Locus 2076

Sequence ID X_DroMel_CAF1
Location 5,673,094 – 5,673,223
Length 129
Max. P 0.918792
window3374 window3375

overview

Window 4

Location 5,673,094 – 5,673,189
Length 95
Sequences 3
Columns 109
Reading direction reverse
Mean pairwise identity 83.85
Mean single sequence MFE -19.93
Consensus MFE -14.17
Energy contribution -15.83
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -2.62
Structure conservation index 0.71
SVM decision value 1.12
SVM RNA-class probability 0.918792
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5673094 95 - 22224390
AAAAUAAUGUGCGAAAACCCAAAUCAAAU-----AGAACCAAUUUUCGCAUACCCUAAUUCCCCCAACAA---------AUGCACCCAAAUGCUGAAUAAAGCAAGCCA
.......((((((((((......((....-----.)).....))))))))))..................---------...........((((......))))..... ( -13.70)
>DroSec_CAF1 12141 109 - 1
AAAAUAGUGUGCGAAAACCCAAAUCAAAUAUAGUAGAACCAAUUUUCGCAUACUGGGGCUUCCCCAAAAACCGUUCUCAGUGCACCUAAAUGCUGAAUAAAGCUAGCCA
.....((((((((((((......((..........)).....))))))))))))((((...))))...........(((((..........)))))............. ( -22.60)
>DroSim_CAF1 12630 104 - 1
AAAAUAGUGUGCGAAAACCCAAAUCAAAU-----AGAACCAAUUUUCGCAUACUGGGGCUUCCCCAAAAACCGUUCUCAGUGCACCUAAAUGCUGAAUAAAGCUAGCCA
.....((((((((((((......((....-----.)).....))))))))))))((((...))))...........(((((..........)))))............. ( -23.50)
>consensus
AAAAUAGUGUGCGAAAACCCAAAUCAAAU_____AGAACCAAUUUUCGCAUACUGGGGCUUCCCCAAAAACCGUUCUCAGUGCACCUAAAUGCUGAAUAAAGCUAGCCA
.....((((((((((((......((..........)).....))))))))))))(((.....)))..........................(((......)))...... (-14.17 = -15.83 +   1.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 5,673,123 – 5,673,223
Length 100
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 81.60
Mean single sequence MFE -21.93
Consensus MFE -13.06
Energy contribution -15.40
Covariance contribution 2.34
Combinations/Pair 1.07
Mean z-score -2.41
Structure conservation index 0.60
SVM decision value 0.50
SVM RNA-class probability 0.758621
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5673123 100 - 22224390
GCCCUAAAUGUUAUUCCCUGCAAUCAAGCUAGCGAAAAUAAUGUGCGAAAACCCAAAUCAAAU-----AGAACCAAUUUUCGCAUACCCUAAUUCCCCCAACAA---------A
........((((.(((.((((......)).)).))).....((((((((((......((....-----.)).....)))))))))).............)))).---------. ( -14.50)
>DroSec_CAF1 12170 114 - 1
GCCCUAACUGUUAUUCCUGCAAAUCAAGCCAGAGAAAAUAGUGUGCGAAAACCCAAAUCAAAUAUAGUAGAACCAAUUUUCGCAUACUGGGGCUUCCCCAAAAACCGUUCUCAG
((((((((((((.(((((((.......).))).)))))))))(((((((((......((..........)).....)))))))))..))))))..................... ( -25.20)
>DroSim_CAF1 12659 109 - 1
GCCCUAACUGUUAUUCCUGCAAAUCAAGCUAGAGAAAAUAGUGUGCGAAAACCCAAAUCAAAU-----AGAACCAAUUUUCGCAUACUGGGGCUUCCCCAAAAACCGUUCUCAG
((((((((((((.(((((((.......)).)).)))))))))(((((((((......((....-----.)).....)))))))))..))))))..................... ( -26.10)
>consensus
GCCCUAACUGUUAUUCCUGCAAAUCAAGCUAGAGAAAAUAGUGUGCGAAAACCCAAAUCAAAU_____AGAACCAAUUUUCGCAUACUGGGGCUUCCCCAAAAACCGUUCUCAG
((((((((((((.((((((..........))).)))))))))(((((((((......((..........)).....)))))))))..))))))..................... (-13.06 = -15.40 +   2.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:39 2006