Locus 2060

Sequence ID 2L_DroMel_CAF1
Location 5,569,360 – 5,569,471
Length 111
Max. P 0.983575
window3314 window3315

overview

Window 4

Location 5,569,360 – 5,569,471
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.09
Mean single sequence MFE -25.94
Consensus MFE -25.12
Energy contribution -25.62
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.97
SVM decision value 1.68
SVM RNA-class probability 0.971883
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5569360 111 + 22407834
---------CAGGCCGACUGGCACUCACACUUGGCUCUUGCAAAAACGUGUCUAUUACAAUUCAAUUUGACAAUAGGUGCACACAAAAGCCAACCCAAGCCGCAAGCCAACCAUCCAGCC
---------..(((.(..(((.........((((((..(((......(..((((((.(((......)))..))))))..)........((........)).))))))))))))..).))) ( -23.90)
>DroSec_CAF1 14046 111 + 1
---------CAGGCCGACUGGCACUCACACUUGGCUUUUGCAAAAACGUGUCUAUUACAAUUCAAUUUGACAAUAGGUGCACACAAAAGCCAACCCAAGCCGCAAGCCAACCAUCCAGCC
---------..(((....((((........((((((((((.......(..((((((.(((......)))..))))))..)...)))))))))).....))))...)))............ ( -26.52)
>DroSim_CAF1 15596 120 + 1
CUCUGGUCGCAGGCCGACUGGCACUCACACUUGGCUUUUGCAAAAACGUGUCUAUUACAAUUCAAUUUGACAAUAGGUGCACACAAAAGCCAACCCAAGCCGCAAGCCAACCAUCCAGCC
..((((..(..(((....((((........((((((((((.......(..((((((.(((......)))..))))))..)...)))))))))).....))))...)))...)..)))).. ( -30.32)
>DroYak_CAF1 14322 111 + 1
---------CAGGCCGACUGGCACUCACACUUGGCUCUUGCAAAAACGUGUCUAUUACAAUUCAAUUUGACAAUAGGUGCACACAAAAGCCAACCCAAGCCGCAAGCCAACCAUCCAACC
---------..(((....((((........((((((.(((.......(..((((((.(((......)))..))))))..)...))).)))))).....))))...)))............ ( -23.02)
>consensus
_________CAGGCCGACUGGCACUCACACUUGGCUCUUGCAAAAACGUGUCUAUUACAAUUCAAUUUGACAAUAGGUGCACACAAAAGCCAACCCAAGCCGCAAGCCAACCAUCCAGCC
...........(((....((((........((((((((((.......(..((((((.(((......)))..))))))..)...)))))))))).....))))...)))............ (-25.12 = -25.62 +   0.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,569,360 – 5,569,471
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.09
Mean single sequence MFE -39.75
Consensus MFE -39.61
Energy contribution -39.17
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -2.23
Structure conservation index 1.00
SVM decision value 1.95
SVM RNA-class probability 0.983575
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5569360 111 - 22407834
GGCUGGAUGGUUGGCUUGCGGCUUGGGUUGGCUUUUGUGUGCACCUAUUGUCAAAUUGAAUUGUAAUAGACACGUUUUUGCAAGAGCCAAGUGUGAGUGCCAGUCGGCCUG---------
(((((..((((..(((..((.(((((.((.((...(((((....((((((.(((......)))))))))))))).....))..)).)))))))..)))))))..)))))..--------- ( -40.00)
>DroSec_CAF1 14046 111 - 1
GGCUGGAUGGUUGGCUUGCGGCUUGGGUUGGCUUUUGUGUGCACCUAUUGUCAAAUUGAAUUGUAAUAGACACGUUUUUGCAAAAGCCAAGUGUGAGUGCCAGUCGGCCUG---------
(((((..((((..(((..((.(((((.((.((...(((((....((((((.(((......)))))))))))))).....))..)).)))))))..)))))))..)))))..--------- ( -39.60)
>DroSim_CAF1 15596 120 - 1
GGCUGGAUGGUUGGCUUGCGGCUUGGGUUGGCUUUUGUGUGCACCUAUUGUCAAAUUGAAUUGUAAUAGACACGUUUUUGCAAAAGCCAAGUGUGAGUGCCAGUCGGCCUGCGACCAGAG
..((((..((((((((.(((.((((.(((((((((((((((...((((((.(((......))))))))).)))......))))))))))).).))))))).)))))))).....)))).. ( -41.90)
>DroYak_CAF1 14322 111 - 1
GGUUGGAUGGUUGGCUUGCGGCUUGGGUUGGCUUUUGUGUGCACCUAUUGUCAAAUUGAAUUGUAAUAGACACGUUUUUGCAAGAGCCAAGUGUGAGUGCCAGUCGGCCUG---------
(((((..((((..(((..((.(((((.((.((...(((((....((((((.(((......)))))))))))))).....))..)).)))))))..)))))))..)))))..--------- ( -37.50)
>consensus
GGCUGGAUGGUUGGCUUGCGGCUUGGGUUGGCUUUUGUGUGCACCUAUUGUCAAAUUGAAUUGUAAUAGACACGUUUUUGCAAAAGCCAAGUGUGAGUGCCAGUCGGCCUG_________
(((((..((((..(((..((.(((((.((.((...(((((....((((((.(((......)))))))))))))).....))..)).)))))))..)))))))..)))))........... (-39.61 = -39.17 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:18 2006