Locus 3940

Sequence ID X_DroMel_CAF1
Location 10,496,337 – 10,496,436
Length 99
Max. P 0.875664
window6473 window6474

overview

Window 3

Location 10,496,337 – 10,496,436
Length 99
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 92.41
Mean single sequence MFE -35.16
Consensus MFE -32.19
Energy contribution -32.00
Covariance contribution -0.19
Combinations/Pair 1.14
Mean z-score -1.73
Structure conservation index 0.92
SVM decision value 0.89
SVM RNA-class probability 0.875664
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10496337 99 + 22224390
CCCACUCAUUUCGAAGCUCCGCUUUUCUGUGCUAAUUUCUGCUCCAGUUACGCGGCGGGCAAAUUGGCGAACAUUUUGCGGA-----UGGAGUGAAUGGAUGGG
.(((.((((((((....(((((.......((((((((((((((.(......).))))))..))))))))........)))))-----)))))))).)))..... ( -32.86)
>DroSec_CAF1 27483 104 + 1
CCCACUCAUUUCCAAGCUUCGCUUUUCUGUGCUAAUUUCUGCUCCAGUUACGCGGCUGGCAAAUUGGUGAGCAUUUUGCGGAUGGGAUGGAGUGAAUGGGUGGG
(((((((((((....((((((((..(((((((((((((.....(((((......))))).)))))))).........)))))..)).))))))))))))))))) ( -36.70)
>DroSim_CAF1 28009 104 + 1
CCCACUCAUUUCCAAGCUUCGCUUUUCUGUGCUAAUUUCUGCUCCAGUUACGCGGCGGGCAAAUUGGUGAGCAUUUUGCGGAUGGGAUGGAGUGAAUGGGUGGG
(((((((((((....((((((((..((((((((((((((((((.(......).))))))..))))))).........)))))..)).))))))))))))))))) ( -37.00)
>DroEre_CAF1 29071 99 + 1
CCCACUCAUUUUCAAGCUUCGCUUUUCUGUGCUAAUUUCUGCUCCAGUUACGCGGCGGGAAAAUUGGUGAGCAUUUUGCGAA-----UGGAGUGAAUGGGUGGG
(((((((((((......(((((.....((((((((((((((((.(......).)))))))..))))))..)))....)))))-----......))))))))))) ( -34.10)
>consensus
CCCACUCAUUUCCAAGCUUCGCUUUUCUGUGCUAAUUUCUGCUCCAGUUACGCGGCGGGCAAAUUGGUGAGCAUUUUGCGGA_____UGGAGUGAAUGGGUGGG
((((((((((((((...(((((.....((((((((((((((((.(......).))))))..)))))))..)))....))))).....))))...)))))))))) (-32.19 = -32.00 +  -0.19)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 10,496,337 – 10,496,436
Length 99
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 92.41
Mean single sequence MFE -27.16
Consensus MFE -23.11
Energy contribution -23.68
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.59
Structure conservation index 0.85
SVM decision value 0.30
SVM RNA-class probability 0.678271
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10496337 99 - 22224390
CCCAUCCAUUCACUCCA-----UCCGCAAAAUGUUCGCCAAUUUGCCCGCCGCGUAACUGGAGCAGAAAUUAGCACAGAAAAGCGGAGCUUCGAAAUGAGUGGG
((((..((((.......-----(((((....(((.(.....((((((((.........))).))))).....).))).....))))).......))))..)))) ( -25.74)
>DroSec_CAF1 27483 104 - 1
CCCACCCAUUCACUCCAUCCCAUCCGCAAAAUGCUCACCAAUUUGCCAGCCGCGUAACUGGAGCAGAAAUUAGCACAGAAAAGCGAAGCUUGGAAAUGAGUGGG
....((((((((.((((........(((((.((.....)).))))).((((((....(((..((........)).)))....)))..)))))))..)))))))) ( -29.20)
>DroSim_CAF1 28009 104 - 1
CCCACCCAUUCACUCCAUCCCAUCCGCAAAAUGCUCACCAAUUUGCCCGCCGCGUAACUGGAGCAGAAAUUAGCACAGAAAAGCGAAGCUUGGAAAUGAGUGGG
....((((((((.((((........(((((.((.....)).)))))..(((((....(((..((........)).)))....)))..)).))))..)))))))) ( -28.70)
>DroEre_CAF1 29071 99 - 1
CCCACCCAUUCACUCCA-----UUCGCAAAAUGCUCACCAAUUUUCCCGCCGCGUAACUGGAGCAGAAAUUAGCACAGAAAAGCGAAGCUUGAAAAUGAGUGGG
....(((((((......-----...((.....))......((((((..(((((....(((..((........)).)))....)))..))..))))))))))))) ( -25.00)
>consensus
CCCACCCAUUCACUCCA_____UCCGCAAAAUGCUCACCAAUUUGCCCGCCGCGUAACUGGAGCAGAAAUUAGCACAGAAAAGCGAAGCUUGGAAAUGAGUGGG
....((((((((.((((........(((((.((.....)).)))))..(((((....(((..((........)).)))....)))..)).))))..)))))))) (-23.11 = -23.68 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:21 2006