Locus 4055

Sequence ID 2L_DroMel_CAF1
Location 11,737,268 – 11,737,377
Length 109
Max. P 0.715462
window6390 window6391

overview

Window 0

Location 11,737,268 – 11,737,377
Length 109
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 92.49
Mean single sequence MFE -32.73
Consensus MFE -26.45
Energy contribution -27.07
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -1.74
Structure conservation index 0.81
SVM decision value 0.29
SVM RNA-class probability 0.669120
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11737268 109 + 22407834
AGCAAAACUGGACCGAAGUCCUUGUAAUGACCAACGACUGGCAGGUGGUCGCUUAUCAUCCGGGGGCAAAGGCAAAAGGCCAUCAUAGCAGUCAAGUGGUUGCCAAAAA----
.((((.(((.(((....(((((((..((((....(((((.......)))))....)))).)))))))...(((.....))).........))).)))..))))......---- ( -30.50)
>DroSec_CAF1 197120 109 + 1
AGCAAAACUGGACCGAAGUCCUUGUAAUGACCAAUGACUGGCAGGUGGUCGCUUAUCAUUCGUGGGCAAAGGCAAAAGGCCAUCAUACCAGUCAAGUGGUUGCCAAAAA----
.((...((.((((....))))..))...(((((.(((((((...(((((.((((((.....))))))...(((.....)))))))).)))))))..)))))))......---- ( -35.40)
>DroSim_CAF1 196913 109 + 1
AGCAAAACUGGACCGAAGUCCUUGUAAUGACCAACGACUGGCAGGUGGUCGCUUAUCAUCCGUGGGCAAAGGCAGAAGGCCAUUAUACCAGUCAAGUGGUUGCCAAAAA----
.((...((.((((....))))..))...(((((..((((((...(((((.((((((.....))))))...(((.....)))))))).))))))...)))))))......---- ( -32.40)
>DroYak_CAF1 190626 110 + 1
AGCAAAACUGGACCGAAGUCCUUGUAAUGACCAACGACUGGCAGGUGGUCGCUUAUCAUCCGCGGG--AUGCCAAAAGGCGAUCAUACCA-UCAAGUGGUUGCCAAAAAAUAU
.((...((.((((....))))..))...(((((..((.(((...((((((((((..(((((...))--))).....)))))))))).)))-))...))))))).......... ( -32.60)
>consensus
AGCAAAACUGGACCGAAGUCCUUGUAAUGACCAACGACUGGCAGGUGGUCGCUUAUCAUCCGUGGGCAAAGGCAAAAGGCCAUCAUACCAGUCAAGUGGUUGCCAAAAA____
.((...((.((((....))))..))...(((((..((((((..(((((((.........(....)((....))....)))))))...))))))...))))))).......... (-26.45 = -27.07 +   0.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,737,268 – 11,737,377
Length 109
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 92.49
Mean single sequence MFE -32.97
Consensus MFE -27.41
Energy contribution -28.48
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.83
SVM decision value 0.39
SVM RNA-class probability 0.715462
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11737268 109 - 22407834
----UUUUUGGCAACCACUUGACUGCUAUGAUGGCCUUUUGCCUUUGCCCCCGGAUGAUAAGCGACCACCUGCCAGUCGUUGGUCAUUACAAGGACUUCGGUCCAGUUUUGCU
----.....(((((..(((.(((((.......(((.....))).......((.((((((.((((((.........)))))).))))))....))....))))).))).))))) ( -29.00)
>DroSec_CAF1 197120 109 - 1
----UUUUUGGCAACCACUUGACUGGUAUGAUGGCCUUUUGCCUUUGCCCACGAAUGAUAAGCGACCACCUGCCAGUCAUUGGUCAUUACAAGGACUUCGGUCCAGUUUUGCU
----.....((((((((..(((((((((.(.(((((((...(.((((....)))).)..))).).)))).))))))))).))))........((((....)))).....)))) ( -36.20)
>DroSim_CAF1 196913 109 - 1
----UUUUUGGCAACCACUUGACUGGUAUAAUGGCCUUCUGCCUUUGCCCACGGAUGAUAAGCGACCACCUGCCAGUCGUUGGUCAUUACAAGGACUUCGGUCCAGUUUUGCU
----.....((((((((..(((((((((....(((.....))).........((.((.....)).))...))))))))).))))........((((....)))).....)))) ( -33.90)
>DroYak_CAF1 190626 110 - 1
AUAUUUUUUGGCAACCACUUGA-UGGUAUGAUCGCCUUUUGGCAU--CCCGCGGAUGAUAAGCGACCACCUGCCAGUCGUUGGUCAUUACAAGGACUUCGGUCCAGUUUUGCU
.........((((((((..(((-(((((((.((((.((....(((--((...)))))..)))))).))..))))).))).))))........((((....)))).....)))) ( -32.80)
>consensus
____UUUUUGGCAACCACUUGACUGGUAUGAUGGCCUUUUGCCUUUGCCCACGGAUGAUAAGCGACCACCUGCCAGUCGUUGGUCAUUACAAGGACUUCGGUCCAGUUUUGCU
.........((((((((..(((((((((....(((.....))).........((.((.....)).))...))))))))).))))........((((....)))).....)))) (-27.41 = -28.48 +   1.06)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:12 2006