Locus 178

Sequence ID 4_DroMel_CAF1
Location 1,102,421 – 1,102,581
Length 160
Max. P 0.990532
window283 window284

overview

Window 3

Location 1,102,421 – 1,102,541
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -31.91
Consensus MFE -26.10
Energy contribution -26.34
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.64
Structure conservation index 0.82
SVM decision value 0.70
SVM RNA-class probability 0.825915
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1102421 120 - 1281640
GAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGUUUGAAGUCAAACUUAUAAAUUGCAAUGGGAUCAGCAGUAGUAAUUAUUAUGCUUCGAAUUUGGAGAGUCACAAGGGCUGCA
(((((((......)))))))....((((((((..(..(((((((((...........(((((..........)))))............)))))))))..)..))))).)))........ ( -31.80)
>DroSec_CAF1 16185 120 - 1
GAGCCAAUCUUAUUUGGCUUCUAAUCGGACUCGUCUGGUUUGAAGUCAAGCUUAUAAAUUGCAAUGGGAUCAGCAGUAGUAAUUAUUAUGCUUCGAAUUUGGAGAGUCACAAGGGCUGCA
..((..(((((((((((((((.(((((((....))))))).))))))).((.........))))))))))..)).(((((..........(((((....)))))..........))))). ( -34.85)
>DroSim_CAF1 6819 119 - 1
GAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGU-UGAAGUCAAGCUUAUAAAUUGCAAUGGGAUCAGCAGUAGUAAUUAUUAUGCUUCGAAUUUGGAGAGUCACAAGGGCUGCA
..((..(((((((((((((((.(((..((....))..))-)))))))).((.........))))))))))..)).(((((..........(((((....)))))..........))))). ( -32.75)
>DroEre_CAF1 15694 120 - 1
GAGCUAAUCUUAUUUGGCUUCUCAUUGGACUUGUCUGGUUUGAAGUCAAAUUAAUAAAUUGCAAUGGGAUAAGCAGUAGUAAUUACUAUACUUCUAAUUUGGAGACACACAAGGGCUGCA
..(((.(((((((((((((((..((..((....))..))..)))))))((((....))))..)))))))).))).(((((..........((((......))))..........))))). ( -31.05)
>DroYak_CAF1 7682 120 - 1
GAGCCAAUCUUAUAUGGCUUCUCAUUGGACUCGUCUGGUUUGAAGUCAAACUAAUAAAUUGCAAUGGAAUCAGCAGUAGUAAUUACUAUGCUUCGAAUUUGGAGACACAUAAGGGCUGCA
.((((...(((((.((.((((((((((.(......(((((((....)))))))......).))))))....((((.((((....))))))))........)))).)).)))))))))... ( -29.10)
>consensus
GAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGUUUGAAGUCAAACUUAUAAAUUGCAAUGGGAUCAGCAGUAGUAAUUAUUAUGCUUCGAAUUUGGAGAGUCACAAGGGCUGCA
..((..(((((((((((((((..((((((....))))))..)))))))..............))))))))..)).(((((..........((((......))))..........))))). (-26.10 = -26.34 +   0.24) 

alignment

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secondary structure

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dotplot

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Window 4

Location 1,102,461 – 1,102,581
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.33
Mean single sequence MFE -30.56
Consensus MFE -27.70
Energy contribution -27.38
Covariance contribution -0.32
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.91
SVM decision value 2.22
SVM RNA-class probability 0.990532
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1102461 120 - 1281640
CAUGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGUUUGAAGUCAAACUUAUAAAUUGCAAUGGGAUCAGCAGUAGU
..((((((..(((((....(((....)))...)))))...))))))......(((((((((.(((..((....))..))).))))))))).......(((((..........)))))... ( -32.10)
>DroSec_CAF1 16225 120 - 1
CAUGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUUUGGCUUCUAAUCGGACUCGUCUGGUUUGAAGUCAAGCUUAUAAAUUGCAAUGGGAUCAGCAGUAGU
..((((((..(((((....(((....)))...)))))...))))))(((((((((((((((.(((((((....))))))).))))))).((.........)))))))))).......... ( -34.20)
>DroSim_CAF1 6859 119 - 1
CAUGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGU-UGAAGUCAAGCUUAUAAAUUGCAAUGGGAUCAGCAGUAGU
..((((((..(((((....(((....)))...)))))...))))))(((((((((((((((.(((..((....))..))-)))))))).((.........)))))))))).......... ( -32.10)
>DroEre_CAF1 15734 120 - 1
CAAGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCUAAUCUUAUUUGGCUUCUCAUUGGACUUGUCUGGUUUGAAGUCAAAUUAAUAAAUUGCAAUGGGAUAAGCAGUAGU
...(((((..(((((....(((....)))...)))))...)))))......((((((((((..((..((....))..))..))))))))))......(((((..........)))))... ( -28.30)
>DroYak_CAF1 7722 120 - 1
CAAGGCUCAGUACGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUAUGGCUUCUCAUUGGACUCGUCUGGUUUGAAGUCAAACUAAUAAAUUGCAAUGGAAUCAGCAGUAGU
...(((((.((.(((....(((....)))...)))..)).))))).........(((((((..((..((....))..))..))))))).........(((((..........)))))... ( -26.10)
>consensus
CAUGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGUUUGAAGUCAAACUUAUAAAUUGCAAUGGGAUCAGCAGUAGU
...(((((..(((((....(((....)))...)))))...))))).......(((((((((..((((((....))))))..))))))))).......(((((..........)))))... (-27.70 = -27.38 +  -0.32) 

alignment

Postscript

secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:16 2006