Locus 7892

Sequence ID 3L_DroMel_CAF1
Location 21,039,737 – 21,039,895
Length 158
Max. P 0.761586
window12845 window12846

overview

Window 5

Location 21,039,737 – 21,039,855
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.80
Mean single sequence MFE -20.90
Consensus MFE -19.49
Energy contribution -19.80
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.93
SVM decision value 0.32
SVM RNA-class probability 0.685940
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21039737 118 - 23771897
CCAACUUCCUCGACUCACUACGAAAAUGGCAAUAAAUGCAGCGGGUUGCAGGAAAAAUGCAA--AAAAAAAAUAAAAAUUUGACUUGCCAUAAAAAUUGAAAUCCAAAAUGUGGCAGCAG
.....(((((((((((.((.(......)(((.....))))).)))))).)))))...(((..--.....((((....))))....(((((((....(((.....)))..)))))))))). ( -24.00)
>DroSec_CAF1 94960 118 - 1
CCAACUUCCUCGACUCACUACGAAAAUGGCAAUAAAUGCAGCGGAUUGCAGGAAAAAUGCAA--AAAAAAAAUAAAAAUUUGACUUGCCAUAAAAAUUGAAAUCCAAAAUGUGGCGGCAG
.....((((((((..(.((.(......)(((.....))))).)..))).)))))...(((..--.....((((....))))....(((((((....(((.....)))..)))))))))). ( -18.20)
>DroSim_CAF1 1194 120 - 1
CCAACUUCCUCGACUCACUACGAAAAUGGCAAUAAAUGCAGCGGGUUGCAGGAAAAAUGCAAGAAAAAAAAAUAAAAAUUUGACUUGCCAUAAAAAUUGAAAUCCAAAAUGUGGCAGCAG
.....(((((((((((.((.(......)(((.....))))).)))))).)))))...(((.........((((....))))....(((((((....(((.....)))..)))))))))). ( -24.00)
>DroEre_CAF1 17034 115 - 1
CCAACUUCCUCGACUCACUACGAAAAUGGCAAUAAAUGCAGCGGGUUGCAGAAAAAAUU-----AAAAAAAAUACAAAUUUGACUUGCCAUAAAAAUUGAAAUCCAAAAUGUGGCAGCAG
.....(((..((((((.((.(......)(((.....))))).))))))..)))......-----....................((((((((....(((.....)))..))))))))... ( -17.40)
>consensus
CCAACUUCCUCGACUCACUACGAAAAUGGCAAUAAAUGCAGCGGGUUGCAGGAAAAAUGCAA__AAAAAAAAUAAAAAUUUGACUUGCCAUAAAAAUUGAAAUCCAAAAUGUGGCAGCAG
.....(((((((((((.((.(......)(((.....))))).)))))).)))))..............................((((((((....(((.....)))..))))))))... (-19.49 = -19.80 +   0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,039,777 – 21,039,895
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.22
Mean single sequence MFE -27.60
Consensus MFE -24.05
Energy contribution -24.67
Covariance contribution 0.63
Combinations/Pair 1.05
Mean z-score -1.98
Structure conservation index 0.87
SVM decision value 0.50
SVM RNA-class probability 0.761586
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21039777 118 + 23771897
AAUUUUUAUUUUUUUU--UUGCAUUUUUCCUGCAACCCGCUGCAUUUAUUGCCAUUUUCGUAGUGAGUCGAGGAAGUUGGAAUUUGCAUAGAAAAAUGGAAAUUAACAAGACCAUUUGAC
(((((((((((((((.--.((((...((((.((..((((....(((((((((.......))))))))))).))..)).))))..)))).)))))))))))))))................ ( -29.40)
>DroSec_CAF1 95000 118 + 1
AAUUUUUAUUUUUUUU--UUGCAUUUUUCCUGCAAUCCGCUGCAUUUAUUGCCAUUUUCGUAGUGAGUCGAGGAAGUUGGAAUUUGCAUAGAAAAAUGGAAAUUAACAAGACCAUUUGAC
(((((((((((((((.--.((((...((((.((..(((..((.(((((((((.......))))))))))).))).)).))))..)))).)))))))))))))))................ ( -29.90)
>DroSim_CAF1 1234 120 + 1
AAUUUUUAUUUUUUUUUCUUGCAUUUUUCCUGCAACCCGCUGCAUUUAUUGCCAUUUUCGUAGUGAGUCGAGGAAGUUGGAAUUUGCAUAGAAAAAUGGAAAUUAACAAGACCAUUUGAC
(((((((((((((((....((((...((((.((..((((....(((((((((.......))))))))))).))..)).))))..)))).)))))))))))))))................ ( -28.80)
>DroEre_CAF1 17074 115 + 1
AAUUUGUAUUUUUUUU-----AAUUUUUUCUGCAACCCGCUGCAUUUAUUGCCAUUUUCGUAGUGAGUCGAGGAAGUUGGAAUUUGCAUAGAAAAAUGGAAAUUAACAAGACCAUUUGAC
....((((....((((-----(((((((((.(((......)))(((((((((.......))))))))).)))))))))))))..)))).....((((((............))))))... ( -22.30)
>consensus
AAUUUUUAUUUUUUUU__UUGCAUUUUUCCUGCAACCCGCUGCAUUUAUUGCCAUUUUCGUAGUGAGUCGAGGAAGUUGGAAUUUGCAUAGAAAAAUGGAAAUUAACAAGACCAUUUGAC
(((((((((((((((....((((...((((.((..((((....(((((((((.......))))))))))).))..)).))))..)))).)))))))))))))))................ (-24.05 = -24.67 +   0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:41 2006