Locus 1253

Sequence ID 3L_DroMel_CAF1
Location 3,609,660 – 3,609,767
Length 107
Max. P 0.901071
window1964 window1965

overview

Window 4

Location 3,609,660 – 3,609,767
Length 107
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 91.21
Mean single sequence MFE -36.22
Consensus MFE -27.60
Energy contribution -28.00
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.76
SVM decision value 0.24
SVM RNA-class probability 0.650714
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3609660 107 + 23771897
GAGCGACAGAUCACCUGGGC-------CGAAAGUGGCGGAGAGCGGACCAGGUGAGCGGAACACCUGGUGAGCAGAGUAUCCGACAGAUACAGAUACGAAAGGUGAGCGAGAGC
..........((((((..((-------((....)))).....((..((((((((.......))))))))..))...(((((.....))))).........))))))((....)) ( -36.60)
>DroSec_CAF1 134263 107 + 1
GAGCGACAGAUCACCUGGGC-------CGAAAGUGGCGGAGAGCGAUCCAGGUGAGCGGAACACCUGGUGAGCAGAGUAUCCGACAGAUACAGAUACGAAAGGUGAGCGAGAGC
..........((((((..((-------((....)))).....((...(((((((.......)))))))...))...(((((.....))))).........))))))((....)) ( -34.60)
>DroSim_CAF1 140166 107 + 1
GAGCGACAGAUCACCUGGGC-------CGAAAGUCGCGGAGAGCGAUCCAGGUGAGCGGAACACCUGGUGAGCAGAGUAUCCGACAGAUACAGAUACGAAAGGUGAGCGAGAGC
..((..(...(((((((((.-------(....)((((.....)))))))))))))...)..(((((..((......(((((.....))))).....))..))))).))...... ( -35.50)
>DroEre_CAF1 156630 101 + 1
GAGCGUCAGAUCACCUGGGC-------CGAAACUGGCGGAGAGCGAUCCAGGUGAGCGGAACACCUGGUGAGCAGAGUAUCCGACAG------AUACGAAAGGUGAGCGAGAGC
..........((((((..((-------((....)))).....((...(((((((.......)))))))...))...(((((.....)------))))...))))))((....)) ( -34.80)
>DroYak_CAF1 139203 108 + 1
GAGCGACAGAUCACCUGGGCCUGGGCCCGAAACGCGAGGAGAGCGAUCCAGGUGAGCGGAACACCUGGUGAGCAGAGUAUCCGACAG------AUACGAAAGGUGAGCGAGAGC
..........((((((((((....))))....(....)....((...(((((((.......)))))))...))...(((((.....)------))))...))))))((....)) ( -39.60)
>consensus
GAGCGACAGAUCACCUGGGC_______CGAAAGUGGCGGAGAGCGAUCCAGGUGAGCGGAACACCUGGUGAGCAGAGUAUCCGACAGAUACAGAUACGAAAGGUGAGCGAGAGC
..........((((((..........................((...(((((((.......)))))))...))...(((((...........)))))...))))))((....)) (-27.60 = -28.00 +   0.40)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 5

Location 3,609,660 – 3,609,767
Length 107
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 91.21
Mean single sequence MFE -34.44
Consensus MFE -25.34
Energy contribution -26.54
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.59
Structure conservation index 0.74
SVM decision value 1.02
SVM RNA-class probability 0.901071
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3609660 107 - 23771897
GCUCUCGCUCACCUUUCGUAUCUGUAUCUGUCGGAUACUCUGCUCACCAGGUGUUCCGCUCACCUGGUCCGCUCUCCGCCACUUUCG-------GCCCAGGUGAUCUGUCGCUC
((....(.((((((...(((((((.......)))))))...((..((((((((.......))))))))..)).....(((......)-------))..)))))).)....)).. ( -35.10)
>DroSec_CAF1 134263 107 - 1
GCUCUCGCUCACCUUUCGUAUCUGUAUCUGUCGGAUACUCUGCUCACCAGGUGUUCCGCUCACCUGGAUCGCUCUCCGCCACUUUCG-------GCCCAGGUGAUCUGUCGCUC
((....(.((((((...(((((((.......)))))))...((...(((((((.......)))))))...)).....(((......)-------))..)))))).)....)).. ( -33.00)
>DroSim_CAF1 140166 107 - 1
GCUCUCGCUCACCUUUCGUAUCUGUAUCUGUCGGAUACUCUGCUCACCAGGUGUUCCGCUCACCUGGAUCGCUCUCCGCGACUUUCG-------GCCCAGGUGAUCUGUCGCUC
((....(.((((((...(((((((.......)))))))...(((..(((((((.......))))))).((((.....)))).....)-------))..)))))).)....)).. ( -34.40)
>DroEre_CAF1 156630 101 - 1
GCUCUCGCUCACCUUUCGUAU------CUGUCGGAUACUCUGCUCACCAGGUGUUCCGCUCACCUGGAUCGCUCUCCGCCAGUUUCG-------GCCCAGGUGAUCUGACGCUC
((((....((((((.(((...------(((.((((......((...(((((((.......)))))))...))..)))).)))...))-------)...))))))...)).)).. ( -33.60)
>DroYak_CAF1 139203 108 - 1
GCUCUCGCUCACCUUUCGUAU------CUGUCGGAUACUCUGCUCACCAGGUGUUCCGCUCACCUGGAUCGCUCUCCUCGCGUUUCGGGCCCAGGCCCAGGUGAUCUGUCGCUC
((....(.((((((...((((------(.....)))))........(((((((.......)))))))..(((.......)))....((((....)))))))))).)....)).. ( -36.10)
>consensus
GCUCUCGCUCACCUUUCGUAUCUGUAUCUGUCGGAUACUCUGCUCACCAGGUGUUCCGCUCACCUGGAUCGCUCUCCGCCACUUUCG_______GCCCAGGUGAUCUGUCGCUC
((....(.((((((...(((((((.......)))))))...((...(((((((.......)))))))...))..........................)))))).)....)).. (-25.34 = -26.54 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

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