Locus 7733

Sequence ID 3R_DroMel_CAF1
Location 20,762,626 – 20,762,801
Length 175
Max. P 0.669230
window12468 window12469

overview

Window 8

Location 20,762,626 – 20,762,727
Length 101
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 83.23
Mean single sequence MFE -38.82
Consensus MFE -27.78
Energy contribution -29.01
Covariance contribution 1.23
Combinations/Pair 1.20
Mean z-score -2.02
Structure conservation index 0.72
SVM decision value 0.29
SVM RNA-class probability 0.669230
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20762626 101 - 27905053
AGGCAGCGGUCGCUCCCCUGAGUCUUCGGAUUGCGAGCGGGGUACCUUUAUCUUAAAGAUGCACAAGCGCCGCAGUAGUAGCGAGGACCAGGUGGAGGGCC
.......((((.((((((((.(((((((.(((((..((((.((.....((((.....)))).....)).)))).)))))..))))))))))).)))))))) ( -46.40)
>DroSec_CAF1 5031 101 - 1
AGGAAGCGGUCGCUCCCCUGAGUCUCCGGAUUGCGAGCGGGGUACUUUUAUCUUAAAGAUGAACAAGCGCCGCAGUAGUAGCGAAGACCAGGUGGAGGGCC
.......((((.((((((((.((((.((.(((((..((((.((...((((((.....))))))...)).)))).)))))..)).)))))))).)))))))) ( -45.00)
>DroSim_CAF1 5789 101 - 1
AGGAAGCGGUCGCUCCCCUGAGUCUCCGGAUUGCGAGCGGGGUACCUUUAUCUUAAAGAUGAACAAACGCCGCAGUAGUAGCGAAGACCAGGUGGAGGGCC
.......((((.((((((((.((((.((.(((((..((((.((...((((((.....))))))...)).)))).)))))..)).)))))))).)))))))) ( -44.70)
>DroEre_CAF1 6560 101 - 1
AGGCAGUGGUCGGUCCCCUGAGUCUCCGGAUCGCGAGCGGGGUACGUUUAUCUUAAAGAUGAACAAACGCCGCAGUAGUAGCGAGGACCAGGUGGAGGGCC
.......((((..(((((((.(((..((.((..(..((((.((..(((((((.....)))))))..)).)))).)..))..))..))))))).))).)))) ( -41.00)
>DroWil_CAF1 8183 79 - 1
-------GGUACAUCCCC------CCCAGAU---------GGAACCUUUAUCCUGAAGAUGAACAAGCGCCGCAGCAGCUCUGAGGAUCAGGUGGAGGGUC
-------.......((((------(((....---------)).((((..(((((..(((.(.....((......))..)))).))))).)))))).))).. ( -18.60)
>DroYak_CAF1 4758 101 - 1
AGGCAGUGGUCGUUCCCCUGAGUCUCCGGAUCGAGAGCGGGGUACGUUUAUCUUAAAGAUGAACAAGCGCCGCAGUAGUAGCGAGGACCAGGUGGAGGGUC
.......(..(.((((((((.(((..((...(....((((.((..(((((((.....)))))))..)).))))....)...))..))))))).)))))..) ( -37.20)
>consensus
AGGCAGCGGUCGCUCCCCUGAGUCUCCGGAUUGCGAGCGGGGUACCUUUAUCUUAAAGAUGAACAAGCGCCGCAGUAGUAGCGAGGACCAGGUGGAGGGCC
.......((((.((((((((.((((.((........((((.((...((((((.....))))))...)).))))........)).)))))))).)))))))) (-27.78 = -29.01 +   1.23)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,762,697 – 20,762,801
Length 104
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 83.72
Mean single sequence MFE -43.72
Consensus MFE -31.53
Energy contribution -33.82
Covariance contribution 2.28
Combinations/Pair 1.20
Mean z-score -1.81
Structure conservation index 0.72
SVM decision value 0.07
SVM RNA-class probability 0.568307
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20762697 104 - 27905053
GCAGGCACCGCCGGCUCCUUGGUGACCUCAGAUGAGGAGAUGGAGUUUUUCGAUGCCGAGGAGCACGGCUAUUCAGGCAGCGGUCGCUCCCCUGAGUCUUCGGA
(.((((...((((((((((((((..((((....))))..((.(((...))).)))))))))))).))))...(((((.(((....)))..))))))))).)... ( -45.80)
>DroVir_CAF1 33944 94 - 1
UCAGGGCCCCCCGGCACGAAUUUAACCUCAGACGACGAGACCGAAUUUUUCGAUGCCGAGGAAUACGGCUAC---------GGCCGAACAGGCGAAUCGCCA-A
........((.(((((((((.((...(((.......)))....))...)))).))))).))....((((...---------.))))....((((...)))).-. ( -30.40)
>DroSec_CAF1 5102 104 - 1
GCCGGCACCGCCGGCUCCUUGGUGACCUCAGAUGAGGAGAUGGAGUUUUUCGAUGCCGAGGAGCACGGCUAUUCAGGAAGCGGUCGCUCCCCUGAGUCUCCGGA
.((((....((((((((((((((..((((....))))..((.(((...))).)))))))))))).)))).(((((((.(((....)))..)))))))..)))). ( -50.10)
>DroSim_CAF1 5860 104 - 1
GCCGGCACCGCCGGCUCCUUGGUGACCUCAGAUGAGGAGAUGGAGUUUUUCGAUGCCGAGGAGCACGGCUAUUCAGGAAGCGGUCGCUCCCCUGAGUCUCCGGA
.((((....((((((((((((((..((((....))))..((.(((...))).)))))))))))).)))).(((((((.(((....)))..)))))))..)))). ( -50.10)
>DroEre_CAF1 6631 104 - 1
GCCGGCACCGCCGGUUCCUUGGUGACCUCAGAUGAGGAGAUGGAGUUUUUCGACGCCGAGGAGCACGGCUAUUCAGGCAGUGGUCGGUCCCCUGAGUCUCCGGA
.((((....(((((((((((((((.((((....)))).((.........))..))))))))))).)))).(((((((....((.....)))))))))..)))). ( -46.00)
>DroYak_CAF1 4829 104 - 1
GCUGGCACCGCCGGCUCCUUGGUGACCUCAGACGAGGAGAUGGAAUUUUUCGACGCCGAAGAGCACGGCUAUUCAGGCAGUGGUCGUUCCCCUGAGUCUCCGGA
.((((....((((((((.((((((.((((....))))...((((....)))).)))))).)))).)))).(((((((....((.....)))))))))..)))). ( -39.90)
>consensus
GCCGGCACCGCCGGCUCCUUGGUGACCUCAGAUGAGGAGAUGGAGUUUUUCGAUGCCGAGGAGCACGGCUAUUCAGGCAGCGGUCGCUCCCCUGAGUCUCCGGA
.((((....(((((((((((((((.((((....)))).....(((...)))..))))))))))).)))).(((((((....((.....)))))))))..)))). (-31.53 = -33.82 +   2.28)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:11 2006