Locus 6060

Sequence ID 3R_DroMel_CAF1
Location 15,928,654 – 15,928,772
Length 118
Max. P 0.763522
window9884 window9885

overview

Window 4

Location 15,928,654 – 15,928,772
Length 118
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 96.33
Mean single sequence MFE -33.38
Consensus MFE -30.31
Energy contribution -30.20
Covariance contribution -0.11
Combinations/Pair 1.12
Mean z-score -1.23
Structure conservation index 0.91
SVM decision value 0.51
SVM RNA-class probability 0.763522
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15928654 118 + 27905053
UCAUCAGCGCUCGUCCGCUGGCCAUAAAAAGUUACAGACUUUUAAGUGUCCUGCGUUUGCAUUUUAUUUUAGUUUAUUGGUCGGCAAUGGCAAAUGAAAAUGCCAGCUGAGAGAUGAG
((.(((((........((((((((..(((((((...)))))))(((((...(((....)))...)))))........))))))))..(((((........))))))))))))...... ( -33.10)
>DroSec_CAF1 45623 118 + 1
UCAUCAGCGCUCGUCCGAUGGCCAUAAAAAGUUACAGACUUUUAAGUGUCCUGCGUUGGCAUUUUAUUUUAGUUUAUUGGUCGGCAAUGGCAAAUGAAAAUGCCAGCUGAGAGAUGAG
((.(((((((.((.((((((..(...(((((((...)))))))(((((.((......))))))).......)..)))))).))))..(((((........))))))))))))...... ( -34.30)
>DroSim_CAF1 35727 118 + 1
UCAUCAGCGCUCGUCCGAUGGCCAUAAAAAGUUACAGACUUUUAAGUGUCCUGCGUUGGCAUUUUAUUUUAGUUUAUUGGUCGGCAAUGGCAAAUGAAAAUGCCAGCUGAGAGAUGAG
((.(((((((.((.((((((..(...(((((((...)))))))(((((.((......))))))).......)..)))))).))))..(((((........))))))))))))...... ( -34.30)
>DroEre_CAF1 34963 118 + 1
UCAUCAGCGCUCGUCCGCUGGCCAUAAAAAGUUAGAGACUUUUAAGUGUCCUGCGUUGGCAUUUUAUUUUAGUUUAUUGGUUGGCAAUGGCAAAUGAAAAUGCCAGCUGAGAGGAGAG
((.(((((........((..((((..(((((((...)))))))(((((.((......))))))).............))))..))..(((((........))))))))))...))... ( -34.40)
>DroYak_CAF1 47876 118 + 1
UCAUCAGCGCUCGUCCGCUGGCCAUAAAAAGUUACAGACUUUUAAGUGUCCUGCGUUGGCGUUUUAUUUUAGUUUAUUGGUUGGCAAUGGCAAAUGAAAAUGCCAGCUGAGAGGAGAG
((.(((((.......(((.((.(((.(((((((...)))))))..))).)).))).(((((((((...((.(((.((((.....))))))).))..))))))))))))))...))... ( -32.50)
>DroAna_CAF1 29780 118 + 1
UCAUCAGCGCUCGUCCGUUGGCCAUAAAAAGUUACAGACUUUUAAGUGUCCUGCGUUGGCAUUUUAUUUUAGUUUAUUGGUUGGCAAUGGCAAAUGAGAAUGCCGGCUGAGAGGGGAG
...((..(.((((.((((..((((..(((((((...)))))))(((((.((......))))))).............))))..))...((((........)))))).)))).)..)). ( -31.70)
>consensus
UCAUCAGCGCUCGUCCGCUGGCCAUAAAAAGUUACAGACUUUUAAGUGUCCUGCGUUGGCAUUUUAUUUUAGUUUAUUGGUCGGCAAUGGCAAAUGAAAAUGCCAGCUGAGAGAUGAG
((.(((((........((((((((..(((((((...)))))))(((((.((......))))))).............))))))))..(((((........))))))))))))...... (-30.31 = -30.20 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,928,654 – 15,928,772
Length 118
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 96.33
Mean single sequence MFE -26.95
Consensus MFE -23.48
Energy contribution -23.65
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.87
SVM decision value 0.39
SVM RNA-class probability 0.716246
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15928654 118 - 27905053
CUCAUCUCUCAGCUGGCAUUUUCAUUUGCCAUUGCCGACCAAUAAACUAAAAUAAAAUGCAAACGCAGGACACUUAAAAGUCUGUAACUUUUUAUGGCCAGCGGACGAGCGCUGAUGA
......((((((((((((........)))))..((((.((.................(((....)))((.((...((((((.....))))))..)).))...)).)).))))))).)) ( -28.20)
>DroSec_CAF1 45623 118 - 1
CUCAUCUCUCAGCUGGCAUUUUCAUUUGCCAUUGCCGACCAAUAAACUAAAAUAAAAUGCCAACGCAGGACACUUAAAAGUCUGUAACUUUUUAUGGCCAUCGGACGAGCGCUGAUGA
......((((((((((((........)))))..((((.((.................(((....)))((.((...((((((.....))))))..)).))...)).)).))))))).)) ( -27.60)
>DroSim_CAF1 35727 118 - 1
CUCAUCUCUCAGCUGGCAUUUUCAUUUGCCAUUGCCGACCAAUAAACUAAAAUAAAAUGCCAACGCAGGACACUUAAAAGUCUGUAACUUUUUAUGGCCAUCGGACGAGCGCUGAUGA
......((((((((((((........)))))..((((.((.................(((....)))((.((...((((((.....))))))..)).))...)).)).))))))).)) ( -27.60)
>DroEre_CAF1 34963 118 - 1
CUCUCCUCUCAGCUGGCAUUUUCAUUUGCCAUUGCCAACCAAUAAACUAAAAUAAAAUGCCAACGCAGGACACUUAAAAGUCUCUAACUUUUUAUGGCCAGCGGACGAGCGCUGAUGA
......((((((((((((((((.((((...((((.....))))......))))))))))))).(((.((.((...((((((.....))))))..)).)).))).......))))).)) ( -27.80)
>DroYak_CAF1 47876 118 - 1
CUCUCCUCUCAGCUGGCAUUUUCAUUUGCCAUUGCCAACCAAUAAACUAAAAUAAAACGCCAACGCAGGACACUUAAAAGUCUGUAACUUUUUAUGGCCAGCGGACGAGCGCUGAUGA
......((((((((((((........)))))...........................(((..(((.((.((...((((((.....))))))..)).)).)))...).))))))).)) ( -25.80)
>DroAna_CAF1 29780 118 - 1
CUCCCCUCUCAGCCGGCAUUCUCAUUUGCCAUUGCCAACCAAUAAACUAAAAUAAAAUGCCAACGCAGGACACUUAAAAGUCUGUAACUUUUUAUGGCCAACGGACGAGCGCUGAUGA
......(((((((.((((........))))...(((..((.................(((....)))((.((...((((((.....))))))..)).))...))..).))))))).)) ( -24.70)
>consensus
CUCACCUCUCAGCUGGCAUUUUCAUUUGCCAUUGCCAACCAAUAAACUAAAAUAAAAUGCCAACGCAGGACACUUAAAAGUCUGUAACUUUUUAUGGCCAGCGGACGAGCGCUGAUGA
......(((((((.((((........))))...(((..((.................(((....)))((.((...((((((.....))))))..)).))...))..).))))))).)) (-23.48 = -23.65 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:38 2006