Locus 7962

Sequence ID X_DroMel_CAF1
Location 19,847,447 – 19,847,584
Length 137
Max. P 0.930646
window13064 window13065 window13066

overview

Window 4

Location 19,847,447 – 19,847,553
Length 106
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 97.48
Mean single sequence MFE -29.61
Consensus MFE -29.55
Energy contribution -29.33
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 1.00
SVM decision value 0.98
SVM RNA-class probability 0.894289
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19847447 106 + 22224390
CAGCUGGCUGUCCUGCUCCUCCGCACCUUCGUCCUUCGCUCAUCCUGGCCUCUGGUUUAUUUUAGAGCAGGAAUAGAAAGAAAAUUUCUAUGCUAUCGCUGUCUCU
((((((((..((((((((......(((...(.((............)).)...)))........))))))))(((((((.....)))))))))))..))))..... ( -28.84)
>DroSec_CAF1 5301 106 + 1
CAGCUGGCUGUCCUGCUCCUCCGCACCUUCGUCCUUUGCCCGUCCUGGCCUCUGGUUUAUUUUAGAGCAGGAAUAGAAAGAAAAUUUCUAUGCUAUCGCUGUCUCU
((((((((..((((((((....((......))((...(((......)))....)).........))))))))(((((((.....)))))))))))..))))..... ( -30.00)
>DroSim_CAF1 1973 106 + 1
CAGCUGGCUGUCCUGCUCCGCCGCACCUUCGUCCUUUGCCCGUCCUGGCCUCUGGUUUAUUUUAGAGCAGGAAUAGAAAGAAAAUUUCUAUGCUAUCGCUGUCUCU
((((((((..((((((((....((......))((...(((......)))....)).........))))))))(((((((.....)))))))))))..))))..... ( -30.00)
>consensus
CAGCUGGCUGUCCUGCUCCUCCGCACCUUCGUCCUUUGCCCGUCCUGGCCUCUGGUUUAUUUUAGAGCAGGAAUAGAAAGAAAAUUUCUAUGCUAUCGCUGUCUCU
((((((((..((((((((....((......))((...(((......)))....)).........))))))))(((((((.....)))))))))))..))))..... (-29.55 = -29.33 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 19,847,447 – 19,847,553
Length 106
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 97.48
Mean single sequence MFE -33.00
Consensus MFE -32.30
Energy contribution -32.63
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.98
SVM decision value 1.21
SVM RNA-class probability 0.930646
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19847447 106 - 22224390
AGAGACAGCGAUAGCAUAGAAAUUUUCUUUCUAUUCCUGCUCUAAAAUAAACCAGAGGCCAGGAUGAGCGAAGGACGAAGGUGCGGAGGAGCAGGACAGCCAGCUG
.....((((....(((((((((.....)))))))(((((((((........((........)).........(.((....)).)...)))))))))..))..)))) ( -30.60)
>DroSec_CAF1 5301 106 - 1
AGAGACAGCGAUAGCAUAGAAAUUUUCUUUCUAUUCCUGCUCUAAAAUAAACCAGAGGCCAGGACGGGCAAAGGACGAAGGUGCGGAGGAGCAGGACAGCCAGCUG
.....((((....(((((((((.....)))))))(((((((((..............(((......)))...(.((....)).)...)))))))))..))..)))) ( -34.20)
>DroSim_CAF1 1973 106 - 1
AGAGACAGCGAUAGCAUAGAAAUUUUCUUUCUAUUCCUGCUCUAAAAUAAACCAGAGGCCAGGACGGGCAAAGGACGAAGGUGCGGCGGAGCAGGACAGCCAGCUG
.....((((....(((((((((.....)))))))(((((((((..............(((......)))...(.((....)).)...)))))))))..))..)))) ( -34.20)
>consensus
AGAGACAGCGAUAGCAUAGAAAUUUUCUUUCUAUUCCUGCUCUAAAAUAAACCAGAGGCCAGGACGGGCAAAGGACGAAGGUGCGGAGGAGCAGGACAGCCAGCUG
.....((((....(((((((((.....)))))))(((((((((..............(((......)))...(.((....)).)...)))))))))..))..)))) (-32.30 = -32.63 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 19,847,487 – 19,847,584
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 88.32
Mean single sequence MFE -17.00
Consensus MFE -16.69
Energy contribution -16.47
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -0.90
Structure conservation index 0.98
SVM decision value 0.17
SVM RNA-class probability 0.616230
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19847487 97 - 22224390
CAAACACAAGGACACACAAACAACAGUCGGCAGAGACAGCGAUAGCAUAGAAAUUUUCUUUCUAUUCCUGCUCUAAAAUAAACCAGAGGCCAGGAUG
..........(((............)))(((((((.(((.(((((...(((.....)))..))))).)))))))........(....))))...... ( -16.60)
>DroSec_CAF1 5341 81 - 1
C----------------AAACAACAGUCGGCAGAGACAGCGAUAGCAUAGAAAUUUUCUUUCUAUUCCUGCUCUAAAAUAAACCAGAGGCCAGGACG
.----------------........((((((((((.(((.(((((...(((.....)))..))))).)))))))........(....))))..))). ( -17.20)
>DroSim_CAF1 2013 97 - 1
CAAACACAAGGACACACAAACAACAGUCGGCAGAGACAGCGAUAGCAUAGAAAUUUUCUUUCUAUUCCUGCUCUAAAAUAAACCAGAGGCCAGGACG
.........................((((((((((.(((.(((((...(((.....)))..))))).)))))))........(....))))..))). ( -17.20)
>consensus
CAAACACAAGGACACACAAACAACAGUCGGCAGAGACAGCGAUAGCAUAGAAAUUUUCUUUCUAUUCCUGCUCUAAAAUAAACCAGAGGCCAGGACG
.........................((((((((((.(((.(((((...(((.....)))..))))).)))))))........(....))))..))). (-16.69 = -16.47 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:53 2006