Locus 1708

Sequence ID X_DroMel_CAF1
Location 4,768,200 – 4,768,358
Length 158
Max. P 0.999972
window2801 window2802 window2803 window2804

overview

Window 1

Location 4,768,200 – 4,768,318
Length 118
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 88.80
Mean single sequence MFE -49.33
Consensus MFE -44.51
Energy contribution -44.40
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.83
Structure conservation index 0.90
SVM decision value 1.73
SVM RNA-class probability 0.974584
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4768200 118 + 22224390
CCAGUAUCCUGUAGUUGGACUCAAACAAGUCCCUC-CUUCCGCUCGACAGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCC
.(((....))).....(((((......)))))...-....((((..((((.((((((((((((..((((..((((((...))))))..))))..)))))))))))).))))..)))).. ( -49.30)
>DroSec_CAF1 6703 119 + 1
CCAGUGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGA
.(((....))).....(((((......)))))......((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..)))))) ( -49.30)
>DroSim_CAF1 7305 119 + 1
CCAGCGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGA
(((((........)))))....................((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..)))))) ( -49.40)
>consensus
CCAGUGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGA
.(((....))).....(((((......)))))......((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..)))))) (-44.51 = -44.40 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,768,200 – 4,768,318
Length 118
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 88.80
Mean single sequence MFE -55.87
Consensus MFE -52.30
Energy contribution -50.53
Covariance contribution -1.77
Combinations/Pair 1.13
Mean z-score -3.56
Structure conservation index 0.94
SVM decision value 2.30
SVM RNA-class probability 0.992042
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4768200 118 - 22224390
GGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCUGUCGAGCGGAAG-GAGGGACUUGUUUGAGUCCAACUACAGGAUACUGG
..(((((.(((((((((((((((((..(.(((.((((((...)))))).))).)..))))))))))))))))).)))))...(-(..((((((....))))))..)).(((....))). ( -60.70)
>DroSec_CAF1 6703 119 - 1
UCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACACUGG
((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).))..((..((((((....))))))..)).(((....))). ( -53.50)
>DroSim_CAF1 7305 119 - 1
UCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACGCUGG
(((((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).....((..((((((....))))))..))...)))...... ( -53.40)
>consensus
UCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACACUGG
...((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).........((((((....)))))).....(((....))). (-52.30 = -50.53 +  -1.77)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,768,239 – 4,768,358
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 75.07
Mean single sequence MFE -48.13
Consensus MFE -39.52
Energy contribution -39.67
Covariance contribution 0.14
Combinations/Pair 1.08
Mean z-score -3.23
Structure conservation index 0.82
SVM decision value 5.07
SVM RNA-class probability 0.999972
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4768239 119 + 22224390
CGCUCGACAGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCAGGAGCGAACUUGUUGGAGUCAAACUACAGGCUACCAGGG
((((..((((.((((((((((((..((((..((((((...))))))..))))..)))))))))))).))))..)))).((((......))))((((((((........)))).)))).. ( -51.40)
>DroSec_CAF1 6743 119 + 1
UGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUGUUGGAGUCAAACUUCAGGCUACCAGGG
.((((.((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))....(....))))).......((((((((........)))).)))).. ( -49.30)
>DroSim_CAF1 7345 93 + 1
UGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGU--------------------------
.(((((((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))....(....)...)))))....-------------------------- ( -43.70)
>consensus
UGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUUGGAGUCAAACU_CAGGCUACCAGGG
(((((.((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))....(....))))))......((((((((........)))).)))).. (-39.52 = -39.67 +   0.14)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,768,239 – 4,768,358
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 75.07
Mean single sequence MFE -48.37
Consensus MFE -42.00
Energy contribution -40.23
Covariance contribution -1.77
Combinations/Pair 1.17
Mean z-score -4.33
Structure conservation index 0.87
SVM decision value 4.59
SVM RNA-class probability 0.999925
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4768239 119 - 22224390
CCCUGGUAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCUGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCUGUCGAGCG
........(((.(.(((..((((......)))).))).).)))((((.(((((((((((((((((..(.(((.((((((...)))))).))).)..))))))))))))))))).)))). ( -55.40)
>DroSec_CAF1 6743 119 - 1
CCCUGGUAGCCUGAAGUUUGACUCCAACAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCA
....((.(((..((...(((....)))...))..)))))....((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))). ( -47.60)
>DroSim_CAF1 7345 93 - 1
--------------------------ACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCA
--------------------------....((((((.......))...(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))). ( -42.10)
>consensus
CCCUGGUAGCCUG_AGUUUGACUCCAACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCA
...........................................((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))). (-42.00 = -40.23 +  -1.77)

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 10:17:08 2006