Locus 7223

Sequence ID	X_DroMel_CAF1
Location	18,065,530 – 18,065,810
Length	280
Max. P	0.815035

overview

Window 9

Location	18,065,530 – 18,065,650
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-38.47
Consensus MFE	-37.87
Energy contribution	-38.20
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.98
SVM decision value	0.66
SVM RNA-class probability	0.815035
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18065530 120 - 22224390
AGCUGCUGCUGUCGAUUUUGGAGGCCCAGGCACUUGGCUCUGCCAGUUUCCACUGUUUUCGCCACUCGGGUUUUCCCGCCAUUUUUGUUUUCCUUCUCCCUUGGCAGCGAGGCAAACAAA
.(((..(((((((((....(((((...(((((..((((.....((((....)))).....))))..((((....)))).......))))).)))))....))))))))).)))....... ( -37.60)
>DroSec_CAF1 3366 120 - 1
AGCUGCUGCUGUCGAUUUUGGAGGGCCAGGCACUUGGCUCUGCCAGUUUCCACUGUUUUCGCCACUCGGGUUUUCCCGCCAUUUUUGUUUUCCUUCUCCCUUGGCAGCGAGGCAAACAAA
.(((..(((((((((..((((((((((((....)))))))).))))..))................((((....))))........................))))))).)))....... ( -38.90)
>DroSim_CAF1 6503 120 - 1
AGCUGCUGCUGUCGAUUUUGGAGGGCCAGGCACUUGGCUCUGCCAGUUUCCACUGUUUUCGCCACUCGGGUUUUCCCGCCAUUUUUGUUUUCCUUCUCCCUUGGCAGCGAGGCAAACAAA
.(((..(((((((((..((((((((((((....)))))))).))))..))................((((....))))........................))))))).)))....... ( -38.90)
>consensus
AGCUGCUGCUGUCGAUUUUGGAGGGCCAGGCACUUGGCUCUGCCAGUUUCCACUGUUUUCGCCACUCGGGUUUUCCCGCCAUUUUUGUUUUCCUUCUCCCUUGGCAGCGAGGCAAACAAA
.(((..(((((((((....((((((..(((((..((((.....((((....)))).....))))..((((....)))).......)))))))))))....))))))))).)))....... (-37.87 = -38.20 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	18,065,570 – 18,065,690
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-41.80
Consensus MFE	-39.67
Energy contribution	-41.17
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.95
SVM decision value	0.24
SVM RNA-class probability	0.647152
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18065570 120 + 22224390
GGCGGGAAAACCCGAGUGGCGAAAACAGUGGAAACUGGCAGAGCCAAGUGCCUGGGCCUCCAAAAUCGACAGCAGCAGCUGACUCGUGGAACAGCAGGCACAACUUCAUUACCGUUGAGC
((((((....))))..((((.....((((....)))).....)))).(((((((....((((....(((((((....))))..)))))))....)))))))..........))....... ( -42.20)
>DroSec_CAF1 3406 120 + 1
GGCGGGAAAACCCGAGUGGCGAAAACAGUGGAAACUGGCAGAGCCAAGUGCCUGGCCCUCCAAAAUCGACAGCAGCAGCUGACUCGGGGAACAGCAGGCACAACUUCAUUACCGUUGAGC
((((((....))))..((((.....((((....)))).....)))).(((((((....(((....((((((((....))))..)))))))....)))))))..........))....... ( -41.60)
>DroSim_CAF1 6543 120 + 1
GGCGGGAAAACCCGAGUGGCGAAAACAGUGGAAACUGGCAGAGCCAAGUGCCUGGCCCUCCAAAAUCGACAGCAGCAGCUGACUCGGGGAACAGCAGGCACAACUUCAUUACCGUUGAGC
((((((....))))..((((.....((((....)))).....)))).(((((((....(((....((((((((....))))..)))))))....)))))))..........))....... ( -41.60)
>consensus
GGCGGGAAAACCCGAGUGGCGAAAACAGUGGAAACUGGCAGAGCCAAGUGCCUGGCCCUCCAAAAUCGACAGCAGCAGCUGACUCGGGGAACAGCAGGCACAACUUCAUUACCGUUGAGC
((((((....))))..((((.....((((....)))).....)))).(((((((....(((.....(((((((....))))..))).)))....)))))))..........))....... (-39.67 = -41.17 +   1.50)

alignment

secondary structure

dotplot

Window 1

Location	18,065,690 – 18,065,810
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.61
Mean single sequence MFE	-40.43
Consensus MFE	-39.44
Energy contribution	-39.67
Covariance contribution	0.22
Combinations/Pair	1.03
Mean z-score	-1.55
Structure conservation index	0.98
SVM decision value	0.19
SVM RNA-class probability	0.628431
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18065690 120 + 22224390
UGGCGGCGCGUGGGCGUGCCGAGAUUUAUUCAAUUUAAUUUGGCAUCGGCGUCAAGUCGGGCGUUGGUGUCGAGGCAUGUGAUUAAAAAUUGUUUACCAAGUUCAUUGACAUCGACCCGG
((((((((((....)))))))...((((.(((......(((((((((((((((......))))))))))))))).....))).)))).........)))..................... ( -39.10)
>DroSec_CAF1 3526 120 + 1
UGGCGGCGCGUGGGCGUGCCGAGAUUUAUUCAAUUUAAUUUGGCAUCGGCGUCAAGUAGGGCGUUGGUGUCGAGGCAUGUGAUUAAAAAUUGUUUACCAAGUUCAUUGACAUCGAACCGG
((((((((((....)))))))...((((.(((......(((((((((((((((......))))))))))))))).....))).)))).........))).((((.........))))... ( -40.70)
>DroSim_CAF1 6663 120 + 1
UGGCGGCGCGUGGGCGUGCCGAGAUUUAUUCAAUUUAAUUUGGCAUCGGCGUCAAGUCGGGCGUUGGUGUCGAGGCAUGUGAUUAAAAAUUGUUUACCAAGUUCAUUGACAUCGAGCCGG
...((((.((((.(((((((..((.....))........((((((((((((((......))))))))))))))))))))).................(((.....))).)).)).)))). ( -41.50)
>consensus
UGGCGGCGCGUGGGCGUGCCGAGAUUUAUUCAAUUUAAUUUGGCAUCGGCGUCAAGUCGGGCGUUGGUGUCGAGGCAUGUGAUUAAAAAUUGUUUACCAAGUUCAUUGACAUCGAACCGG
((((((((((....)))))))...((((.(((......(((((((((((((((......))))))))))))))).....))).)))).........))).((((.........))))... (-39.44 = -39.67 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:20 2006