Locus 1805

Sequence ID 2L_DroMel_CAF1
Location 4,981,561 – 4,981,655
Length 94
Max. P 0.894045
window2906 window2907

overview

Window 6

Location 4,981,561 – 4,981,655
Length 94
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 85.90
Mean single sequence MFE -35.64
Consensus MFE -25.22
Energy contribution -25.58
Covariance contribution 0.36
Combinations/Pair 1.10
Mean z-score -2.37
Structure conservation index 0.71
SVM decision value 0.98
SVM RNA-class probability 0.894045
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4981561 94 + 22407834
CUGACUGCAACCUGCACUGCUCCAAAUGGAGUGGCUG-CCAACACUGCUUGC--------GCCAGUCGUUGUGCAGCACUGGUCGAGUCAGCAGCAGCAAAA----G
.((.((((.....((((..((((....))))..).))-).....(((((((.--------((((((.(((....))))))))))))).)))..))))))...----. ( -36.50)
>DroSec_CAF1 1876 94 + 1
UUGACUGCAACCUGCACAGCUCCAAAUGGAGUGGCUG-CCAACACUGCUUGC--------GCCAGUCGGUGUGCAGCACUGGUCGAGUCAGCAGCAGCAAAA----G
(((.((((....(((...(((((....)))))(((((-(((...((((..((--------(((....)))))))))...))))..)))).))))))))))..----. ( -35.30)
>DroSim_CAF1 1876 94 + 1
CUGACUGCAAGCUGCACAGCUCCAAAUGGAGUGGCUG-CCAACACUGCUUGC--------GCCAGUCGUUGUGCAGCACUGGUCGAGUCAGCAGCAGCAAAA----G
.((.((((..((((.((.(((((....))))).((((-((((((((((....--------).)))).)))).))))).........)))))).))))))...----. ( -37.50)
>DroEre_CAF1 1830 107 + 1
CAAACUGCAAGUUGCACUACUCCAAUUGGAGUGCCUGACCAACACUGCUGGCCAACUUGCGCCAGUCGUUGUGCAGCACUAGUCAAGUCAGCAGCAGCAAAAAGCAG
....((((..(((((((((((((....))))))..........((.(((((((.....).)))))).)).))))))).............((....)).....)))) ( -35.40)
>DroYak_CAF1 1879 98 + 1
CUAACUGCAAGUUGCACUACUCCAAUUGGAGUUGCUGGCCAACACUGCUUGC---------UCAGUCGUUGUGCAGCACUGGUCAAGUCAGCAGCAGCAAAAAGUAG
....((((...((((.....(((....)))(((((((((...((.((((.((---------.(((...))).)))))).)).....))))))))).))))...)))) ( -33.50)
>consensus
CUGACUGCAAGCUGCACUGCUCCAAAUGGAGUGGCUG_CCAACACUGCUUGC________GCCAGUCGUUGUGCAGCACUGGUCGAGUCAGCAGCAGCAAAA____G
....((((..(((((((.(((((....)))))........(((((((...((........)))))).)))))))))).((((.....))))..)))).......... (-25.22 = -25.58 +   0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,981,561 – 4,981,655
Length 94
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 85.90
Mean single sequence MFE -38.71
Consensus MFE -25.38
Energy contribution -26.02
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -2.57
Structure conservation index 0.66
SVM decision value 0.77
SVM RNA-class probability 0.847215
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4981561 94 - 22407834
C----UUUUGCUGCUGCUGACUCGACCAGUGCUGCACAACGACUGGC--------GCAAGCAGUGUUGG-CAGCCACUCCAUUUGGAGCAGUGCAGGUUGCAGUCAG
.----...........(((((((((((.(.(((((.((((.((((.(--------....))))))))))-))))).((((....)))).......))))).)))))) ( -41.10)
>DroSec_CAF1 1876 94 - 1
C----UUUUGCUGCUGCUGACUCGACCAGUGCUGCACACCGACUGGC--------GCAAGCAGUGUUGG-CAGCCACUCCAUUUGGAGCUGUGCAGGUUGCAGUCAA
.----....(((((.((((.......)))).((((((((((((..((--------....))...)))))-......((((....)))).)))))))...)))))... ( -36.70)
>DroSim_CAF1 1876 94 - 1
C----UUUUGCUGCUGCUGACUCGACCAGUGCUGCACAACGACUGGC--------GCAAGCAGUGUUGG-CAGCCACUCCAUUUGGAGCUGUGCAGCUUGCAGUCAG
.----....(((((.((((((.......(.(((((.((((.((((.(--------....))))))))))-))))).((((....))))..)).))))..)))))... ( -39.60)
>DroEre_CAF1 1830 107 - 1
CUGCUUUUUGCUGCUGCUGACUUGACUAGUGCUGCACAACGACUGGCGCAAGUUGGCCAGCAGUGUUGGUCAGGCACUCCAAUUGGAGUAGUGCAACUUGCAGUUUG
((((...((((.(((((((.(((((((((..((((....(((((......)))))....))))..))))))))))).(((....))))))))))))...)))).... ( -45.20)
>DroYak_CAF1 1879 98 - 1
CUACUUUUUGCUGCUGCUGACUUGACCAGUGCUGCACAACGACUGA---------GCAAGCAGUGUUGGCCAGCAACUCCAAUUGGAGUAGUGCAACUUGCAGUUAG
.........((((((((((....(.((((..((((...........---------....))))..))))))))))(((((....)))))..........)))))... ( -30.96)
>consensus
C____UUUUGCUGCUGCUGACUCGACCAGUGCUGCACAACGACUGGC________GCAAGCAGUGUUGG_CAGCCACUCCAUUUGGAGCAGUGCAGCUUGCAGUCAG
.........(((((..(((((..(.((((..((((.((.....))((........))..))))..)))).).....((((....))))..)).)))...)))))... (-25.38 = -26.02 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:44 2006