Locus 920

Sequence ID 3R_DroMel_CAF1
Location 3,109,644 – 3,109,764
Length 120
Max. P 0.971886
window1458 window1459

overview

Window 8

Location 3,109,644 – 3,109,764
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -24.67
Consensus MFE -23.19
Energy contribution -23.30
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.63
Structure conservation index 0.94
SVM decision value 0.08
SVM RNA-class probability 0.575079
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3109644 120 + 27905053
AAGAAAGGGAGAGGAAGAGUCUUAAAAAAUAGCAGAGUUGCCAUUGAAAAAUACAAUUUAUUAUAAAUUGUUGUUUUUAGUGCCCAACUAGAAUUGGGUUAGACAAAGCGACGAUUGAGG
........((((.......)))).........(((.((((((((((((((..((((((((...))))))))..)))))))))(((((......))))).........)))))..)))... ( -23.20)
>DroSim_CAF1 2551 120 + 1
AAGAAAGGGAGAGGAAGAGCCUUAAAAAAUAGCAGAGUUGCCAUUGAAAAAUACAAUUUAUUAUAAAUUGUUGUUUUUAGUGCCCAACUAGAAUUGGGUUAGACAAAGCGACGAUUGAGG
..........((((.....)))).........(((.((((((((((((((..((((((((...))))))))..)))))))))(((((......))))).........)))))..)))... ( -25.40)
>DroYak_CAF1 248 120 + 1
AAGAAAGGGAGAGGAAGAGCCUUAAAAAAUAGCAGAGUUGCCAUUGAAAAAUACAAUUUAUUAUAAAUUGUUGUUUUUAGUGCCCAACUAGAAUUGGGUUAGACAAAGCGCCGAUUGAGC
......(((.((((.....))))........((......))(((((((((..((((((((...))))))))..))))))))))))..((..(((((((((......))).)))))).)). ( -25.40)
>consensus
AAGAAAGGGAGAGGAAGAGCCUUAAAAAAUAGCAGAGUUGCCAUUGAAAAAUACAAUUUAUUAUAAAUUGUUGUUUUUAGUGCCCAACUAGAAUUGGGUUAGACAAAGCGACGAUUGAGG
..........((((.....)))).........(((.((((((((((((((..((((((((...))))))))..)))))))))(((((......))))).........)))))..)))... (-23.19 = -23.30 +   0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,109,644 – 3,109,764
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -21.13
Consensus MFE -19.92
Energy contribution -19.70
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.97
Structure conservation index 0.94
SVM decision value 1.68
SVM RNA-class probability 0.971886
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3109644 120 - 27905053
CCUCAAUCGUCGCUUUGUCUAACCCAAUUCUAGUUGGGCACUAAAAACAACAAUUUAUAAUAAAUUGUAUUUUUCAAUGGCAACUCUGCUAUUUUUUAAGACUCUUCCUCUCCCUUUCUU
................((((..((((((....))))))...(((((...((((((((...)))))))).......(((((((....)))))))))))))))).................. ( -20.10)
>DroSim_CAF1 2551 120 - 1
CCUCAAUCGUCGCUUUGUCUAACCCAAUUCUAGUUGGGCACUAAAAACAACAAUUUAUAAUAAAUUGUAUUUUUCAAUGGCAACUCUGCUAUUUUUUAAGGCUCUUCCUCUCCCUUUCUU
...........((((((.....((((((....))))))...........((((((((...)))))))).......(((((((....)))))))...)))))).................. ( -20.80)
>DroYak_CAF1 248 120 - 1
GCUCAAUCGGCGCUUUGUCUAACCCAAUUCUAGUUGGGCACUAAAAACAACAAUUUAUAAUAAAUUGUAUUUUUCAAUGGCAACUCUGCUAUUUUUUAAGGCUCUUCCUCUCCCUUUCUU
(((.....)))((((((.....((((((....))))))...........((((((((...)))))))).......(((((((....)))))))...)))))).................. ( -22.50)
>consensus
CCUCAAUCGUCGCUUUGUCUAACCCAAUUCUAGUUGGGCACUAAAAACAACAAUUUAUAAUAAAUUGUAUUUUUCAAUGGCAACUCUGCUAUUUUUUAAGGCUCUUCCUCUCCCUUUCUU
................((((..((((((....))))))...(((((...((((((((...)))))))).......(((((((....)))))))))))))))).................. (-19.92 = -19.70 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:26 2006