Locus 1995

Sequence ID 3L_DroMel_CAF1
Location 5,471,641 – 5,471,731
Length 90
Max. P 0.999496
window3124 window3125

overview

Window 4

Location 5,471,641 – 5,471,731
Length 90
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 71.36
Mean single sequence MFE -27.25
Consensus MFE -16.96
Energy contribution -19.28
Covariance contribution 2.31
Combinations/Pair 1.04
Mean z-score -2.49
Structure conservation index 0.62
SVM decision value 3.47
SVM RNA-class probability 0.999262
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5471641 90 + 23771897
GAUGUUU--------------------------UCGUUUAUUUUUGUGGAUAGUCGGUUCCAAAUAGUUUGUUACAAACUAAAGCGGAUAGUUUGUAACGGGCUGCCUUCUUGGAU
.......--------------------------(((.((((((....)))))).))).(((((.(((((((((((((((((.......))))))))))))))))).....))))). ( -25.20)
>DroSec_CAF1 33185 90 + 1
GAUGUUU--------------------------UCGCUUAUUUUUGUGGAUAUUCGGUUCCAAAAAGUUUGUUACAAACUAAAGCGGUUAGUCUGUAGCGGGCUACCUUUUUGGAU
((....(--------------------------((((........)))))...))...((((((((((((((((((.(((((.....))))).)))))))))))....))))))). ( -25.90)
>DroSim_CAF1 34738 90 + 1
GAUGUUU--------------------------UGGCUUAUUUUUGUGGAUAUUCGGUUCCAAACAGUUUGUUACAAACUAAAGCGUUUAGUUUGUAGCGGGCUACCGUUUUGGAU
((....(--------------------------(.((........)).))...))...((((((((((((((((((((((((.....)))))))))))))))))...).)))))). ( -25.30)
>DroYak_CAF1 20639 116 + 1
GGUAUUUCGUAUAAAGUUUUUGAACAUAUGAAGACGUUUAUGGUUCAGAAAAGUCGGUUCCAAACAGGUUGUUACAAACUAAGGCAGCUAGUUUGGCGCGUGCACUUUUCUUGGAC
.........((((((((((((........)))))).))))))((((((((((((((((.((((((.(((((((.........))))))).)))))).)).)).))))))).))))) ( -32.60)
>consensus
GAUGUUU__________________________UCGCUUAUUUUUGUGGAUAGUCGGUUCCAAACAGUUUGUUACAAACUAAAGCGGUUAGUUUGUAGCGGGCUACCUUCUUGGAU
..........................................................((((((.(((((((((((((((((.....))))))))))))))))).....)))))). (-16.96 = -19.28 +   2.31)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 5,471,641 – 5,471,731
Length 90
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 71.36
Mean single sequence MFE -18.12
Consensus MFE -12.36
Energy contribution -13.05
Covariance contribution 0.69
Combinations/Pair 1.16
Mean z-score -2.43
Structure conservation index 0.68
SVM decision value 3.66
SVM RNA-class probability 0.999496
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5471641 90 - 23771897
AUCCAAGAAGGCAGCCCGUUACAAACUAUCCGCUUUAGUUUGUAACAAACUAUUUGGAACCGACUAUCCACAAAAAUAAACGA--------------------------AAACAUC
.((((((..((....))(((((((((((.......)))))))))))......)))))).........................--------------------------....... ( -19.50)
>DroSec_CAF1 33185 90 - 1
AUCCAAAAAGGUAGCCCGCUACAGACUAACCGCUUUAGUUUGUAACAAACUUUUUGGAACCGAAUAUCCACAAAAAUAAGCGA--------------------------AAACAUC
.(((((((((((((....))))(((((((.....)))))))........)))))))))..((..(((........)))..)).--------------------------....... ( -19.00)
>DroSim_CAF1 34738 90 - 1
AUCCAAAACGGUAGCCCGCUACAAACUAAACGCUUUAGUUUGUAACAAACUGUUUGGAACCGAAUAUCCACAAAAAUAAGCCA--------------------------AAACAUC
.((((((.((((.....(.((((((((((.....)))))))))).)..)))))))))).........................--------------------------....... ( -17.40)
>DroYak_CAF1 20639 116 - 1
GUCCAAGAAAAGUGCACGCGCCAAACUAGCUGCCUUAGUUUGUAACAACCUGUUUGGAACCGACUUUUCUGAACCAUAAACGUCUUCAUAUGUUCAAAAACUUUAUACGAAAUACC
.....((((((((.(......((((((((.....))))))))......((.....))....)))))))))((((.(((..........)))))))..................... ( -16.60)
>consensus
AUCCAAAAAGGUAGCCCGCUACAAACUAACCGCUUUAGUUUGUAACAAACUGUUUGGAACCGAAUAUCCACAAAAAUAAACGA__________________________AAACAUC
.((((((..((....))(.((((((((((.....)))))))))).)......)))))).......................................................... (-12.36 = -13.05 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:03 2006