Locus 3647

Sequence ID 3R_DroMel_CAF1
Location 9,852,309 – 9,852,440
Length 131
Max. P 0.971831
window5862 window5863 window5864

overview

Window 2

Location 9,852,309 – 9,852,413
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 86.97
Mean single sequence MFE -29.55
Consensus MFE -23.62
Energy contribution -24.43
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.80
SVM decision value 0.46
SVM RNA-class probability 0.743709
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9852309 104 - 27905053
CCCUUAAAUAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCGCAUGGAGCUUUCAGCAUUGUUCUGCAGAGAGUUGUUGACUUGGCCUUUUACUAGCUAAA
........((((......(((((((.....(((((((..(((.....)))(((((((.(((......))).)))))))))))))).))))))).....)))).. ( -33.40)
>DroSim_CAF1 59110 104 - 1
CCCUUAAAUAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCGCAUGGAGCUUUCAGCAUUGUUCUGCAGAGAGUUGUUCACUUGGCCUUUUACUAGCUAAA
........((((......(((((((.....(((..((..(((.....)))(((((((.(((......))).)))))))))..))).))))))).....)))).. ( -28.10)
>DroEre_CAF1 57608 93 - 1
-CCUUGAAUAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCCCAUGGAGCUU----------UCUGCUUAGUGUUGUUGACUUUGCCUUUUACUAGCUAAA
-.......((((......((((((......((((((((((.((......((((..----------...)))).))))))))))))..)))))).....)))).. ( -26.00)
>DroYak_CAF1 58312 94 - 1
CCCUUAAACAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCCCAUGGAGCUU----------UUUGUGGAGUGUUGUUGACAUGGCCUUUUACUAGCUAAA
.........(((......(((((((......(((((((((.((.(((..((....----------))..))).)))))))))))..))))))).....)))... ( -30.70)
>consensus
CCCUUAAAUAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCCCAUGGAGCUU__________UCUGCAGAGAGUUGUUGACUUGGCCUUUUACUAGCUAAA
........((((......(((((((.....(((((((((((.((....)).((...............))...).)))))))))).))))))).....)))).. (-23.62 = -24.43 +   0.81)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,852,344 – 9,852,440
Length 96
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 87.63
Mean single sequence MFE -28.40
Consensus MFE -21.88
Energy contribution -23.12
Covariance contribution 1.25
Combinations/Pair 1.04
Mean z-score -2.04
Structure conservation index 0.77
SVM decision value 0.85
SVM RNA-class probability 0.865260
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9852344 96 + 27905053
CAGAACAAUGCUGAAAGCUCCAUGCGGUGGCUGCCGACUAUCAAGGCCCUUAUCAAGGCUAUUUAAGGGUGAGCAAGUCAGCAGCUUAAGAGAUAA
........((((((..((((....((((....)))).........(((((((...........)))))))))))...))))))............. ( -28.00)
>DroSim_CAF1 59145 96 + 1
CAGAACAAUGCUGAAAGCUCCAUGCGGUGGCUGCCGACUAUCAAGGCCCUUAUCAAGGCUAUUUAAGGGUGAGCAAGUCGGCAGCUUAAAAGAUAA
(((.......)))...((.....))...(((((((((((.((...(((((((...........)))))))))...))))))))))).......... ( -31.30)
>DroEre_CAF1 57643 85 + 1
CAGA----------AAGCUCCAUGGGGUGGCUGCCGACUAUCAAGGCCCUUAUCAAGGCUAUUCAAGG-GGAGCAAGUCAGCAGCCUAAGAGAUAA
....----------..((((....))))((((((.((((.....((((........)))).(((....-)))...)))).)))))).......... ( -25.50)
>DroYak_CAF1 58347 86 + 1
CAAA----------AAGCUCCAUGGGGUGGCUGCCGACUAUCAAGGCCCUUAUCAAGGCUGUUUAAGGGGGAGCAAGUCAGCAGCCUAAGAGAUAA
....----------..((((....))))((((((.((((.((....((((((.((....))..)))))).))...)))).)))))).......... ( -28.80)
>consensus
CAGA__________AAGCUCCAUGCGGUGGCUGCCGACUAUCAAGGCCCUUAUCAAGGCUAUUUAAGGGGGAGCAAGUCAGCAGCCUAAGAGAUAA
................((((....))))((((((.((((.((...(((((((...........)))))))))...)))).)))))).......... (-21.88 = -23.12 +   1.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,852,344 – 9,852,440
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 87.63
Mean single sequence MFE -28.10
Consensus MFE -24.36
Energy contribution -24.54
Covariance contribution 0.19
Combinations/Pair 1.14
Mean z-score -2.29
Structure conservation index 0.87
SVM decision value 1.68
SVM RNA-class probability 0.971831
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9852344 96 - 27905053
UUAUCUCUUAAGCUGCUGACUUGCUCACCCUUAAAUAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCGCAUGGAGCUUUCAGCAUUGUUCUG
...........((((((((((...(((((((((...........))))))...))).))))))))))........(((((..........))))). ( -27.70)
>DroSim_CAF1 59145 96 - 1
UUAUCUUUUAAGCUGCCGACUUGCUCACCCUUAAAUAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCGCAUGGAGCUUUCAGCAUUGUUCUG
...........((((((((((...(((((((((...........))))))...))).))))))))))........(((((..........))))). ( -29.90)
>DroEre_CAF1 57643 85 - 1
UUAUCUCUUAGGCUGCUGACUUGCUCC-CCUUGAAUAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCCCAUGGAGCUU----------UCUG
....((((..(((((((((((.....(-(((((...........)))))).......))))))))))).......))))...----------.... ( -26.80)
>DroYak_CAF1 58347 86 - 1
UUAUCUCUUAGGCUGCUGACUUGCUCCCCCUUAAACAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCCCAUGGAGCUU----------UUUG
....((((..(((((((((((......((((((...........)))))).......))))))))))).......))))...----------.... ( -28.02)
>consensus
UUAUCUCUUAAGCUGCUGACUUGCUCACCCUUAAAUAGCCUUGAUAAGGGCCUUGAUAGUCGGCAGCCACCCCAUGGAGCUU__________UCUG
....((((..(((((((((((......((((((...........)))))).......))))))))))).......))))................. (-24.36 = -24.54 +   0.19)

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 11:06:30 2006