Locus 2343

Sequence ID X_DroMel_CAF1
Location 6,269,856 – 6,270,077
Length 221
Max. P 0.995872
window3811 window3812 window3813 window3814

overview

Window 1

Location 6,269,856 – 6,269,958
Length 102
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 78.27
Mean single sequence MFE -32.07
Consensus MFE -20.02
Energy contribution -21.65
Covariance contribution 1.63
Combinations/Pair 1.10
Mean z-score -2.03
Structure conservation index 0.62
SVM decision value 0.88
SVM RNA-class probability 0.872770
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6269856 102 - 22224390
CCUCUCCCAUUCGCA------------AAACCCAAUCCGAAAGCCAGGCCAACGCCCACCUUUUGCGACUGGGGCC-CGAAAACGAGGCCACUUGAAAG---CCAAGCCAGCGGAGAA
..(((((...(((((------------(((.......(....)...(((....)))....))))))))((((((((-((....)).)))).((((....---.)))))))).))))). ( -35.40)
>DroSim_CAF1 13406 101 - 1
CCUCUCCCAUUCGCA------------A-UCCCAAUCCGAAAGCCAGGCCAACGCCCACCUUUUGGGUUUUGGGCC-CGAAAACGAGGCCACUUGACAG---CCAAGCCAGCGGAGAA
..((((((.((((..------------.-.(((((((((((((...(((....)))...)))))))))..))))..-)))).....(((...(((....---.)))))).).))))). ( -32.20)
>DroEre_CAF1 1087 107 - 1
CCUUUCCCAUUCCCAAUCCCAUGCCC-------AAUCCAAAAGCCAGGCCAACGCCCACCUUUUGGGUUUUGGGCC-CGAAAACGAGGCCACUUGACGG---CGAAGCCGGCGUAGAA
....................(((((.-------...(((((((...(((....)))...)))))))(((..(((((-((....)).)))).)..)))((---(...)))))))).... ( -32.50)
>DroYak_CAF1 9255 118 - 1
CCUUGUCCAUUCCCAUUCCCAUUCCCAUUGCCAAAGCAAAAAGCCAGGCCAACGCCCACCUUUUGGGUUCUCGGCCCCAAAAACGAGGCCACUUGACAGCCGCCAAGCCAGCGGAGAA
..(((((................((((((((....))))((((...(((....)))...)))))))).....((((.(......).))))....)))))((((.......)))).... ( -28.20)
>consensus
CCUCUCCCAUUCCCA____________A__CCCAAUCCAAAAGCCAGGCCAACGCCCACCUUUUGGGUUUUGGGCC_CGAAAACGAGGCCACUUGACAG___CCAAGCCAGCGGAGAA
..((((((.........................((((((((((...(((....)))...))))))))))...((((.((....)).)))).((((........))))...).))))). (-20.02 = -21.65 +   1.63)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,269,892 – 6,269,998
Length 106
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 72.81
Mean single sequence MFE -30.15
Consensus MFE -19.86
Energy contribution -20.43
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.10
Structure conservation index 0.66
SVM decision value 2.30
SVM RNA-class probability 0.992014
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6269892 106 - 22224390
GUCGCCAUGGGCGUGGCUUCCCCCUACCGCUUACCAUUCACCUCUCCCAUUCGCA------------AAACCCAAUCCGAAAGCCAGGCCAACGCCCACCUUUUGCGACUGGGGCC-CG
........((((((((..........))))...............((((.(((((------------(((.......(....)...(((....)))....)))))))).)))))))-). ( -32.30)
>DroSim_CAF1 13442 105 - 1
GUCGCCAUGGGCGUGGCUUCCCCCUACCGCUUCCCAUUCACCUCUCCCAUUCGCA------------A-UCCCAAUCCGAAAGCCAGGCCAACGCCCACCUUUUGGGUUUUGGGCC-CG
........((((((((..........)))).........................------------.-..((((((((((((...(((....)))...)))))))))..))))))-). ( -28.10)
>DroEre_CAF1 1123 110 - 1
GCCGCCAUAGGCGUGGUUUCCCCUUACCGAUU-CCAUACACCUUUCCCAUUCCCAAUCCCAUGCCC-------AAUCCAAAAGCCAGGCCAACGCCCACCUUUUGGGUUUUGGGCC-CG
(((......)))((((..((........))..-)))).........................((((-------((((((((((...(((....)))...)))))))))..))))).-.. ( -32.40)
>DroYak_CAF1 9294 107 - 1
ACCGCCAUGGGCGUGGCUG-----------UC-CCAUACACCUUGUCCAUUCCCAUUCCCAUUCCCAUUGCCAAAGCAAAAAGCCAGGCCAACGCCCACCUUUUGGGUUCUCGGCCCCA
...(((...(((.((((((-----------(.-....))............................((((....))))..))))).)))...(((((.....)))))....))).... ( -27.80)
>consensus
GCCGCCAUGGGCGUGGCUUCCCCCUACCGCUU_CCAUACACCUCUCCCAUUCCCA____________A__CCCAAUCCAAAAGCCAGGCCAACGCCCACCUUUUGGGUUUUGGGCC_CG
...(((...(((.((((((.............................................................)))))).)))...(((((.....)))))....))).... (-19.86 = -20.43 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,269,930 – 6,270,037
Length 107
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 74.78
Mean single sequence MFE -19.79
Consensus MFE -18.09
Energy contribution -17.87
Covariance contribution -0.22
Combinations/Pair 1.08
Mean z-score -1.36
Structure conservation index 0.91
SVM decision value 2.63
SVM RNA-class probability 0.995872
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6269930 107 - 22224390
CCUCAAGUUUUCUUAGCCGCACACCGCAAAACGCCCGCAGUCGCCAUGGGCGUGGCUUCCCCCUACCGCUUACCAUUCACCUCUCCCAUUCGCA------------AAACCCAAUCCGA
......(((((...((((((.....))...((((((((....))...))))))))))..........((......................)))------------))))......... ( -18.85)
>DroSim_CAF1 13480 106 - 1
CCUCAAGUUUUCUUAGCCGCACACCGCAAAACGCCCACAGUCGCCAUGGGCGUGGCUUCCCCCUACCGCUUCCCAUUCACCUCUCCCAUUCGCA------------A-UCCCAAUCCGA
......((......((((((.....))...(((((((.........))))))))))).......))............................------------.-........... ( -18.02)
>DroYak_CAF1 9333 107 - 1
CCUCAAGUUUUCUUAGCCGCAUACCGCAAAACGCCCACAACCGCCAUGGGCGUGGCUG-----------UC-CCAUACACCUUGUCCAUUCCCAUUCCCAUUCCCAUUGCCAAAGCAAA
......((.....(((((((.....))...(((((((.........))))))))))))-----------..-....))............................((((....)))). ( -22.50)
>consensus
CCUCAAGUUUUCUUAGCCGCACACCGCAAAACGCCCACAGUCGCCAUGGGCGUGGCUUCCCCCUACCGCUU_CCAUUCACCUCUCCCAUUCGCA____________A_ACCCAAUCCGA
..............((((((.....))...(((((((.........))))))))))).............................................................. (-18.09 = -17.87 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,269,958 – 6,270,077
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.66
Mean single sequence MFE -23.09
Consensus MFE -19.75
Energy contribution -19.62
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -1.63
Structure conservation index 0.86
SVM decision value 0.50
SVM RNA-class probability 0.759876
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6269958 119 - 22224390
CGCACACUUAACUCAAGUUUCAUUCAAUUAUUGUUAAGCACCUCAAGUUUUCUUAGCCGCACACCGCAAA-ACGCCCGCAGUCGCCAUGGGCGUGGCUUCCCCCUACCGCUUACCAUUCA
.((...((((((...((((......))))...))))))........((......((((((.....))...-((((((((....))...)))))))))).......)).)).......... ( -24.52)
>DroSim_CAF1 13507 119 - 1
CGCACACUUAACUCAAGUUUCAUUCAAUUAUUGUUAAGCACCUCAAGUUUUCUUAGCCGCACACCGCAAA-ACGCCCACAGUCGCCAUGGGCGUGGCUUCCCCCUACCGCUUCCCAUUCA
.((...((((((...((((......))))...))))))........((......((((((.....))...-(((((((.........))))))))))).......)).)).......... ( -24.22)
>DroEre_CAF1 1194 119 - 1
CGCACACUUAACUCAAGUUUCAUUCAAUUAUUGUUAAGCACCUCAAGUUUUCUUAGCCGCACACCGCAAAGACGCCCACAGCCGCCAUAGGCGUGGUUUCCCCUUACCGAUU-CCAUACA
.((...((((((...((((......))))...))))))............((((.((........)).)))).))((((.(((......)))))))................-....... ( -19.60)
>DroYak_CAF1 9373 107 - 1
CGCACACUUAACUCAAGUUUCAUUCAAUUAUUGUUAAGCACCUCAAGUUUUCUUAGCCGCAUACCGCAAA-ACGCCCACAACCGCCAUGGGCGUGGCUG-----------UC-CCAUACA
......((((((...((((......))))...))))))........((.....(((((((.....))...-(((((((.........))))))))))))-----------..-....)). ( -24.00)
>consensus
CGCACACUUAACUCAAGUUUCAUUCAAUUAUUGUUAAGCACCUCAAGUUUUCUUAGCCGCACACCGCAAA_ACGCCCACAGCCGCCAUGGGCGUGGCUUCCCCCUACCGCUU_CCAUACA
......((((((...((((......))))...))))))................((((((.....))....(((((((.........)))))))))))...................... (-19.75 = -19.62 +  -0.12)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:16 2006