Locus 1976

Sequence ID X_DroMel_CAF1
Location 5,404,821 – 5,404,916
Length 95
Max. P 0.980614
window3219 window3220

overview

Window 9

Location 5,404,821 – 5,404,916
Length 95
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 78.70
Mean single sequence MFE -47.70
Consensus MFE -39.43
Energy contribution -43.27
Covariance contribution 3.84
Combinations/Pair 1.08
Mean z-score -2.01
Structure conservation index 0.83
SVM decision value 1.87
SVM RNA-class probability 0.980614
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5404821 95 + 22224390
GGCCGCUGCCACCGCCGCAUGGGCAUUGAAGUAGGCCAUUCGCGAGGCGGCCGCCAUGGUCAUUUGGUGGUGCUCCCUGUACUGAUGGUGGUGCG-------------
...(((.((((((((((.((((.(((.(.....((((..((....)).)))).).))).)))).))))(((((.....)))))...)))))))))------------- ( -38.40)
>DroPse_CAF1 33392 99 + 1
GGCGGCCGCCACCGCUGCAUGGGCGUUGAAGUAGGCCAUGCGGGAGGCGGCUGCCAUGGUCAUUUGAUGGUGAUCCCUGUAGUGGU---------GCUGCUGCUGAUC
((((((((((.((.(.((((((.(.........).))))))))).))))))))))..(((((((....)))))))...(((((...---------...)))))..... ( -48.50)
>DroPer_CAF1 37183 108 + 1
GGCGGCCGCCACCGCUGCAUGGGCGUUGAAGUAGGCCAUGCGGGAGGCGGCUGCCAUGGUCAUUUGAUGGUGAUCCCUGUAGUGGUGCUGGUGGUGCUGCUGCUGAUC
((((((((((.((.(.((((((.(.........).))))))))).))))))))))..(((((((....)))))))...((((..(..(.....)..)..))))..... ( -56.20)
>consensus
GGCGGCCGCCACCGCUGCAUGGGCGUUGAAGUAGGCCAUGCGGGAGGCGGCUGCCAUGGUCAUUUGAUGGUGAUCCCUGUAGUGGUG_UGGUG__GCUGCUGCUGAUC
((((((((((.((..(((((((.(.........).))))))))).))))))))))..(((((((....)))))))...((((((((((.....))))))))))..... (-39.43 = -43.27 +   3.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 5,404,821 – 5,404,916
Length 95
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 78.70
Mean single sequence MFE -35.23
Consensus MFE -26.27
Energy contribution -27.27
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.75
SVM decision value 0.33
SVM RNA-class probability 0.690694
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5404821 95 - 22224390
-------------CGCACCACCAUCAGUACAGGGAGCACCACCAAAUGACCAUGGCGGCCGCCUCGCGAAUGGCCUACUUCAAUGCCCAUGCGGCGGUGGCAGCGGCC
-------------(((..(.((((..((.((.((.......))...)))).)))).)(((((((((((...(((..........)))..))))).)))))).)))... ( -30.70)
>DroPse_CAF1 33392 99 - 1
GAUCAGCAGCAGC---------ACCACUACAGGGAUCACCAUCAAAUGACCAUGGCAGCCGCCUCCCGCAUGGCCUACUUCAACGCCCAUGCAGCGGUGGCGGCCGCC
((((.((....))---------.((......))))))................(((.((((((.(((((((((.(.........).)))))).).)).)))))).))) ( -37.50)
>DroPer_CAF1 37183 108 - 1
GAUCAGCAGCAGCACCACCAGCACCACUACAGGGAUCACCAUCAAAUGACCAUGGCAGCCGCCUCCCGCAUGGCCUACUUCAACGCCCAUGCAGCGGUGGCGGCCGCC
((((.((....))..........((......))))))................(((.((((((.(((((((((.(.........).)))))).).)).)))))).))) ( -37.50)
>consensus
GAUCAGCAGCAGC__CACCA_CACCACUACAGGGAUCACCAUCAAAUGACCAUGGCAGCCGCCUCCCGCAUGGCCUACUUCAACGCCCAUGCAGCGGUGGCGGCCGCC
...............................((.....)).............(((.((((((.(((((((((.(.........).)))))).).)).)))))).))) (-26.27 = -27.27 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:20 2006