Locus 7774

Sequence ID 3L_DroMel_CAF1
Location 20,739,828 – 20,740,028
Length 200
Max. P 0.814884
window12658 window12659

overview

Window 8

Location 20,739,828 – 20,739,948
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.67
Mean single sequence MFE -31.28
Consensus MFE -25.54
Energy contribution -26.38
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -1.50
Structure conservation index 0.82
SVM decision value 0.33
SVM RNA-class probability 0.690269
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20739828 120 + 23771897
AACCGAACAGCAGCCCAACUGGAUCUUCGACUACCAGCGUAAAGUGUCCCAGCAAAUGAUAUUUUACAACCGACAGCUGACCACGAUCCGAAUCGUGGUGAACUACCAAAUCGAAGACUU
.......(((........)))..(((((((....((((((((((((((.........))))))))))........))))((((((((....))))))))...........)))))))... ( -31.80)
>DroSec_CAF1 15308 120 + 1
GGCCGAACAGCAGCCCAACUGGAUCUUCGACUACCAGCGUAAAGUGUCCCAGCAAAUGAUAUUUUACAACCGACAGCUGACCACGAUCCGAAUUGUGGUGAACUACCAAAUCGAAGACUU
(((.(.....).)))........(((((((....((((((((((((((.........))))))))))........))))((((((((....))))))))...........)))))))... ( -31.00)
>DroSim_CAF1 18406 120 + 1
GGCCGAACAGCAGCCCAACUGGAUCUUCGACUACCAGCGUAAAGUGUCCCAGCAAAUGAUAUUUUACAACCGACAGCUGACCACGAUCCGAAUCGUGGUGAACUACCAAAUCGAAGACUU
(((.(.....).)))........(((((((....((((((((((((((.........))))))))))........))))((((((((....))))))))...........)))))))... ( -33.10)
>DroEre_CAF1 17053 120 + 1
GGUCGAGCAGCAGCCCAACUGGAUAUUCGACUACCAACGUAAAGUGUCCAAGCAAUUGAUAUUUUACCACCGACAGCUGACCACGUUCCGAAUCGUGGUGAACUACCAAAUCGAAGACUU
..((((.((((...((....))................((((((((((.((....))))))))))))........))))((((((........))))))...........))))...... ( -28.90)
>DroYak_CAF1 29720 120 + 1
GGUCGAACAGCAGCCCAACUGGAUAUUCGACUACCAACGUAAAGUGUCGCAGCAAUUGAUAUUUUACCACCGCCAGCUGACCACGUUCCGAAUCGUGGUAAACUACCGAAUGGAAGACUU
(((((((.(.(((.....)))..).))))))).(((..(((((((((((.(....))))))))))))...((..((...((((((........))))))...))..))..)))....... ( -31.60)
>consensus
GGCCGAACAGCAGCCCAACUGGAUCUUCGACUACCAGCGUAAAGUGUCCCAGCAAAUGAUAUUUUACAACCGACAGCUGACCACGAUCCGAAUCGUGGUGAACUACCAAAUCGAAGACUU
...(((.((((.......((((...........)))).((((((((((.........))))))))))........))))((((((((....))))))))...........)))....... (-25.54 = -26.38 +   0.84)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,739,908 – 20,740,028
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -39.51
Consensus MFE -32.32
Energy contribution -32.88
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.82
SVM decision value 0.66
SVM RNA-class probability 0.814884
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20739908 120 - 23771897
GCGAUGACCAUUGGUCCUUGGGAGUGGGCACGUCAUUGUCUAGUUGAAUGGAACACACGCUAAUGGUGGACUCCUCUACUAAGUCUUCGAUUUGGUAGUUCACCACGAUUCGGAUCGUGG
((((((((.....((((........))))..)))))))).....((((.(((...(((.(....))))...))).((((((((((...))))))))))))))(((((((....))))))) ( -38.40)
>DroSec_CAF1 15388 120 - 1
GCGAUGACCAUUGGUCCUUGGGAGUGGGCACCUCAUUGUCUAGUUCAAUGGAACACACGCUAAUGGUGGACUCGUCCACCAAGUCUUCGAUUUGGUAGUUCACCACAAUUCGGAUCGUGG
.......((((.(((((((((..(((((((......))))..((((....)))).))).))))(((((((((.....((((((((...)))))))))))))))))......))))))))) ( -39.90)
>DroSim_CAF1 18486 120 - 1
GCGAUGACCAUUGGUCCUUGGGAGUGGGCACCUCAUUGUCUAGUUCAAUGGAACACACGCUAAUGGUGGACUCGUCCACCAAGUCUUCGAUUUGGUAGUUCACCACGAUUCGGAUCGUGG
......(((((((((((...(((.((((((......)))))).)))...)).......)))))))))(((....)))((((((((...))))))))......(((((((....))))))) ( -40.91)
>DroEre_CAF1 17133 120 - 1
GCGAUGACCAUUGUUCCUUUGGAGUGUGCACCUCAUUGUCUAGUUCAAUGGAACACACGCUAAUGGUCGUCUCAUCCACCAAGUCUUCGAUUUGGUAGUUCACCACGAUUCGGAACGUGG
(.(((((((((((((((.(((((.((.(((......))).)).))))).)))))).......))))))))).)....((((((((...))))))))......(((((........))))) ( -40.81)
>DroYak_CAF1 29800 120 - 1
GCGUUGACCAUUGUUCCUUUGGAGUGGGCACCUCAUUGUCUAAUUCAAUGGAACACACGCUAAUGGUCGACUCAUCCACCAAGUCUUCCAUUCGGUAGUUUACCACGAUUCGGAACGUGG
(.(((((((((((((((.(((((.((((((......)))))).))))).)))))).......))))))))).).....(((....((((..(((...........)))...))))..))) ( -37.51)
>consensus
GCGAUGACCAUUGGUCCUUGGGAGUGGGCACCUCAUUGUCUAGUUCAAUGGAACACACGCUAAUGGUGGACUCAUCCACCAAGUCUUCGAUUUGGUAGUUCACCACGAUUCGGAUCGUGG
.......((((.(((((.....((((......((((((.......))))))......))))..(((((((((.....((((((((...)))))))))))))))))......))))))))) (-32.32 = -32.88 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:39 2006