Locus 6386

Sequence ID 2R_DroMel_CAF1
Location 19,975,744 – 19,975,856
Length 112
Max. P 0.999929
window10194 window10195

overview

Window 4

Location 19,975,744 – 19,975,856
Length 112
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 93.66
Mean single sequence MFE -36.92
Consensus MFE -33.18
Energy contribution -33.98
Covariance contribution 0.80
Combinations/Pair 1.12
Mean z-score -3.10
Structure conservation index 0.90
SVM decision value 4.61
SVM RNA-class probability 0.999929
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19975744 112 + 20766785
GCAGCCAGCUUUCACUUUCCCAGGCUUUUCAUCCCAUCCGCCCCAGCAUGCACUUGACUUUUCGCCAUGUGCAUGUGCUGGUGGGAUCUUCUUGCCCGAUACUCGUUGGCUC
..(((((((.............(((.....((((((((.((....((((((((.((.(.....).)).)))))))))).))))))))......))).(.....)))))))). ( -39.80)
>DroSec_CAF1 16818 112 + 1
GCAGCCAGCUUCCACUUUCCCAGGCUUUUCAUCCCAUCCGCCCCUGCAUGCACUUGACUUUUCGCCAUGUGCAUGUGUUGGUGGGAUCUUCUUGCCCGGUACUCGUUGGCUC
..(((((((..........((.(((.....((((((((.((....((((((((.((.(.....).)).)))))))))).))))))))......))).)).....))))))). ( -39.26)
>DroSim_CAF1 17449 112 + 1
GCAGCCAGCUUCCACUUUCCCAGGCUUUUCAUCCCAUCCGCCCCUGCAUGCACUUGACUUUUCGCCAUGUGCAUGUGUUGGAGGGAUCUUCUUGCCCGGUACUCGUUGGCUC
..(((((((..........((.(((.....(((((.((((.(...((((((((.((.(.....).)).))))))))).)))))))))......))).)).....))))))). ( -37.56)
>DroEre_CAF1 16912 110 + 1
GCAGCCAGCUUCCACUUUCCCAGGCUUUUCA-CCCAUCCAC-CCUGCAUGCACUUGACUUUUCACCAUAUGGGUGUGUUGGCGGGAUCUUCUUGCCCGGUACUCAUCGGCUC
..(((((((((..........)))))....(-((....(((-((...(((....(((....))).)))..)))))....((((((.....)))))).))).......)))). ( -26.10)
>DroYak_CAF1 17456 112 + 1
GCAGCCAGCUUCCACUUUCCCAGGCUUUUCAUCCCAGCCGCCCCUGCAUGCACUUGACUUUUCGCCAUGUGCAUGUGUUGCUGGGAUCUUCAUGCCCGGUACUCGUUGGCUC
..(((((((..........((.(((.....((((((((.((....((((((((.((.(.....).)).)))))))))).))))))))......))).)).....))))))). ( -41.86)
>consensus
GCAGCCAGCUUCCACUUUCCCAGGCUUUUCAUCCCAUCCGCCCCUGCAUGCACUUGACUUUUCGCCAUGUGCAUGUGUUGGUGGGAUCUUCUUGCCCGGUACUCGUUGGCUC
..(((((((..........((.(((.....((((((((.((....((((((((.((.........)).)))))))))).))))))))......))).)).....))))))). (-33.18 = -33.98 +   0.80)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,975,744 – 19,975,856
Length 112
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 93.66
Mean single sequence MFE -43.34
Consensus MFE -37.58
Energy contribution -37.98
Covariance contribution 0.40
Combinations/Pair 1.12
Mean z-score -3.56
Structure conservation index 0.87
SVM decision value 4.23
SVM RNA-class probability 0.999844
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19975744 112 - 20766785
GAGCCAACGAGUAUCGGGCAAGAAGAUCCCACCAGCACAUGCACAUGGCGAAAAGUCAAGUGCAUGCUGGGGCGGAUGGGAUGAAAAGCCUGGGAAAGUGAAAGCUGGCUGC
.((((........((((((......((((((((((((..(((((.((((.....)))).)))))))))))......)))))).....))))))...(((....))))))).. ( -45.20)
>DroSec_CAF1 16818 112 - 1
GAGCCAACGAGUACCGGGCAAGAAGAUCCCACCAACACAUGCACAUGGCGAAAAGUCAAGUGCAUGCAGGGGCGGAUGGGAUGAAAAGCCUGGGAAAGUGGAAGCUGGCUGC
.((((........((((((......((((((((..(.(((((((.((((.....)))).)))))))....)..)).)))))).....))))))...(((....))))))).. ( -44.50)
>DroSim_CAF1 17449 112 - 1
GAGCCAACGAGUACCGGGCAAGAAGAUCCCUCCAACACAUGCACAUGGCGAAAAGUCAAGUGCAUGCAGGGGCGGAUGGGAUGAAAAGCCUGGGAAAGUGGAAGCUGGCUGC
.((((........((((((......((((((((..(.(((((((.((((.....)))).)))))))....)..))).))))).....))))))...(((....))))))).. ( -44.70)
>DroEre_CAF1 16912 110 - 1
GAGCCGAUGAGUACCGGGCAAGAAGAUCCCGCCAACACACCCAUAUGGUGAAAAGUCAAGUGCAUGCAGG-GUGGAUGGG-UGAAAAGCCUGGGAAAGUGGAAGCUGGCUGC
.((((........((((((..(.....).((((....(((((.((((.(((....)))....))))..))-)))....))-))....))))))...(((....))))))).. ( -33.90)
>DroYak_CAF1 17456 112 - 1
GAGCCAACGAGUACCGGGCAUGAAGAUCCCAGCAACACAUGCACAUGGCGAAAAGUCAAGUGCAUGCAGGGGCGGCUGGGAUGAAAAGCCUGGGAAAGUGGAAGCUGGCUGC
.((((........((((((......((((((((..(.(((((((.((((.....)))).))))))).....)..)))))))).....))))))...(((....))))))).. ( -48.40)
>consensus
GAGCCAACGAGUACCGGGCAAGAAGAUCCCACCAACACAUGCACAUGGCGAAAAGUCAAGUGCAUGCAGGGGCGGAUGGGAUGAAAAGCCUGGGAAAGUGGAAGCUGGCUGC
.((((........((((((......((((((((..(.(((((((.((((.....)))).)))))))...)...)).)))))).....))))))...(((....))))))).. (-37.58 = -37.98 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:45 2006