Locus 4119

Sequence ID X_DroMel_CAF1
Location 10,850,309 – 10,850,497
Length 188
Max. P 0.887986
window6767 window6768

overview

Window 7

Location 10,850,309 – 10,850,417
Length 108
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 90.48
Mean single sequence MFE -39.69
Consensus MFE -32.12
Energy contribution -33.38
Covariance contribution 1.25
Combinations/Pair 1.03
Mean z-score -2.09
Structure conservation index 0.81
SVM decision value 0.95
SVM RNA-class probability 0.887986
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10850309 108 + 22224390
UUGCUGGCAGACAGGUGGCCACAAGCUUGGCUCUAAAUGCAGAGCACUUGGGGCGCG---CUUGUUAAGGCCACUCAACUCCAUUAGCACACGGUGGCUGCACUGGAAAGA
.((((((..((..(((((((((((((...(((((((.(((...))).)))))))..)---)))))...)))))))....))..))))))..(((((....)))))...... ( -41.20)
>DroSec_CAF1 4298 110 + 1
-CGUUGGCAGACAGGUGGCCACAAGCUUGGCUCUAAAUGCAGAGCACUUGGGGCACGCUGCUUGUUAAGGCCACUCAACUCCAUUAGCACACGGUGACUGCACUGCAAAGA
-.....((((...(((((((((((((.(((((((((.(((...))).))))))).))..))))))...)))))))...........(((...(....)))).))))..... ( -41.00)
>DroSim_CAF1 4395 110 + 1
-CGUUGGCAGACAGGUGGCCACAAGCUUGGCUCUAAAUGCAGAGCACUUGGGGCACGCUGCUUGUUAAGGCCACUCAACUCCAUUAGCACACGGUGGCUGCACUGGAAAGA
-...(((.((...(((((((((((((.(((((((((.(((...))).))))))).))..))))))...)))))))...)))))........(((((....)))))...... ( -40.40)
>DroYak_CAF1 4378 107 + 1
UUGCUGGCAAAUAGGUGGCCACAAGCCUGGCUCUAAAUGCAGAACACUUGGGGCAUG---CUUGUUAAGGCCACUCAACUCCAUUAGCAGAACG-GGCUACACUGGAAAGA
(((((((......(((((((((((((...(((((((.((.....)).)))))))..)---)))))...)))))))........)))))))..((-(......)))...... ( -36.14)
>consensus
_CGCUGGCAGACAGGUGGCCACAAGCUUGGCUCUAAAUGCAGAGCACUUGGGGCACG___CUUGUUAAGGCCACUCAACUCCAUUAGCACACGGUGGCUGCACUGGAAAGA
..(((((.((...(((((((((((((...(((((((.((.....)).))))))).....))))))...)))))))...)))))...))...(((((....)))))...... (-32.12 = -33.38 +   1.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,850,377 – 10,850,497
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.18
Mean single sequence MFE -32.73
Consensus MFE -28.31
Energy contribution -28.20
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.02
Structure conservation index 0.86
SVM decision value 0.32
SVM RNA-class probability 0.686565
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10850377 120 + 22224390
CACUCAACUCCAUUAGCACACGGUGGCUGCACUGGAAAGAAAUUCGCUACUUGCGAACGCCUGGACUUUCACAGCUUGGGCAUAGAUCACCGCACUUAGCUUUCAGUGCAGUCAUUCUCA
.....................((((((((((((((((.((..(((((.....))))).(((..(.((.....)).)..))).....))...((.....)))))))))))))))))).... ( -38.10)
>DroSec_CAF1 4368 118 + 1
CACUCAACUCCAUUAGCACACGGUGACUGCACUGCAAAGAAAAUCGCUACCUGCGAACGCCUGGACUUUCAUAGCCUGGACAUAGAUCACCGUAUUUAGUUCUCAGUGCAGUCAUU--CA
.....................(((((((((((((...((((..((((.....))))..(((.((.((.....)))).)).)..................)))))))))))))))))--.. ( -32.10)
>DroSim_CAF1 4465 118 + 1
CACUCAACUCCAUUAGCACACGGUGGCUGCACUGGAAAGAAAAUCGCUACCUGCGAACGCCUGGACUUUCAUAGCCUGGACAUAGAUCACCGCAUUUAGUUCUCAAUGCAGUCAUU--CA
.....................((((((((((.(((((..(((.((((.....))))..(((.((.((.....)))).)).).............)))..))).)).))))))))))--.. ( -28.00)
>consensus
CACUCAACUCCAUUAGCACACGGUGGCUGCACUGGAAAGAAAAUCGCUACCUGCGAACGCCUGGACUUUCAUAGCCUGGACAUAGAUCACCGCAUUUAGUUCUCAGUGCAGUCAUU__CA
.....................(((((((((((((.........((((.....))))..(((.((.((.....)))).)).)......................))))))))))))).... (-28.31 = -28.20 +  -0.11)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:48 2006