF1 17834 110 + 1
CGCUUUAAAGCAAUCCGGAAGCGAACAGGAAAAGUUUGCUGGGCCAAGUUCGCGCCCAGCGCCCAAGUGGUGGGUGGC-GGUUGCAUGGGCAUGUUGCAACUAGCAGCGCA
.((((....((((.(((...((((((.((...((....))...))..))))))(((((.(((....))).)))))..)-))))))..))))..(((((.....)))))... ( -42.90)
>DroSim_CAF1 29646 110 + 1
CGCUUUAAAGCAAUCCGCAAGCGAACAGGAAAAGUUUGCUGGGCCAAGUUCGCGCCCAGCGCCCAAGUGGUGGGUGGC-GGUUGCAUGGGCAUGUUGCAACUAGCAGCGCA
.((((....((((.((((..((((((.((...((....))...))..))))))(((((.(((....))).))))).))-))))))..))))..(((((.....)))))... ( -46.50)
>DroEre_CAF1 21436 110 + 1
CGCUUUAAAGCAAUCCGCAACCGAACAGGAAAAGUUUGCUGGGCCAAGUUCGCGCCCAGUGCCCAAGUGGUGGGUGGC-UGUUGCAUGGGUAUGUUGCAAGUUGCAGCGGG
((((.....(((((..((((((((((.......)))))(((((((......).))))))((((((.(..(..(....)-..)..).)))))).)))))..))))))))).. ( -41.90)
>DroYak_CAF1 27895 111 + 1
CGCUUUAAAGCAAUCCGCAACUGAACAGGAAAAGUUUGCUGGGCCAAGUUCGCGCCCAGUGCCCAAGUGGUGGGUGGCAUGUUGCAUGGGCAUGUUGCAACUUGCAGCGGC
.(((....)))...((((....((((.......))))((((((((......).)))))))(((((.....))))).(((.((((((.........)))))).))).)))). ( -39.20)
>consensus
CGCUUUAAAGCAAUCCGCAACCGAACAGGAAAAGUUUGCUGGGCCAAGUUCGCGCCCAGCGCCCAAGUGGUGGGUGGC_GGUUGCAUGGGCAUGUUGCAACUAGCAGCGCA
.((((....((((((.((...(((((.((...((....))...))..)))))((((((.(((....))).)))))))).))))))..)))).((((((.....)))))).. (-38.72 = -38.76 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 24,474,781 – 24,474,881
Length 100
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 88.56
Mean single sequence MFE -44.58
Consensus MFE -33.68
Energy contribution -34.44
Covariance contribution 0.76
Combinations/Pair 1.03
Mean z-score -1.58
Structure conservation index 0.76
SVM decision value 0.09
SVM RNA-class probability 0.579726
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24474781 100 + 27905053
CUGGGCCAAGUUCGCGCCCAGCGCCCAAGUGGUGGGUGGC-GGUUGCAUGGGCAUGUUGCAACUAGCAGCGCACCACUGGCAAC-------UGGCAACUAGCAUGUGC--
(((((((......).)))))).(((..(((((((.((.((-(((((((.........))))))).)).)).))))))))))...-------..((.....))......-- ( -42.20)
>DroSec_CAF1 17872 107 + 1
CUGGGCCAAGUUCGCGCCCAGCGCCCAAGUGGUGGGUGGC-GGUUGCAUGGGCAUGUUGCAACUAGCAGCGCACCACUGGCAACUGGCAACUGGCAACUUGCAUGUGC--
.((((((......).)))))((((.(((((.((.((((.(-((((((.(((((..(((((.....))))))).)))...))))))).).))).)).)))))...))))-- ( -46.50)
>DroSim_CAF1 29684 100 + 1
CUGGGCCAAGUUCGCGCCCAGCGCCCAAGUGGUGGGUGGC-GGUUGCAUGGGCAUGUUGCAACUAGCAGCGCACCACUGGCAAC-------UGGCAACUUGCAUGUGC--
(((((((......).)))))).(((..(((((((.((.((-(((((((.........))))))).)).)).))))))))))...-------..((.....))......-- ( -42.50)
>DroEre_CAF1 21474 107 + 1
CUGGGCCAAGUUCGCGCCCAGUGCCCAAGUGGUGGGUGGC-UGUUGCAUGGGUAUGUUGCAAGUUGCAGCGGGCAACUGUUAACUGGCAACCGGCAACUUGCAUGUGC--
(((((((......).))))))((((((.(..(..(....)-..)..).))))))...(((((((((((((((....)))))..(.(....).))))))))))).....-- ( -48.30)
>DroYak_CAF1 27933 110 + 1
CUGGGCCAAGUUCGCGCCCAGUGCCCAAGUGGUGGGUGGCAUGUUGCAUGGGCAUGUUGCAACUUGCAGCGGCCAACUGGUAACUGGUAACUGGGAACUUGCAUGUGCUG
...(((((.((..(..((((((..(((..((.(((.((((.(((((((...((.....))....))))))))))).))).))..)))..))))))..)..)).)).))). ( -43.40)
>consensus
CUGGGCCAAGUUCGCGCCCAGCGCCCAAGUGGUGGGUGGC_GGUUGCAUGGGCAUGUUGCAACUAGCAGCGCACCACUGGCAACUGG_AACUGGCAACUUGCAUGUGC__
(((((((......).))))))((((((.....))))))((.((((((.(((...((((((.....))))))..)))..(....).........)))))).))........ (-33.68 = -34.44 +   0.76)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:28:14 2006