Locus 5294

Sequence ID 3R_DroMel_CAF1
Location 13,820,929 – 13,821,033
Length 104
Max. P 0.971317
window8635 window8636

overview

Window 5

Location 13,820,929 – 13,821,033
Length 104
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 89.61
Mean single sequence MFE -41.60
Consensus MFE -33.58
Energy contribution -33.78
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.81
SVM decision value 1.67
SVM RNA-class probability 0.971317
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13820929 104 + 27905053
GCGUAGGUGGAUGAGCGAGUGGGAGGUCCUUGUCGCAGGACCUCGUCGAAACUGCAGCAAUACCUGCUCGCAG------CGCUAC-CCCACUCAGCACUUUGCUCUGACAU
..(((((..((.(.((((((((((((((((......))))))))((.(...((((((((.....)))).))))------..).))-.)))))).)).)))..).)).)).. ( -41.10)
>DroSec_CAF1 92799 101 + 1
GCG---GUGGAUGAGCGAGUGGGAGGUCCUUGUCGCAGGACCUCGUCGAAACUGCAGCAAUACCUGCUCGUCC------CGCUCC-CCCACCCACCACUUUGCUCUGACAU
..(---((((.((.(.((((((((((((((......))))))))(.(((....((((......))))))).))------))))).-).)).)))))............... ( -41.40)
>DroSim_CAF1 94858 101 + 1
GCG---GUGGAUGAGCGAGUGGGAGGUCCUUGUCGCAGGACCUCGUCGAAACUGCAGCAAUACCUGCACGUCC------CGCUUC-CCCACCCACCACUUUGCUCUGACAU
..(---((((.((.(.((((((((((((((......))))))))...((...(((((......)))))..)))------))))).-).)).)))))............... ( -40.20)
>DroEre_CAF1 90737 108 + 1
GCG---GUGGAUGAGCGAGUGGGAGGUCCUUGUCGCAGGACCUCGUCGAAACUGCAGCAAUACCUGCCCGCCCUCGCCUCGCCCCGCUCUCCCACCACUUUGCUCUGACAU
(((---(.((.((((((((.((((((((((......)))))))).........((((......))))...)))))).))))))))))........................ ( -41.80)
>DroYak_CAF1 100062 105 + 1
GCG---GUGGAUGAGCGAGUGGGAGGUCCUUGUCGCAGGACCUCGUCGAAACUGCAGCAAUACCUGCUCGCCCUCGCCCCGCU---CUCUCCCACCACUUUGCUCUGACAU
..(---((((..(((.((((((((((((((......))))))))(.(((....((((((.....)))).))..)))).)))))---).))))))))............... ( -43.50)
>consensus
GCG___GUGGAUGAGCGAGUGGGAGGUCCUUGUCGCAGGACCUCGUCGAAACUGCAGCAAUACCUGCUCGCCC______CGCUCC_CCCACCCACCACUUUGCUCUGACAU
......(((...((((((((((((((((((......)))))))).........((((......))))...........................)))).))))))...))) (-33.58 = -33.78 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,820,929 – 13,821,033
Length 104
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 89.61
Mean single sequence MFE -48.78
Consensus MFE -34.08
Energy contribution -34.28
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -3.12
Structure conservation index 0.70
SVM decision value 1.10
SVM RNA-class probability 0.915468
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13820929 104 - 27905053
AUGUCAGAGCAAAGUGCUGAGUGGG-GUAGCG------CUGCGAGCAGGUAUUGCUGCAGUUUCGACGAGGUCCUGCGACAAGGACCUCCCACUCGCUCAUCCACCUACGC
......((((........((((((.-((...(------((((.(((((...))))))))))....))((((((((......))))))))))))))))))............ ( -40.40)
>DroSec_CAF1 92799 101 - 1
AUGUCAGAGCAAAGUGGUGGGUGGG-GGAGCG------GGACGAGCAGGUAUUGCUGCAGUUUCGACGAGGUCCUGCGACAAGGACCUCCCACUCGCUCAUCCAC---CGC
.............((((((((((((-.(((((------..((..((((......)))).))..))..((((((((......))))))))...))).)))))))))---))) ( -53.00)
>DroSim_CAF1 94858 101 - 1
AUGUCAGAGCAAAGUGGUGGGUGGG-GAAGCG------GGACGUGCAGGUAUUGCUGCAGUUUCGACGAGGUCCUGCGACAAGGACCUCCCACUCGCUCAUCCAC---CGC
.............((((((((((((-((.(((------..((.(((((......)))))))..)).)((((((((......))))))))....)).)))))))))---))) ( -49.80)
>DroEre_CAF1 90737 108 - 1
AUGUCAGAGCAAAGUGGUGGGAGAGCGGGGCGAGGCGAGGGCGGGCAGGUAUUGCUGCAGUUUCGACGAGGUCCUGCGACAAGGACCUCCCACUCGCUCAUCCAC---CGC
.............(((((((..(((((((.((((((....((((.(((...))))))).))))))..((((((((......))))))))...)))))))..))))---))) ( -53.10)
>DroYak_CAF1 100062 105 - 1
AUGUCAGAGCAAAGUGGUGGGAGAG---AGCGGGGCGAGGGCGAGCAGGUAUUGCUGCAGUUUCGACGAGGUCCUGCGACAAGGACCUCCCACUCGCUCAUCCAC---CGC
.............((((((((...(---((((((.(((((.(..((((......)))).))))))..((((((((......))))))))...))))))).)))))---))) ( -47.60)
>consensus
AUGUCAGAGCAAAGUGGUGGGUGGG_GGAGCG______GGGCGAGCAGGUAUUGCUGCAGUUUCGACGAGGUCCUGCGACAAGGACCUCCCACUCGCUCAUCCAC___CGC
........((...((((((((((((...................((((......)))).........((((((((......))))))))...)))))))).))))....)) (-34.08 = -34.28 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:16 2006