Locus 6112

Sequence ID 3L_DroMel_CAF1
Location 16,210,287 – 16,210,519
Length 232
Max. P 0.990583
window9816 window9817 window9818

overview

Window 6

Location 16,210,287 – 16,210,407
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.58
Mean single sequence MFE -34.56
Consensus MFE -32.78
Energy contribution -33.38
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.95
SVM decision value 1.46
SVM RNA-class probability 0.955999
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16210287 120 - 23771897
GAUCACGCAUCCUGUCCUCGACCUACUUUUAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGUAACUUUGUGCGCCUCAUUGCUCCACACGUCGCCUGGCAUUUAA
......((((((((((((.((...........)).))))..))))))))...(((....)))...(((((((........)))))))(((.....((..(....)..))..)))...... ( -35.40)
>DroSec_CAF1 29109 120 - 1
GAUCACGCAUCCUGUCCUCGACCUACUUUCAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCACACGCACAAAUUGGCAACUUUUUGCGCCCCAUUGCUCCACACGUCGCCUGGCAUUUAA
......((((((((((((.((...........)).))))..))))))))....((....))....((.((((..(....)..)))).)).(((..((..(....)..)).)))....... ( -31.60)
>DroSim_CAF1 30980 120 - 1
GAUCACGCAUCCUGUCCUCGACCUACUUUCAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGCAACUUUGUGCGCCCCAUUGCUCCACACGUCGCCUGGCAUUUAA
......((((((((((((.((...........)).))))..))))))))...(((....)))...(((((((..(....))))))))(((.....((..(....)..))..)))...... ( -36.00)
>DroEre_CAF1 28615 120 - 1
GAUCACGCAUCCUGUCCUCGACCUACUUUCAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGCAACUUUGUGCGCCUCAUUGCUCCACACGUCGCCUGGCAUUUAA
......((((((((((((.((...........)).))))..))))))))...(((....)))...(((((((..(....))))))))(((.....((..(....)..))..)))...... ( -36.70)
>DroYak_CAF1 65694 120 - 1
GAUCACACAUCCUGUCCUCGACCUACUUUAAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGCAACUUUGUGCGCCUCAUUGCUCCACACGUCGCCUGGCAUUUAA
.......(((((((((((.((...........)).))))..)))))))....(((....)))...(((((((..(....))))))))(((.....((..(....)..))..)))...... ( -33.10)
>consensus
GAUCACGCAUCCUGUCCUCGACCUACUUUCAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGCAACUUUGUGCGCCUCAUUGCUCCACACGUCGCCUGGCAUUUAA
......((((((((((((.((...........)).))))..))))))))...(((....)))...(((((((..(....))))))))(((.....((..(....)..))..)))...... (-32.78 = -33.38 +   0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,210,327 – 16,210,447
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.25
Mean single sequence MFE -35.90
Consensus MFE -34.06
Energy contribution -34.74
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.76
Structure conservation index 0.95
SVM decision value 2.22
SVM RNA-class probability 0.990583
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16210327 120 - 23771897
AUAAUUGCCAGAAGAAGCCGUCCAAGUGCCGCACCCACUGGAUCACGCAUCCUGUCCUCGACCUACUUUUAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGUAAC
....(((((((.....((.(((((.(((.......))))))))...((((((((((((.((...........)).))))..))))))))...(((....)))...)).....))))))). ( -35.80)
>DroSec_CAF1 29149 120 - 1
AUAAUUGCCAGAAGAAGCCGUCCAAGUGCCGCACCCACUGGAUCACGCAUCCUGUCCUCGACCUACUUUCAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCACACGCACAAAUUGGCAAC
....(((((((.....((.(((((.(((.......))))))))...((((((((((((.((...........)).))))..))))))))....((....))....)).....))))))). ( -36.90)
>DroSim_CAF1 31020 120 - 1
AUAAUUGCCAGAAGAAGCCGUCCAAGUGCCGCACCCACUGGAUCACGCAUCCUGUCCUCGACCUACUUUCAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGCAAC
....(((((((.....((.(((((.(((.......))))))))...((((((((((((.((...........)).))))..))))))))...(((....)))...)).....))))))). ( -37.80)
>DroEre_CAF1 28655 120 - 1
AUAAUUGCCACAAGAAGCCGUCCAAGUGCCGCACCCACUGGAUCACGCAUCCUGUCCUCGACCUACUUUCAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGCAAC
....((((((......((.(((((.(((.......))))))))...((((((((((((.((...........)).))))..))))))))...(((....)))...))......)))))). ( -37.00)
>DroYak_CAF1 65734 120 - 1
AUAAUUGCUCCAAGAAGCCGUCCAAGUGCCGCACCCACUGGAUCACACAUCCUGUCCUCGACCUACUUUAAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGCAAC
................((((.....((((.((((((...((((.....))))..((((.((...........)).))))...))).)))...(((....)))...))))....))))... ( -32.00)
>consensus
AUAAUUGCCAGAAGAAGCCGUCCAAGUGCCGCACCCACUGGAUCACGCAUCCUGUCCUCGACCUACUUUCAUUCUGGGAAUCGGGAUGCCCUCGGGAAACCGCACGCACAAAUUGGCAAC
....(((((((.....((.(((((.(((.......))))))))...((((((((((((.((...........)).))))..))))))))...(((....)))...)).....))))))). (-34.06 = -34.74 +   0.68)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,210,407 – 16,210,519
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.58
Mean single sequence MFE -41.10
Consensus MFE -34.68
Energy contribution -35.16
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -1.36
Structure conservation index 0.84
SVM decision value 0.28
SVM RNA-class probability 0.667610
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16210407 112 + 23771897
CAGUGGGUGCGGCACUUGGACGGCUUCUUCUGGCAAUUAUGAAUGAAAUCCUUUCAGGAGCGAAAUCCGUUCCACCGGCAGUCGCCCAAGGUCGCUCCAAAGCUUGGU--------CUCU
.(((.((.(((((.(((((.(((((....((((......((((.(.....).))))((((((.....)))))).)))).))))).)))))))))).))...)))....--------.... ( -41.60)
>DroSec_CAF1 29229 112 + 1
CAGUGGGUGCGGCACUUGGACGGCUUCUUCUGGCAAUUAUGAAUGAAAUCCUUUCAGGAGCGAAAUCCGUUCCACCGGCAGUCACCCAAGGUCGCUCCAAAGCUUGGU--------CUCU
.(((.((.(((((.(((((..((((....((((......((((.(.....).))))((((((.....)))))).)))).))))..)))))))))).))...)))....--------.... ( -38.50)
>DroSim_CAF1 31100 112 + 1
CAGUGGGUGCGGCACUUGGACGGCUUCUUCUGGCAAUUAUGAAUGAAAUCCUUUCAGGAGCGAAAUCCGUUCCACCGGCAGUCGCCCAAGGUCGCUCCAAAGCUUGGU--------CUCU
.(((.((.(((((.(((((.(((((....((((......((((.(.....).))))((((((.....)))))).)))).))))).)))))))))).))...)))....--------.... ( -41.60)
>DroEre_CAF1 28735 120 + 1
CAGUGGGUGCGGCACUUGGACGGCUUCUUGUGGCAAUUAUGAAUGAAAUCCUUUCAGGAGCGAAAUCCGCUCCACCGGCAGUCGCCCAAGGUCGCUCGCUCGCUCGGUCGGUCCGUCGCU
.((((((((((((.(((((.(((((.((.((........((((.(.....).))))((((((.....)))))))).)).))))).))))))))))..)))))))(((.....)))..... ( -47.00)
>DroYak_CAF1 65814 112 + 1
CAGUGGGUGCGGCACUUGGACGGCUUCUUGGAGCAAUUAUGAAUGAAAUCCUUUCAGGAGCGAAAUCCGUUCCACCGGCAGUUGCCCAAGGUCGCUCGGUCUCUCGGU--------CUCU
......(.(((((.(((((.(((((.((((((((.....((((.(.....).))))(((......)))))))))..)).))))).)))))))))).)(..(....)..--------)... ( -36.80)
>consensus
CAGUGGGUGCGGCACUUGGACGGCUUCUUCUGGCAAUUAUGAAUGAAAUCCUUUCAGGAGCGAAAUCCGUUCCACCGGCAGUCGCCCAAGGUCGCUCCAAAGCUUGGU________CUCU
.(((.((.(((((.(((((.(((((.((...........((((.(.....).))))((((((.....))))))...)).))))).)))))))))).))...)))................ (-34.68 = -35.16 +   0.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:20 2006