Locus 5254

Sequence ID 3R_DroMel_CAF1
Location 13,706,235 – 13,706,331
Length 96
Max. P 0.974746
window8578 window8579

overview

Window 8

Location 13,706,235 – 13,706,331
Length 96
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 92.71
Mean single sequence MFE -28.20
Consensus MFE -24.17
Energy contribution -24.92
Covariance contribution 0.75
Combinations/Pair 1.04
Mean z-score -2.39
Structure conservation index 0.86
SVM decision value 1.46
SVM RNA-class probability 0.956263
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13706235 96 + 27905053
UUGAAGGGGGCUUCCCCAUUUAUAGGGGUUACCCCUUGUAAGCCUAAAAAUACGUAUCGACUUUGGAUUGGUUUGUUGGUUCUUGGUUUAUUGGUU
...((((((....((((.......))))...))))))(((((((.......(((.((((((....).))))).)))........)))))))..... ( -27.26)
>DroSec_CAF1 16004 95 + 1
UUAAAGGGGGCUUCCCCUUUUAUGGGGAUUACCCCUUGUAAGCCUAA-AAUACGUAUCGACUUUGGAUUGGUUUGUUGGUUCUUGGUUUGUUGGUU
...((((((...(((((......)))))...))))))...((((..(-(((....((((((.............)))))).....))))...)))) ( -30.12)
>DroSim_CAF1 16667 96 + 1
UUAAAGGGGGCUUCCCCUUUUAUAGGGAUUACCCCUUGUAAGCCUAAAAAUACGUAUCGACUUUGGAUUGGUUUGUUGGUUCUUGGUUUGUUGGUU
...((((((...((((........))))...))))))...((((...((((....((((((.............)))))).....))))...)))) ( -25.92)
>DroYak_CAF1 24789 96 + 1
UUAAAGUGGGUUUCCCCAUUAUUGGGGGAUACCCCUUGUAAGCCUAAAAAUACGUAUCGACUUUGGAUUGGAUUGUUGGUUCUUGGUUUGCUGGUU
...(((.(((((((((((....))))))).)))))))(((((((.........((....))...((((..(....)..))))..)))))))..... ( -29.50)
>consensus
UUAAAGGGGGCUUCCCCAUUUAUAGGGAUUACCCCUUGUAAGCCUAAAAAUACGUAUCGACUUUGGAUUGGUUUGUUGGUUCUUGGUUUGUUGGUU
...((((((...(((((......)))))...))))))...((((...((((....((((((.............)))))).....))))...)))) (-24.17 = -24.92 +   0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,706,235 – 13,706,331
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 92.71
Mean single sequence MFE -20.23
Consensus MFE -17.20
Energy contribution -17.02
Covariance contribution -0.19
Combinations/Pair 1.14
Mean z-score -2.81
Structure conservation index 0.85
SVM decision value 1.74
SVM RNA-class probability 0.974746
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13706235 96 - 27905053
AACCAAUAAACCAAGAACCAACAAACCAAUCCAAAGUCGAUACGUAUUUUUAGGCUUACAAGGGGUAACCCCUAUAAAUGGGGAAGCCCCCUUCAA
..............(((................(((((..............)))))....(((((..((((.......))))..))))).))).. ( -20.84)
>DroSec_CAF1 16004 95 - 1
AACCAACAAACCAAGAACCAACAAACCAAUCCAAAGUCGAUACGUAUU-UUAGGCUUACAAGGGGUAAUCCCCAUAAAAGGGGAAGCCCCCUUUAA
.................................(((((..........-...)))))..((((((...(((((......)))))...))))))... ( -21.42)
>DroSim_CAF1 16667 96 - 1
AACCAACAAACCAAGAACCAACAAACCAAUCCAAAGUCGAUACGUAUUUUUAGGCUUACAAGGGGUAAUCCCUAUAAAAGGGGAAGCCCCCUUUAA
.................................(((((..............)))))..((((((...(((((......)))))...))))))... ( -19.14)
>DroYak_CAF1 24789 96 - 1
AACCAGCAAACCAAGAACCAACAAUCCAAUCCAAAGUCGAUACGUAUUUUUAGGCUUACAAGGGGUAUCCCCCAAUAAUGGGGAAACCCACUUUAA
.................................(((((..............)))))..(((((((.(((((.......))))).)))).)))... ( -19.54)
>consensus
AACCAACAAACCAAGAACCAACAAACCAAUCCAAAGUCGAUACGUAUUUUUAGGCUUACAAGGGGUAACCCCCAUAAAAGGGGAAGCCCCCUUUAA
.................................(((((..............)))))....(((((..((((.......))))..)))))...... (-17.20 = -17.02 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:23 2006