Locus 4460

Sequence ID 2R_DroMel_CAF1
Location 14,667,316 – 14,667,423
Length 107
Max. P 0.797341
window7129 window7130

overview

Window 9

Location 14,667,316 – 14,667,423
Length 107
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 92.01
Mean single sequence MFE -38.21
Consensus MFE -27.91
Energy contribution -29.16
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -3.44
Structure conservation index 0.73
SVM decision value 0.54
SVM RNA-class probability 0.776077
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14667316 107 + 20766785
AAUUUAUGGCUAACCCAAACCCAGUUCCUU-GGGGAUGGGG---GGCGGUUAAUUUUCGAAAAGUGGAGCAGCUAGCUGCUCGCUUAUUAAUCCCCAUAAUUUGUUUGGUC
.......((((((((((..(((((....))-)))..))))(---((.(((((((.......(((((.(((((....)))))))))))))))))))).........)))))) ( -39.31)
>DroSim_CAF1 21907 110 + 1
AAUUUAUGGCUAACCCAAACCCAGUUCCUU-GGGGAUGGGGCUGGGGCGUUAAUUUUCGAAAAGUGGAGCAGCUAGCUGCUCGCUUAUUAAUCCCCAUAAUUUGUUUGGUC
.......((((((((((..(((((....))-)))..))))..(((((.((((((.......(((((.(((((....)))))))))))))))))))))........)))))) ( -39.91)
>DroEre_CAF1 22240 104 + 1
AAUUUAUGGCUUACCCAAACCCAGUUCCUU-GGGCAUGG------GGGGUUAAUUUUCGGAAAGUGGAGCAGCUAGCUGCUCGCUUAUUAAUCCCCAUAAUUUGUUUGGUC
...((((((....((((..(((((....))-)))..)))------)((((((((.......(((((.(((((....))))))))))))))))))))))))........... ( -35.31)
>DroYak_CAF1 22262 105 + 1
AAUUUAUGGCUAACCCAAACCCAGUUCCUCCUGGCUGGG------GGGGUUAAUUUUCGAAAAGUGGAGCAGCUAGCUGCUCGCUUAUUAAUCCCCAUAAUUUGUUUGGUC
..............((((((((((((......))))))(------(((((((((.......(((((.(((((....)))))))))))))))))))).......)))))).. ( -38.31)
>consensus
AAUUUAUGGCUAACCCAAACCCAGUUCCUU_GGGCAUGG______GGGGUUAAUUUUCGAAAAGUGGAGCAGCUAGCUGCUCGCUUAUUAAUCCCCAUAAUUUGUUUGGUC
..............(((((((((...((....))..))).....((((((((((.......(((((.(((((....)))))))))))))))))))).......)))))).. (-27.91 = -29.16 +   1.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,667,316 – 14,667,423
Length 107
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 92.01
Mean single sequence MFE -32.33
Consensus MFE -23.91
Energy contribution -24.66
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.82
Structure conservation index 0.74
SVM decision value 0.61
SVM RNA-class probability 0.797341
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14667316 107 - 20766785
GACCAAACAAAUUAUGGGGAUUAAUAAGCGAGCAGCUAGCUGCUCCACUUUUCGAAAAUUAACCGCC---CCCCAUCCCC-AAGGAACUGGGUUUGGGUUAGCCAUAAAUU
...........((((((((.((((((((.((((((....))))))..))).......)))))))...---.((((..(((-(......))))..))))....))))))... ( -31.51)
>DroSim_CAF1 21907 110 - 1
GACCAAACAAAUUAUGGGGAUUAAUAAGCGAGCAGCUAGCUGCUCCACUUUUCGAAAAUUAACGCCCCAGCCCCAUCCCC-AAGGAACUGGGUUUGGGUUAGCCAUAAAUU
..............(((((.((((((((.((((((....))))))..))).......)))))..)))))((((((..(((-(......))))..))))...))........ ( -32.41)
>DroEre_CAF1 22240 104 - 1
GACCAAACAAAUUAUGGGGAUUAAUAAGCGAGCAGCUAGCUGCUCCACUUUCCGAAAAUUAACCCC------CCAUGCCC-AAGGAACUGGGUUUGGGUAAGCCAUAAAUU
...........(((((((((.....(((.((((((....))))))..))))))............(------(((.((((-(......))))).))))....))))))... ( -32.50)
>DroYak_CAF1 22262 105 - 1
GACCAAACAAAUUAUGGGGAUUAAUAAGCGAGCAGCUAGCUGCUCCACUUUUCGAAAAUUAACCCC------CCCAGCCAGGAGGAACUGGGUUUGGGUUAGCCAUAAAUU
...........((((((..........(.((((((....)))))))............(((((((.------(((((((....))..)))))...)))))))))))))... ( -32.90)
>consensus
GACCAAACAAAUUAUGGGGAUUAAUAAGCGAGCAGCUAGCUGCUCCACUUUUCGAAAAUUAACCCC______CCAUCCCC_AAGGAACUGGGUUUGGGUUAGCCAUAAAUU
..((((((.......((((.((((((((.((((((....))))))..))).......)))))))))......(((..((....))...))))))))).............. (-23.91 = -24.66 +   0.75)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:13 2006