Locus 1949

Sequence ID 2L_DroMel_CAF1
Location 5,262,930 – 5,263,032
Length 102
Max. P 0.923344
window3155 window3156

overview

Window 5

Location 5,262,930 – 5,263,032
Length 102
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 85.83
Mean single sequence MFE -31.92
Consensus MFE -22.74
Energy contribution -23.70
Covariance contribution 0.96
Combinations/Pair 1.15
Mean z-score -1.76
Structure conservation index 0.71
SVM decision value 0.19
SVM RNA-class probability 0.625438
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5262930 102 + 22407834
AUUUACUUCUAUUGCAGCAAAGGCUGCAAUUGGCCAGAUUGC---------------AACGGCAGCAACUGCAACUGUGGCAUUGCCAUUUCUGCGCGCGCAUUACAAACUUGGCUC
..........((((((((....)))))))).((((((..(((---------------....)))((...((((...(((((...)))))...))))...)).........)))))). ( -30.90)
>DroSec_CAF1 39722 102 + 1
AUUUACUUCUAUUGCAGCAACGGCUGCACUUGGCCAGCUUGC---------------AACGGCAGCAAGCGCAACUGCGGCAUUGCCAUUUCUGCGCGCGCAUUACAAACUUGGCUC
............((((((....))))))....(((.((((((---------------.......))))))((....)))))...((((....(((....))).........)))).. ( -31.82)
>DroSim_CAF1 41150 102 + 1
AUUUACUUCUAUUGCAGCAACGGCUGCACUUGGCCAGCUUGC---------------AACGGCAGCAACUGCAACUGCGGCAUUGCCAUUUCUGCGCGCGCAUUACAAACUUGGCUC
............((((((....))))))...((((((.(((.---------------...(((((...((((....))))..))))).....(((....)))...))).).))))). ( -29.90)
>DroEre_CAF1 32921 93 + 1
AUUUACUUCUAUUGCAGCCGAGGCUGCACUUGGUCAGGUUG------------------------CAACUGCAACUGUGGCAUUGCCAUUUCUGCGCGCGCAUUGCAAACUUGGCUC
............((((((....))))))...((((((((((------------------------(((..(((...(((((...)))))...)))(....).)))).))))))))). ( -32.60)
>DroYak_CAF1 42007 117 + 1
AUUUACUUCUAUUGCAGCAAAGGCUGCACUUGGCCAGCUUGCCACUGAAGCAACUGCAACUGCGGCAACUGCAACUGCUGCAUUGCCAUUUCUGCGCGCGCAUUACAAACUUGGCUC
............((((((....))))))...(((((((((.......))))....((((.(((((((........)))))))))))......(((....))).........))))). ( -34.40)
>consensus
AUUUACUUCUAUUGCAGCAAAGGCUGCACUUGGCCAGCUUGC_______________AACGGCAGCAACUGCAACUGCGGCAUUGCCAUUUCUGCGCGCGCAUUACAAACUUGGCUC
............((((((....))))))...((((((.(((...................(((((...((((....))))..))))).....(((....)))...))).).))))). (-22.74 = -23.70 +   0.96)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,262,930 – 5,263,032
Length 102
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 85.83
Mean single sequence MFE -38.36
Consensus MFE -26.10
Energy contribution -27.02
Covariance contribution 0.92
Combinations/Pair 1.07
Mean z-score -2.70
Structure conservation index 0.68
SVM decision value 1.15
SVM RNA-class probability 0.923344
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5262930 102 - 22407834
GAGCCAAGUUUGUAAUGCGCGCGCAGAAAUGGCAAUGCCACAGUUGCAGUUGCUGCCGUU---------------GCAAUCUGGCCAAUUGCAGCCUUUGCUGCAAUAGAAGUAAAU
(.((((.(.((((((((.(((.((((.....(((((......)))))..)))))))))))---------------)))).)))))).((((((((....)))))))).......... ( -38.00)
>DroSec_CAF1 39722 102 - 1
GAGCCAAGUUUGUAAUGCGCGCGCAGAAAUGGCAAUGCCGCAGUUGCGCUUGCUGCCGUU---------------GCAAGCUGGCCAAGUGCAGCCGUUGCUGCAAUAGAAGUAAAU
(.((((.((((((((((.((((((((...((((...))))...)))))).....))))))---------------)))))))))))...((((((....))))))............ ( -41.30)
>DroSim_CAF1 41150 102 - 1
GAGCCAAGUUUGUAAUGCGCGCGCAGAAAUGGCAAUGCCGCAGUUGCAGUUGCUGCCGUU---------------GCAAGCUGGCCAAGUGCAGCCGUUGCUGCAAUAGAAGUAAAU
(.((((.((((((((((.(((.((((.....(((((......)))))..)))))))))))---------------)))))))))))...((((((....))))))............ ( -40.10)
>DroEre_CAF1 32921 93 - 1
GAGCCAAGUUUGCAAUGCGCGCGCAGAAAUGGCAAUGCCACAGUUGCAGUUG------------------------CAACCUGACCAAGUGCAGCCUCGGCUGCAAUAGAAGUAAAU
..((((..(((((.........)))))..))))..(((..(((((((....)------------------------))).)))......((((((....))))))......)))... ( -29.90)
>DroYak_CAF1 42007 117 - 1
GAGCCAAGUUUGUAAUGCGCGCGCAGAAAUGGCAAUGCAGCAGUUGCAGUUGCCGCAGUUGCAGUUGCUUCAGUGGCAAGCUGGCCAAGUGCAGCCUUUGCUGCAAUAGAAGUAAAU
..((((..(((((.........)))))..))))..((((((.((.((....)).)).)))))).(((((((..((((......))))..((((((....))))))...))))))).. ( -42.50)
>consensus
GAGCCAAGUUUGUAAUGCGCGCGCAGAAAUGGCAAUGCCGCAGUUGCAGUUGCUGCCGUU_______________GCAAGCUGGCCAAGUGCAGCCUUUGCUGCAAUAGAAGUAAAU
(.((((.((((((..(((....))).....((((((((.......))).))))).....................)))))))))))...((((((....))))))............ (-26.10 = -27.02 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:45 2006