Locus 8436

Sequence ID X_DroMel_CAF1
Location 20,940,688 – 20,940,867
Length 179
Max. P 0.702022
window13861 window13862

overview

Window 1

Location 20,940,688 – 20,940,787
Length 99
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 88.67
Mean single sequence MFE -29.20
Consensus MFE -21.38
Energy contribution -22.88
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.73
SVM decision value 0.35
SVM RNA-class probability 0.702022
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20940688 99 + 22224390
UUUCAUCCGCACUCUGCUCAAAUGGACAGCUGGUCGCCAUAACGCCAUUA--------CGAUCUCGGGCACCUUCACCUCGAAUUCGUCAAGCUCCUUUUUGGGCCA
...............(((((((.(((..(((((.((......))))...(--------(((..(((((........)).)))..))))..))))))..))))))).. ( -24.60)
>DroSec_CAF1 12735 99 + 1
UUUCAUCCGCACUCGGCUCAAAUGGACAGCUGGUCGCCAUAACGCCAUUA--------CGAUCUCGGGCACCUUCACCUCGAAUACGUCGAGCUCCUGUUUGGGCCA
..............(((((((((((..((((((.((......))))....--------((((.(((((........)).)))....)))))))).))))))))))). ( -28.90)
>DroEre_CAF1 11067 107 + 1
UUUCAUCCGCGCUCGGCUCAAAUGGACAGCUGGGCGCCAUAACGCCACAACGCCAUGACGAUCUCUGGCACCUUCACCUCGAAUACGUCUAGCUCCUGUUUGGGCCA
..............(((((((((((..(((((((((...............((((.((.....))))))...(((.....)))..))))))))).))))))))))). ( -35.30)
>DroYak_CAF1 12264 99 + 1
UUUCAUCCACACUCGGCUCAAAUGGACAGCUGGGCGCCAUAACACCACUA--------CGACCUCGGAAACCUUCACCUCGAAUACGUCGAGCUCCUGUUUGGGCCA
..............(((((((((((..((((.((((..............--------.......(....).(((.....)))..)))).)))).))))))))))). ( -28.00)
>consensus
UUUCAUCCGCACUCGGCUCAAAUGGACAGCUGGGCGCCAUAACGCCACUA________CGAUCUCGGGCACCUUCACCUCGAAUACGUCGAGCUCCUGUUUGGGCCA
..............(((((((((((..((((.((((.......(((....................)))...(((.....)))..)))).)))).))))))))))). (-21.38 = -22.88 +   1.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,940,747 – 20,940,867
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.82
Mean single sequence MFE -30.43
Consensus MFE -25.30
Energy contribution -26.55
Covariance contribution 1.25
Combinations/Pair 1.09
Mean z-score -1.36
Structure conservation index 0.83
SVM decision value -0.05
SVM RNA-class probability 0.508158
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20940747 120 + 22224390
GCACCUUCACCUCGAAUUCGUCAAGCUCCUUUUUGGGCCAUAACUCUUUGGCCGAUCUUUCAGUUUUACGAGGGCCUAAACCUUGUGCAAGGCCACAAGGUAAACUCUUAAAUGCAGCAU
(((......(((((....)((.(((((......(.(((((........))))).)......))))).))))))......((((((((......))))))))...........)))..... ( -32.90)
>DroSec_CAF1 12794 116 + 1
GCACCUUCACCUCGAAUACGUCGAGCUCCUGUUUGGGCCAUAACUCUUUGGCCGAUCUUUCAGUUUUACGAGGGCCUAAACCUUGUGCGAGGCCACAUGGUAAACUCUAAAAUACA----
((((......(((((.....))))).....(((((((((....(((...(((.((....)).)))....))))))))))))...))))((((((....)))...))).........---- ( -31.20)
>DroEre_CAF1 11134 119 + 1
GCACCUUCACCUCGAAUACGUCUAGCUCCUGUUUGGGCCAUAACUCUUUCGCCGAUCUUCCAGUUUUACGAGGGCCUAAACCGUGUGCGAGGUCACAUGCUAAACUCUUAAACUCAACA-
(((.....((((((.(((((..........(((((((((....(((....((.(......).)).....))))))))))))))))).))))))....)))...................- ( -28.40)
>DroYak_CAF1 12323 119 + 1
AAACCUUCACCUCGAAUACGUCGAGCUCCUGUUUGGGCCAUAACUCUUUGGCCGAUCUUCCAGUUUUACGAGGGUCUAAACCUUGUGCGCGGCCACAUGGUAAACUCUUAAAUCCAACG-
..((((((..(((((.....)))))...(((..(.(((((........))))).).....)))......))))))....(((.((((......)))).)))..................- ( -29.20)
>consensus
GCACCUUCACCUCGAAUACGUCGAGCUCCUGUUUGGGCCAUAACUCUUUGGCCGAUCUUCCAGUUUUACGAGGGCCUAAACCUUGUGCGAGGCCACAUGGUAAACUCUUAAAUACAACA_
.........(((((.......(((((....)))))(((((........)))))...............)))))......((((((((......))))))))................... (-25.30 = -26.55 +   1.25)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:00 2006