Locus 5361

Sequence ID X_DroMel_CAF1
Location 13,956,932 – 13,957,049
Length 117
Max. P 0.710926
window8699 window8700

overview

Window 9

Location 13,956,932 – 13,957,049
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.01
Mean single sequence MFE -34.41
Consensus MFE -26.71
Energy contribution -27.40
Covariance contribution 0.69
Combinations/Pair 1.04
Mean z-score -1.65
Structure conservation index 0.78
SVM decision value 0.36
SVM RNA-class probability 0.702684
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13956932 117 + 22224390
AGAAGACCCAGCCUCCAGUGGGUUCUAUCCACGGUGGGGCAAUAAAAAUUUAUGAAGCCUGAGGAUGCUGGCGGGGGCAGGGUCUCAGCUGCUUAACCCAUUAAUGACCAAUGAG---AA
.((.(((((.((((((.((.(((...((((....(.((((.((((....))))...)))).)))))))).)))))))).))))))).............................---.. ( -35.80)
>DroSec_CAF1 8151 103 + 1
AGAAGACCCAGCCUCC----------------GGUGGGGCAAUAAAAAUUUAUGAAGCCAGAGGAAGCUAA-GGGGGCAGGGUCUCAGCAGCUUAACCCAUUAAAUACCAAUGAAUGUAA
.((.(((((.((((((----------------.....(((.((((....))))...)))..((....))..-)))))).))))))).................................. ( -27.70)
>DroSim_CAF1 8540 119 + 1
AGAAGACCCAGCCUCCAGUGGGUUUUAUCCACGGUGGGGCAAUAAAAAUUUAUGAAGCCAGAGGAAGCUGA-GGGGGCAGGGUCUCAGCAGCUUAACCCAUUAAAUACCAAUGACUGUAA
.((.(((((.((((((.((((((...)))))).....(((.((((....))))...)))............-)))))).))))))).(((((....................).)))).. ( -35.45)
>DroYak_CAF1 8912 116 + 1
AGAAGACCCAGCCUCCAGUGGGUUUUAUCCACAGUGGGGCAAUAAAAAUUUAUGAAGCCCGAAGAAACUGU-GGGGGCAGGGCUCC---AGCUUAACCCAUUAAAGGCCAGUGCCUGUAA
..((((((((........))))))))..(((((((.((((.((((....))))...))))......)))))-))(((..((((...---.))))..))).....((((....)))).... ( -38.70)
>consensus
AGAAGACCCAGCCUCCAGUGGGUUUUAUCCACGGUGGGGCAAUAAAAAUUUAUGAAGCCAGAGGAAGCUGA_GGGGGCAGGGUCUCAGCAGCUUAACCCAUUAAAGACCAAUGACUGUAA
...((((((.((((((.((((((...)))))).....(((.((((....))))...))).............)))))).))))))................................... (-26.71 = -27.40 +   0.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,956,932 – 13,957,049
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.01
Mean single sequence MFE -33.25
Consensus MFE -23.44
Energy contribution -23.50
Covariance contribution 0.06
Combinations/Pair 1.17
Mean z-score -1.74
Structure conservation index 0.70
SVM decision value 0.38
SVM RNA-class probability 0.710926
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13956932 117 - 22224390
UU---CUCAUUGGUCAUUAAUGGGUUAAGCAGCUGAGACCCUGCCCCCGCCAGCAUCCUCAGGCUUCAUAAAUUUUUAUUGCCCCACCGUGGAUAGAACCCACUGGAGGCUGGGUCUUCU
..---(((((((.....)))))))..........(((((((.(((.(((((..........)))........................((((.......)))).)).))).))))))).. ( -32.50)
>DroSec_CAF1 8151 103 - 1
UUACAUUCAUUGGUAUUUAAUGGGUUAAGCUGCUGAGACCCUGCCCCC-UUAGCUUCCUCUGGCUUCAUAAAUUUUUAUUGCCCCACC----------------GGAGGCUGGGUCUUCU
....((((((((.....)))))))).........(((((((.......-..(((((((...(((...((((....)))).))).....----------------)))))))))))))).. ( -24.50)
>DroSim_CAF1 8540 119 - 1
UUACAGUCAUUGGUAUUUAAUGGGUUAAGCUGCUGAGACCCUGCCCCC-UCAGCUUCCUCUGGCUUCAUAAAUUUUUAUUGCCCCACCGUGGAUAAAACCCACUGGAGGCUGGGUCUUCU
.....(((.(..((((((((....))))).)))..))))........(-(((((((((...(((...((((....)))).))).....((((.......)))).))))))))))...... ( -31.80)
>DroYak_CAF1 8912 116 - 1
UUACAGGCACUGGCCUUUAAUGGGUUAAGCU---GGAGCCCUGCCCCC-ACAGUUUCUUCGGGCUUCAUAAAUUUUUAUUGCCCCACUGUGGAUAAAACCCACUGGAGGCUGGGUCUUCU
....((((.(..(((((((.((((((..((.---((...)).))..((-(((((......((((...((((....)))).)))).)))))))....)))))).)))))))..)))))... ( -44.20)
>consensus
UUACAGUCAUUGGUAUUUAAUGGGUUAAGCUGCUGAGACCCUGCCCCC_UCAGCUUCCUCUGGCUUCAUAAAUUUUUAUUGCCCCACCGUGGAUAAAACCCACUGGAGGCUGGGUCUUCU
...........((((......(((((..........)))))))))(((...(((((((...(((...((((....)))).))).....((((.......)))).))))))))))...... (-23.44 = -23.50 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:07 2006