Locus 6122

Sequence ID 2L_DroMel_CAF1
Location 17,122,320 – 17,122,479
Length 159
Max. P 0.980379
window9764 window9765

overview

Window 4

Location 17,122,320 – 17,122,440
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.50
Mean single sequence MFE -46.22
Consensus MFE -38.88
Energy contribution -40.48
Covariance contribution 1.60
Combinations/Pair 1.12
Mean z-score -2.01
Structure conservation index 0.84
SVM decision value 1.86
SVM RNA-class probability 0.980379
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17122320 120 + 22407834
GCUUUCGUCUGCAUUGCUUAGCUACGAGCUGUGGCGCCUGGCAUUGUCGCUCAAGUGUUUCGGCAAACUGGCUUGCCUUCUGUAAGGCAAGCUGUGCCGAGAGUAAGGUGGCAAGCAGUU
........((((..((((..(((((.....)))))....))))((((((((......((((((((....((((((((((....)))))))))).))))))))....)))))))))))).. ( -51.10)
>DroSec_CAF1 86127 120 + 1
GCUUUCGUCUGCAUUGCUUAGCUACGAGCUGUGGCGCCUGGCAUUGUCGCUCAAGUGUUUCGGCAAACUGACUUGCCAUCUGUAAGGCAAGCUGUGCUGAAAGUAAGGUGGCAAGCAGUU
....((((..((........)).))))((((..((((.((((......)).)).))))..)))).(((((.((((((((((....((((.....)))).......))))))))))))))) ( -44.40)
>DroSim_CAF1 102192 120 + 1
GCUUUCGUCUGCAUUGCUUAGCUACGAGCUGUGGCGCCUGGCAUUGUCGCUCAAGUGUUUCGGCAAACUGACUUGCCUUCUGUAAGGCAAGCUGUGCUGAAAGUAAGGUGGCAAGCAGUU
........((((..((((..(((((.....)))))....))))((((((((......((((((((....(.((((((((....)))))))))..))))))))....)))))))))))).. ( -44.60)
>DroEre_CAF1 88260 120 + 1
GCUUUCGUCUGCAUUGCUUGGCUCCGAGCUGUGGCGCCUCGCAUUGUCGCUCAAGUGUUUCGGCAAACUGGCUUGCCGUCUGUGCGGCAAGCUGUGCAGAAAGCAAGGUGGCAAGAAGUU
((...((((.(((..(((((....))))))))))))....)).((((((((....((((((.(((....((((((((((....)))))))))).))).).))))).))))))))...... ( -46.00)
>DroYak_CAF1 88021 120 + 1
GCUUUCGUCUGCAUUGCUUGGCUCCGUGCAGUGGGGUCUGGCAUUGUCGCUCAAGUGUUUCGGCAAACUGGCUUGCCAUCUGUAAGGCAAGCUGUGCAGAAAGCAAGGUGGCAAGAAGUU
(((((.........((((.(((((((.....))))))).))))((((((((....((((((.(((....((((((((........)))))))).))).).))))).))))))))))))). ( -45.00)
>consensus
GCUUUCGUCUGCAUUGCUUAGCUACGAGCUGUGGCGCCUGGCAUUGUCGCUCAAGUGUUUCGGCAAACUGGCUUGCCAUCUGUAAGGCAAGCUGUGCAGAAAGUAAGGUGGCAAGCAGUU
........((((..((((..(((((.....)))))....))))((((((((....((((((((((....((((((((((....)))))))))).)))))))).)).)))))))))))).. (-38.88 = -40.48 +   1.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,122,360 – 17,122,479
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.81
Mean single sequence MFE -41.60
Consensus MFE -31.58
Energy contribution -32.46
Covariance contribution 0.88
Combinations/Pair 1.16
Mean z-score -1.58
Structure conservation index 0.76
SVM decision value 0.07
SVM RNA-class probability 0.567658
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17122360 119 + 22407834
GCAUUGUCGCUCAAGUGUUUCGGCAAACUGGCUUGCCUUCUGUAAGGCAAGCUGUGCCGAGAGUAAGGUGGCAAGCAGUUUCAGGAC-UGAAGGGAGCGGUCUGAAGGAUAUCUGUCUCU
...((((((((......((((((((....((((((((((....)))))))))).))))))))....))))))))((((..((.((((-((.......))))))....))...)))).... ( -46.50)
>DroSec_CAF1 86167 119 + 1
GCAUUGUCGCUCAAGUGUUUCGGCAAACUGACUUGCCAUCUGUAAGGCAAGCUGUGCUGAAAGUAAGGUGGCAAGCAGUUGCAGGAC-UGAAGGGAGCGGUCUGAAGGAUAUCUGUCUCU
......((((((....((((..((((.(((.((((((((((....((((.....)))).......))))))))))))))))).))))-......))))))......((((....)))).. ( -39.20)
>DroSim_CAF1 102232 119 + 1
GCAUUGUCGCUCAAGUGUUUCGGCAAACUGACUUGCCUUCUGUAAGGCAAGCUGUGCUGAAAGUAAGGUGGCAAGCAGUUGGAGGAC-UGAAGGGAGCGGUCUGAAGGAUAUCUGUCUCU
((.((((((((......((((((((....(.((((((((....)))))))))..))))))))....))))))))))....(((((((-((.......)))))....((....))..)))) ( -38.50)
>DroEre_CAF1 88300 120 + 1
GCAUUGUCGCUCAAGUGUUUCGGCAAACUGGCUUGCCGUCUGUGCGGCAAGCUGUGCAGAAAGCAAGGUGGCAAGAAGUUGCAGGAUGUGGACGAAGCGGUCUAAAGGAUAUCUGGCCUU
...((((((((....((((((.(((....((((((((((....)))))))))).))).).))))).))))))))......((.((((((((((......)))).....)))))).))... ( -41.80)
>DroYak_CAF1 88061 120 + 1
GCAUUGUCGCUCAAGUGUUUCGGCAAACUGGCUUGCCAUCUGUAAGGCAAGCUGUGCAGAAAGCAAGGUGGCAAGAAGUUGCAGGACGUAGAAGGAGCGGCCUGAAGGAUAUCUGCCCCU
((.....(((....)))((((.(((....((((((((........)))))))).))).)))))).(((.((((.((.(((.((((.(((.......))).))))...))).))))))))) ( -42.00)
>consensus
GCAUUGUCGCUCAAGUGUUUCGGCAAACUGGCUUGCCAUCUGUAAGGCAAGCUGUGCAGAAAGUAAGGUGGCAAGCAGUUGCAGGAC_UGAAGGGAGCGGUCUGAAGGAUAUCUGUCUCU
((.((((((((....((((((((((....((((((((((....)))))))))).)))))))).)).)))))))))).................(((((((............))).)))) (-31.58 = -32.46 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:42 2006