Locus 4294

Sequence ID 3R_DroMel_CAF1
Location 11,417,077 – 11,417,182
Length 105
Max. P 0.980190
window6997 window6998

overview

Window 7

Location 11,417,077 – 11,417,182
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.12
Mean single sequence MFE -35.42
Consensus MFE -28.22
Energy contribution -27.74
Covariance contribution -0.48
Combinations/Pair 1.12
Mean z-score -2.39
Structure conservation index 0.80
SVM decision value 1.86
SVM RNA-class probability 0.980190
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11417077 105 + 27905053
GAGGAUUAUUCCAGGCGGAAGGUGAAGCAUAUGCAAAGCAGCUGAGUGAAAAUGCAGUUGGAGCGGCACCCAGGGAAAUUGGGUGGCCAUGGGCUGAA-------AUGUGGC--------
..(((....)))...(....)......(((((....((((((((.((....)).))))).....(((((((((.....)))))).)))....)))...-------)))))..-------- ( -31.20)
>DroSec_CAF1 164723 105 + 1
GAGGAUUAUUCCAGGCGGAAGGUGAAGCAUAUGCAAAGCAGCUGAGUGAAAAUGCAGUUGGAGCGGCACCCAGGGAAAUUGGGUGGCCAUGGGCUGAA-------AUGUGGC--------
..(((....)))...(....)......(((((....((((((((.((....)).))))).....(((((((((.....)))))).)))....)))...-------)))))..-------- ( -31.20)
>DroSim_CAF1 157519 105 + 1
GAGGAUUAUUCCAGGCGGAAGGUGAAGCAUAUGCAAAGCAGCUGAGUGAAAAUGCAGUUGGAGCGCCACCCAGGGAAAUUGGGUGGCCAUGGGCUGAA-------AUGUGGC--------
..(((....)))..((.(.......(((.((((.....((((((.((....)).))))))....(((((((((.....))))))))))))).)))...-------...).))-------- ( -34.92)
>DroEre_CAF1 152471 119 + 1
GAGGAUUACUCCG-GCGGAAGGUGAAGCAUAUGCAAAGCAGCCGAGUGAAAAUGCAGUUGGAGCGGCGCCCAGGGAAACUGGGUGGCCAUGGGCUGAAUAUGGGCAUGUGGCAAUGGAUA
(((.....)))((-.(....).))...(((((((..(.(((((..........((.......))(((((((((.....)))))).)))...)))))....)..))))))).......... ( -41.40)
>DroYak_CAF1 156665 113 + 1
GAGGAUUAUUCCGGGCGGAAGGUGAAGCAUAUGCAAAGCAGCUGAGUGAAAAUGCAGUUGGAGCGGCACCCAGGGAAAUUGGGUGGCCAUGGGCUGAA-------AUGGGGCCAUGGGUA
..(((....)))..((..........((....))....((((((.((....)).))))))..))..(((((((.....))))))).((((((.((...-------...)).))))))... ( -38.40)
>consensus
GAGGAUUAUUCCAGGCGGAAGGUGAAGCAUAUGCAAAGCAGCUGAGUGAAAAUGCAGUUGGAGCGGCACCCAGGGAAAUUGGGUGGCCAUGGGCUGAA_______AUGUGGC________
..(((....)))...(....).....((....))....(((((..(((.....((.......))(.(((((((.....))))))).)))).)))))........................ (-28.22 = -27.74 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,417,077 – 11,417,182
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.12
Mean single sequence MFE -24.44
Consensus MFE -19.26
Energy contribution -19.50
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.08
Structure conservation index 0.79
SVM decision value 1.23
SVM RNA-class probability 0.934133
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11417077 105 - 27905053
--------GCCACAU-------UUCAGCCCAUGGCCACCCAAUUUCCCUGGGUGCCGCUCCAACUGCAUUUUCACUCAGCUGCUUUGCAUAUGCUUCACCUUCCGCCUGGAAUAAUCCUC
--------.......-------..((((....(((.(((((.......))))))))((.......))...........))))....((....))......((((....))))........ ( -21.30)
>DroSec_CAF1 164723 105 - 1
--------GCCACAU-------UUCAGCCCAUGGCCACCCAAUUUCCCUGGGUGCCGCUCCAACUGCAUUUUCACUCAGCUGCUUUGCAUAUGCUUCACCUUCCGCCUGGAAUAAUCCUC
--------.......-------..((((....(((.(((((.......))))))))((.......))...........))))....((....))......((((....))))........ ( -21.30)
>DroSim_CAF1 157519 105 - 1
--------GCCACAU-------UUCAGCCCAUGGCCACCCAAUUUCCCUGGGUGGCGCUCCAACUGCAUUUUCACUCAGCUGCUUUGCAUAUGCUUCACCUUCCGCCUGGAAUAAUCCUC
--------.......-------..((((.....((((((((.......))))))))((.......))...........))))....((....))......((((....))))........ ( -25.10)
>DroEre_CAF1 152471 119 - 1
UAUCCAUUGCCACAUGCCCAUAUUCAGCCCAUGGCCACCCAGUUUCCCUGGGCGCCGCUCCAACUGCAUUUUCACUCGGCUGCUUUGCAUAUGCUUCACCUUCCGC-CGGAGUAAUCCUC
........((...((((....(..(((((...(((..(((((.....))))).)))((.......))..........)))))..).))))..))............-.(((....))).. ( -29.60)
>DroYak_CAF1 156665 113 - 1
UACCCAUGGCCCCAU-------UUCAGCCCAUGGCCACCCAAUUUCCCUGGGUGCCGCUCCAACUGCAUUUUCACUCAGCUGCUUUGCAUAUGCUUCACCUUCCGCCCGGAAUAAUCCUC
.......(((.....-------..((((....(((.(((((.......))))))))((.......))...........))))....((....))..........))).(((....))).. ( -24.90)
>consensus
________GCCACAU_______UUCAGCCCAUGGCCACCCAAUUUCCCUGGGUGCCGCUCCAACUGCAUUUUCACUCAGCUGCUUUGCAUAUGCUUCACCUUCCGCCUGGAAUAAUCCUC
........................((((....(((.(((((.......))))))))((.......))...........))))....((....))......((((....))))........ (-19.26 = -19.50 +   0.24)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:08 2006