Locus 5245

Sequence ID X_DroMel_CAF1
Location 13,685,864 – 13,685,964
Length 100
Max. P 0.980379
window8499 window8500

overview

Window 9

Location 13,685,864 – 13,685,964
Length 100
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.80
Mean single sequence MFE -25.77
Consensus MFE -17.15
Energy contribution -18.05
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -3.05
Structure conservation index 0.67
SVM decision value 1.65
SVM RNA-class probability 0.969951
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13685864 100 + 22224390
AUAAAUAAAUUACAAAAAAUAAUCGAAAAUCGGGGAUCCCACAUCAUGCUCGAU---------------AU-----AUACGAUAUACGAUGCAUGUGGAUCCCCUUUGGAUGGUAGAUCU
.........((((........(((.(((...((((((((.....((((((((((---------------((-----.....)))).))).))))).))))))))))).))).)))).... ( -28.10)
>DroSim_CAF1 3070 103 + 1
AUAAAUAAAUUACAAAAAAUAAUCGAAAAUCGGGGACCCC--AUCAUGAUCGAU---------------AUACGAUAUACUAUAUACGAUACAUGUGGAUCCCCUUUGGAUGGUAGAUCU
.........((((........(((.(((...(((((..((--(.((((((((((---------------(((........))))).)))).))))))).)))))))).))).)))).... ( -24.80)
>DroYak_CAF1 3241 118 + 1
AUAAAUAAAUUACAAAAAAUAAUCGAAAAUCGGGGAUCCC--AUCAUAUACGAUAAUGCGAUAUACAAUAUACGAUAUACGAUAUACGAUACGUGUGGAUCCCCUUUGGAUGGUAGAUCU
.........((((........(((.(((...((((((((.--(((.(((((((((.((.......)).))).)).)))).)))(((((...)))))))))))))))).))).)))).... ( -24.40)
>consensus
AUAAAUAAAUUACAAAAAAUAAUCGAAAAUCGGGGAUCCC__AUCAUGAUCGAU_______________AUACGAUAUACGAUAUACGAUACAUGUGGAUCCCCUUUGGAUGGUAGAUCU
.........((((........(((.(((...((((((((.....((((((((..................................))).))))).))))))))))).))).)))).... (-17.15 = -18.05 +   0.89)

alignment

Postscript

secondary structure

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dotplot

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Window 0

Location 13,685,864 – 13,685,964
Length 100
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.80
Mean single sequence MFE -28.67
Consensus MFE -19.07
Energy contribution -19.41
Covariance contribution 0.34
Combinations/Pair 1.14
Mean z-score -3.28
Structure conservation index 0.67
SVM decision value 1.86
SVM RNA-class probability 0.980379
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13685864 100 - 22224390
AGAUCUACCAUCCAAAGGGGAUCCACAUGCAUCGUAUAUCGUAU-----AU---------------AUCGAGCAUGAUGUGGGAUCCCCGAUUUUCGAUUAUUUUUUGUAAUUUAUUUAU
................((((((((.(((((.((((((((...))-----))---------------).)))))))).....)))))))).......((((((.....))))))....... ( -28.00)
>DroSim_CAF1 3070 103 - 1
AGAUCUACCAUCCAAAGGGGAUCCACAUGUAUCGUAUAUAGUAUAUCGUAU---------------AUCGAUCAUGAU--GGGGUCCCCGAUUUUCGAUUAUUUUUUGUAAUUUAUUUAU
................((((((((.((((.(((((((((........))))---------------).))))))))..--.)))))))).......((((((.....))))))....... ( -27.90)
>DroYak_CAF1 3241 118 - 1
AGAUCUACCAUCCAAAGGGGAUCCACACGUAUCGUAUAUCGUAUAUCGUAUAUUGUAUAUCGCAUUAUCGUAUAUGAU--GGGAUCCCCGAUUUUCGAUUAUUUUUUGUAAUUUAUUUAU
................((((((((..(((...))).(((((((((.((.(((.(((.....))).)))))))))))))--))))))))).......((((((.....))))))....... ( -30.10)
>consensus
AGAUCUACCAUCCAAAGGGGAUCCACAUGUAUCGUAUAUCGUAUAUCGUAU_______________AUCGAACAUGAU__GGGAUCCCCGAUUUUCGAUUAUUUUUUGUAAUUUAUUUAU
................((((((((.(((((.(((..................................)))))))).....)))))))).......((((((.....))))))....... (-19.07 = -19.41 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:10 2006