Locus 8272

Sequence ID 3L_DroMel_CAF1
Location 21,724,503 – 21,724,639
Length 136
Max. P 0.547766
window13528 window13529

overview

Window 8

Location 21,724,503 – 21,724,614
Length 111
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 89.32
Mean single sequence MFE -22.93
Consensus MFE -15.90
Energy contribution -16.40
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.69
SVM decision value -0.04
SVM RNA-class probability 0.510787
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21724503 111 - 23771897
GAUGCACACUCGCAGGUUCGCACAAAUGGCAAUUGCAGCCUGCAAUUGUCAUUGCAUCCUCGUCAUUCGCAUCCUCGACGUCAGACAUCCAAUAUCACUCAGUCACAAUCA
(((((.....((.(((...(((...(((((((((((.....))))))))))))))..)))))......)))))...(((......................)))....... ( -28.85)
>DroSec_CAF1 6412 95 - 1
GAUGCACACUCGCAGGUUCGCACAAAUGGCAAUUGCAGCCUGCG----U------------CUCAUUCGCAUCCUCGACGUCAGACAUCCAAUAUCACUCAGUCGCAAUCA
(((((((....(((((((.(((...........))))))))))(----(------------((.(((((......))).)).))))...............)).)).))). ( -23.20)
>DroSim_CAF1 11431 95 - 1
GAUGCACACUCGCAGGUUCGCACAAAUGGCAAUUGCAGCCUGCG----U------------CUCAUUCGCAUCCUCGACGUCAGACAUCCAAUAUCACUCAGUCGCAAUCA
(((((((....(((((((.(((...........))))))))))(----(------------((.(((((......))).)).))))...............)).)).))). ( -23.20)
>DroYak_CAF1 56975 95 - 1
GAUGCACACUCGCAGAUUCGCACAAAUGGCAAUUGCAGACUGCG----U------------CUCAUUCGCAUCCUCGACGUCAAACAUCCAAUAUCACUCAGUCGCAAUCA
(((((.....(((((.(..(((...........)))..))))))----.------------.......)))))..((((......................))))...... ( -16.47)
>consensus
GAUGCACACUCGCAGGUUCGCACAAAUGGCAAUUGCAGCCUGCG____U____________CUCAUUCGCAUCCUCGACGUCAGACAUCCAAUAUCACUCAGUCGCAAUCA
(((((.....((((((((.(((...........)))))))))))........................)))))...(((......................)))....... (-15.90 = -16.40 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 21,724,543 – 21,724,639
Length 96
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 79.02
Mean single sequence MFE -22.37
Consensus MFE -16.43
Energy contribution -16.77
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.73
SVM decision value 0.03
SVM RNA-class probability 0.547766
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21724543 96 - 23771897
CACACCUCGCAGCGCAC-------AGCUCACAGAUGCACACUCGCAGGUUCGCACAAAUGGCAAUUGCAGCCUGCAAUUGUCAUUGCAUCCUCGUCAUUCGCA
........(((((....-------.)))....(((((......((......))...((((((((((((.....)))))))))))))))))..........)). ( -28.70)
>DroSec_CAF1 6452 87 - 1
CACACCUCGCAGCGCACAGCUCACAGCUCACAGAUGCACACUCGCAGGUUCGCACAAAUGGCAAUUGCAGCCUGCG----U------------CUCAUUCGCA
........((.(.(((((((.....)))....).))).)...((((((((.(((...........)))))))))))----.------------.......)). ( -21.00)
>DroYak_CAF1 57015 80 - 1
CACACCUCGCAGCGUAG-------AGCACACAGAUGCACACUCGCAGAUUCGCACAAAUGGCAAUUGCAGACUGCG----U------------CUCAUUCGCA
........((.((....-------.))....(((((((..((.((((.((.((.(....)))))))))))..))))----)------------)).....)). ( -17.40)
>consensus
CACACCUCGCAGCGCAC_______AGCUCACAGAUGCACACUCGCAGGUUCGCACAAAUGGCAAUUGCAGCCUGCG____U____________CUCAUUCGCA
...........(((...........((........))......(((((((.(((...........))))))))))........................))). (-16.43 = -16.77 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:11:05 2006