Locus 5469

Sequence ID X_DroMel_CAF1
Location 14,212,075 – 14,212,211
Length 136
Max. P 0.988886
window8872 window8873 window8874

overview

Window 2

Location 14,212,075 – 14,212,184
Length 109
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 80.51
Mean single sequence MFE -33.36
Consensus MFE -24.28
Energy contribution -24.24
Covariance contribution -0.04
Combinations/Pair 1.12
Mean z-score -1.68
Structure conservation index 0.73
SVM decision value 0.43
SVM RNA-class probability 0.733489
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14212075 109 - 22224390
AUGAAA--ACACGUGGUUGACGCUUAUGACAGUGGGCCACUUUUGGCGCCACUCCUGGCCAAAAAUUCAUGCCCAGUGUUAACCAAACAAAGUUGCUGUGGCCAUUUGUCC
......--.....(((((((((((......(((((((((....)))).)))))...(((...........))).))))))))))).(((((...((....))..))))).. ( -32.70)
>DroSec_CAF1 123231 111 - 1
AAAAACUUCCACGUGGUUGAACCUACUGGCAGUUGGCCACUUUUGGCGCCACUCCUGGCCAAAAAUUCAUGCCCAGUGUUAACCAAACAAAGUCGCUGCGGCCAUUUGUCC
.............(((((((...((((((((.(((((((....((....))....))))))).......)).))))))))))))).(((((...((....))..))))).. ( -29.50)
>DroSim_CAF1 99495 111 - 1
AAAAACUUCCACGUGGUUGAACCUACUGGCAGUUGGCCACUUUUGGCGCCACUCCUGGCCAAAAAUUCAUGCCCAGUGUUAACCAAACAAAGUCGCUGUGGCCAUUUGUCC
...((((.(((.((((......))))))).))))((((((....((((.(....((((.((........)).))))((((.....))))..).))))))))))........ ( -31.30)
>DroEre_CAF1 110934 89 - 1
----------------------GCCCAUGCAGUGGGCCGCUUUUGGCGCCAUUCCUGGCCAGAAAUCCAUGGCCAGUGUUGACCAAACAAAGUCGCUGUGGCCGCUUGUUC
----------------------((((((...)))))).......((((((((..(((((((........)))))))....(((........)))...)))).))))..... ( -31.80)
>DroYak_CAF1 113183 111 - 1
AAAAACUUCCAUGUGGCUGGAGGUCAUGGCAGUGGGCCACUUUUGGCGCAACUCCUGGCCAGAAAUCCAUGGCCAGUGUUAACCAAACAAAGUCGCUGUGGCCAUUUGUCC
....(((((((......)))))))...(((((..((((((....(((((.....(((((((........)))))))((((.....))))..).))))))))))..))))). ( -41.50)
>consensus
AAAAACUUCCACGUGGUUGAACCUACUGGCAGUGGGCCACUUUUGGCGCCACUCCUGGCCAAAAAUUCAUGCCCAGUGUUAACCAAACAAAGUCGCUGUGGCCAUUUGUCC
...........................(((((..((((((...((((.......((((.((........)).))))((((.....))))..))))..))))))..))))). (-24.28 = -24.24 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,212,110 – 14,212,211
Length 101
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 83.01
Mean single sequence MFE -29.32
Consensus MFE -19.42
Energy contribution -21.80
Covariance contribution 2.38
Combinations/Pair 1.22
Mean z-score -1.72
Structure conservation index 0.66
SVM decision value 0.19
SVM RNA-class probability 0.626470
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14212110 101 + 22224390
CUGGGCAUGAAUUUUUGGCCAGGAGUGGCGCCAAAAGUGGCCCACUGUCAUAAGCGUCAACCACGUGU--UUUCAUUUUUUCAUUGCCCUUCUUUUCUUUUGA
..(((((((((....((((....(((((.((((....)))))))))))))...((((.....))))..--.........)))).))))).............. ( -28.80)
>DroSec_CAF1 123266 103 + 1
CUGGGCAUGAAUUUUUGGCCAGGAGUGGCGCCAAAAGUGGCCAACUGCCAGUAGGUUCAACCACGUGGAAGUUUUUUUUUUCAUUGCCCCUCUUUUAUUUUGA
..(((((((((((((((((.((...((((((.....)).)))).))))))).))))))).....(((((((......)))))))))))).............. ( -30.90)
>DroSim_CAF1 99530 103 + 1
CUGGGCAUGAAUUUUUGGCCAGGAGUGGCGCCAAAAGUGGCCAACUGCCAGUAGGUUCAACCACGUGGAAGUUUUUUUUUUCAUUGCCCCUCUUUUAUUUUGA
..(((((((((((((((((.((...((((((.....)).)))).))))))).))))))).....(((((((......)))))))))))).............. ( -30.90)
>DroYak_CAF1 113218 103 + 1
CUGGCCAUGGAUUUCUGGCCAGGAGUUGCGCCAAAAGUGGCCCACUGCCAUGACCUCCAGCCACAUGGAAGUUUUUCCCUUUACCCAUUCUUUUUUCUUUUGA
(((((((........))))))).........((((((((((.....)))).(((.((((......)))).))).......................)))))). ( -26.70)
>consensus
CUGGGCAUGAAUUUUUGGCCAGGAGUGGCGCCAAAAGUGGCCAACUGCCAGUAGCUUCAACCACGUGGAAGUUUUUUUUUUCAUUGCCCCUCUUUUAUUUUGA
..(((((((((((((((((....(((.(.((((....))))).))))))).)))))))).....(((((((......)))))))))))).............. (-19.42 = -21.80 +   2.38)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,212,110 – 14,212,211
Length 101
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 83.01
Mean single sequence MFE -31.40
Consensus MFE -21.70
Energy contribution -21.82
Covariance contribution 0.12
Combinations/Pair 1.23
Mean z-score -2.91
Structure conservation index 0.69
SVM decision value 2.14
SVM RNA-class probability 0.988886
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14212110 101 - 22224390
UCAAAAGAAAAGAAGGGCAAUGAAAAAAUGAAA--ACACGUGGUUGACGCUUAUGACAGUGGGCCACUUUUGGCGCCACUCCUGGCCAAAAAUUCAUGCCCAG
..............(((((.((((.........--....((((((.((.(....)...)).))))))(((((((..........))))))).))))))))).. ( -30.30)
>DroSec_CAF1 123266 103 - 1
UCAAAAUAAAAGAGGGGCAAUGAAAAAAAAAACUUCCACGUGGUUGAACCUACUGGCAGUUGGCCACUUUUGGCGCCACUCCUGGCCAAAAAUUCAUGCCCAG
..............(((((.((((...............(((((..(.((....))...)..)))))(((((((..........))))))).))))))))).. ( -31.40)
>DroSim_CAF1 99530 103 - 1
UCAAAAUAAAAGAGGGGCAAUGAAAAAAAAAACUUCCACGUGGUUGAACCUACUGGCAGUUGGCCACUUUUGGCGCCACUCCUGGCCAAAAAUUCAUGCCCAG
..............(((((.((((...............(((((..(.((....))...)..)))))(((((((..........))))))).))))))))).. ( -31.40)
>DroYak_CAF1 113218 103 - 1
UCAAAAGAAAAAAGAAUGGGUAAAGGGAAAAACUUCCAUGUGGCUGGAGGUCAUGGCAGUGGGCCACUUUUGGCGCAACUCCUGGCCAGAAAUCCAUGGCCAG
.................((((....((((....)))).((((.(..(((((...(((.....))))))))..)))))))))(((((((........))))))) ( -32.50)
>consensus
UCAAAAGAAAAGAGGGGCAAUGAAAAAAAAAACUUCCACGUGGUUGAACCUAAUGGCAGUGGGCCACUUUUGGCGCCACUCCUGGCCAAAAAUUCAUGCCCAG
..............(((((.((((...............(((((..(............)..)))))(((((((..........))))))).))))))))).. (-21.70 = -21.82 +   0.12)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:42 2006