Locus 1959

Sequence ID X_DroMel_CAF1
Location 5,376,767 – 5,376,886
Length 119
Max. P 0.812026
window3184

overview

Window 4

Location 5,376,767 – 5,376,886
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.46
Mean single sequence MFE -28.60
Consensus MFE -23.68
Energy contribution -23.92
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.55
Structure conservation index 0.83
SVM decision value 0.65
SVM RNA-class probability 0.812026
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5376767 119 + 22224390
CUCUUCCGCAUAAAGUGUUUCGCCAUAUGGACACCGACCUCCUCAGUGGCCAAUGGCUAUCAACUCUAGUCGUUGGGAAAAUGCAAUGCAAAUUGCGAAUUAUUAAAUAAA-AAGCUCAU
...((((..............(((((..(((........)))...)))))(((((((((.......)))))))))))))..((((((....))))))..............-........ ( -27.90)
>DroSec_CAF1 58228 119 + 1
CUCUUCCGCAUAAAGUGUUUCGCCAUAUGGACACCGACCUCCUCAGUGGCCAAUGGCUAUCAACUCUAGUCGUUGGGAAAAUGCAAUGCAAAUUGCGAAUUAUUAAAUAAA-AAGCUCAU
...((((..............(((((..(((........)))...)))))(((((((((.......)))))))))))))..((((((....))))))..............-........ ( -27.90)
>DroSim_CAF1 45180 119 + 1
CUCUUCCGCAUAAAGUGUUUCGCCAUAUGGACACCGACCUCCUCAGUGGCCAAUGGCUAUCAACUCUAGUCGUUGGGAAAAUGCAAUGCAAAUUGCGAAUUAUUAAAUAAA-AAGCUCAU
...((((..............(((((..(((........)))...)))))(((((((((.......)))))))))))))..((((((....))))))..............-........ ( -27.90)
>DroEre_CAF1 51461 118 + 1
CUCUUCCGCAU-AAGCGUUUCGCCAUAUGGACACCGACCUCCUCAGUGGCCAAUGGCUAUCAACUCCGCUCGUUGGGAAAAUGCAAUGCAAAUUGCGAAUUAUUAAAUAAA-GAGCUCAU
(((((.(((..-..)))(((((((((.(((.(((.((.....)).))).))))))))..(((((.......))))))))).((((((....))))))............))-)))..... ( -29.70)
>DroYak_CAF1 50572 108 + 1
------------AAGUGUUUCGCCAUAUGGACAGCGACCUGCUCAGUGGCCAAUGGCUAUCAACUCUAGUCGUUGGGCAAAUGCAAUGCAAAUUGCGAAUUACUAAAUAAAAAAGCUCAU
------------.((((.((((((((.((..(((....)))..)))))))(((((((((.......))))))))).......(((((....)))))))).))))................ ( -29.60)
>consensus
CUCUUCCGCAUAAAGUGUUUCGCCAUAUGGACACCGACCUCCUCAGUGGCCAAUGGCUAUCAACUCUAGUCGUUGGGAAAAUGCAAUGCAAAUUGCGAAUUAUUAAAUAAA_AAGCUCAU
.............(((.(((((((((.(((.(((.((.....)).))).))))))))..(((((.......))))))))).((((((....)))))).................)))... (-23.68 = -23.92 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:49 2006