Locus 4684

Sequence ID 3L_DroMel_CAF1
Location 13,223,657 – 13,223,806
Length 149
Max. P 0.738550
window7379 window7380 window7381

overview

Window 9

Location 13,223,657 – 13,223,768
Length 111
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 92.49
Mean single sequence MFE -18.77
Consensus MFE -14.75
Energy contribution -14.87
Covariance contribution 0.11
Combinations/Pair 1.07
Mean z-score -2.67
Structure conservation index 0.79
SVM decision value 0.44
SVM RNA-class probability 0.738550
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13223657 111 + 23771897
UAAAGGGCUGGGCAAAACCAAAGCAAUAUUUUUCAAAAAUAAUAACAAAACCACCUCGACCACUAGUGGUCAAUUCCCAUUAAAUUCCCCCAGGCAUUAGGCCCUAAAAAA
...((((((((......))...((..(((((.....)))))................(((((....)))))......................))....))))))...... ( -22.40)
>DroSec_CAF1 17062 111 + 1
UAACGGGUUAUACAAAACAAAACCAAUAUUUUUCAAAAAUAAUAACAAAACCACCUCGACCACUAGUGGUCAAUUACCAUUAAAUUCCCCCAGGCAUUAGGCCCUAAAAAA
....(((...................(((((.....)))))................(((((....))))).................))).(((.....)))........ ( -15.80)
>DroYak_CAF1 17021 111 + 1
UAAAGGGCUUGGCAAAACCAAAGCAACAUUUUUGAAAAAUAAUAAUAAAACCACCUCGACCACUAGUGGCCAAUUCCCAUUAAAUUCCCCCAGGCAUUAGGCCCUAAAAAA
...((((((((((.....(((((......))))).............................((((((.......))))))...........))..))))))))...... ( -18.10)
>consensus
UAAAGGGCUAGGCAAAACCAAAGCAAUAUUUUUCAAAAAUAAUAACAAAACCACCUCGACCACUAGUGGUCAAUUCCCAUUAAAUUCCCCCAGGCAUUAGGCCCUAAAAAA
....(((((................................................(((((....)))))...........(((.((....)).))).)))))....... (-14.75 = -14.87 +   0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,223,688 – 13,223,806
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 97.18
Mean single sequence MFE -18.75
Consensus MFE -17.03
Energy contribution -17.03
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.91
SVM decision value 0.34
SVM RNA-class probability 0.694831
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13223688 118 + 23771897
UUCAAAAAUAAUAACAAAACCACCUCGACCACUAGUGGUCAAUUCCCAUUAAAUUCCCCCAGGCAUUAGGCCCUAAAAAACGACUAAACUGUCAGAAAGUCGCGCCAACGCCCACUAA
..........................(((((....))))).....................(((.((.(((..........(((......))).(.....)..))))).)))...... ( -18.50)
>DroSec_CAF1 17093 118 + 1
UUCAAAAAUAAUAACAAAACCACCUCGACCACUAGUGGUCAAUUACCAUUAAAUUCCCCCAGGCAUUAGGCCCUAAAAAACGACUAAACUGUCAGAAAGUCGCGCCAACGCCCACUAA
..........................(((((....))))).....................(((.((.(((..........(((......))).(.....)..))))).)))...... ( -18.50)
>DroYak_CAF1 17052 118 + 1
UUGAAAAAUAAUAAUAAAACCACCUCGACCACUAGUGGCCAAUUCCCAUUAAAUUCCCCCAGGCAUUAGGCCCUAAAAAACGACUAAACUGUCAGAAAGUCGCGCUAACGCCCACUAA
.........................((((...(((.(((((((.((...............)).))).)))))))......(((......))).....)))).((....))....... ( -19.26)
>consensus
UUCAAAAAUAAUAACAAAACCACCUCGACCACUAGUGGUCAAUUCCCAUUAAAUUCCCCCAGGCAUUAGGCCCUAAAAAACGACUAAACUGUCAGAAAGUCGCGCCAACGCCCACUAA
................................((((((...............(((.....(((.....))).........(((......))).)))....(((....))))))))). (-17.03 = -17.03 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,223,688 – 13,223,806
Length 118
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 97.18
Mean single sequence MFE -33.56
Consensus MFE -30.66
Energy contribution -30.33
Covariance contribution -0.33
Combinations/Pair 1.08
Mean z-score -1.74
Structure conservation index 0.91
SVM decision value 0.08
SVM RNA-class probability 0.575941
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13223688 118 - 23771897
UUAGUGGGCGUUGGCGCGACUUUCUGACAGUUUAGUCGUUUUUUAGGGCCUAAUGCCUGGGGGAAUUUAAUGGGAAUUGACCACUAGUGGUCGAGGUGGUUUUGUUAUUAUUUUUGAA
.....((((((((((.(.......((((......)))).......).))).)))))))..((((((.((((..((.(((((((....))))))).....))..))))..))))))... ( -33.34)
>DroSec_CAF1 17093 118 - 1
UUAGUGGGCGUUGGCGCGACUUUCUGACAGUUUAGUCGUUUUUUAGGGCCUAAUGCCUGGGGGAAUUUAAUGGUAAUUGACCACUAGUGGUCGAGGUGGUUUUGUUAUUAUUUUUGAA
.....((((((((((.(.......((((......)))).......).))).)))))))..........(((((((((.(((((((.........)))))))..)))))))))...... ( -32.14)
>DroYak_CAF1 17052 118 - 1
UUAGUGGGCGUUAGCGCGACUUUCUGACAGUUUAGUCGUUUUUUAGGGCCUAAUGCCUGGGGGAAUUUAAUGGGAAUUGGCCACUAGUGGUCGAGGUGGUUUUAUUAUUAUUUUUCAA
.....(((((((((.((..((...((((......))))......)).))))))))))).(..((((.((((((((.(((((((....))))))).....))))))))..))))..).. ( -35.20)
>consensus
UUAGUGGGCGUUGGCGCGACUUUCUGACAGUUUAGUCGUUUUUUAGGGCCUAAUGCCUGGGGGAAUUUAAUGGGAAUUGACCACUAGUGGUCGAGGUGGUUUUGUUAUUAUUUUUGAA
.....(((((((((.((..((...((((......))))......)).)))))))))))..((((((.((((((((.(((((((....))))))).....))))))))..))))))... (-30.66 = -30.33 +  -0.33)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:42 2006