Locus 1309

Sequence ID	X_DroMel_CAF1
Location	3,898,171 – 3,898,278
Length	107
Max. P	0.978239

overview

Window 1

Location	3,898,171 – 3,898,278
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	97.57
Mean single sequence MFE	-28.18
Consensus MFE	-26.90
Energy contribution	-26.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.95
SVM decision value	1.81
SVM RNA-class probability	0.978239
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3898171 107 + 22224390
CUCGCAGCGGGCGAUUUUUCGCCAGUGGCAAAAGAAAGAAAAACAAAAAACGUAUUUACCUCAAAUUAAACAUUAUUAUGCCAGGGGAGGCUGGUCAUUUGAGGGUA
...((.((.(((((....))))).)).)).............................((((((((....(((....)))((((......))))..))))))))... ( -26.90)
>DroSec_CAF1 15541 107 + 1
CUCGCAGCGGGCGAUUUUUCGCCAGUGGCAAAAGAAAGAAAAACAAAAAACGUAUUUACCUCAAAUUAAACAUUAUUAUGCCAGGGGAGGCUGGUCAUUUGAGGGCA
...((.((.(((((....))))).)).)).............................((((((((....(((....)))((((......))))..))))))))... ( -26.90)
>DroSim_CAF1 12677 107 + 1
CUCGCAGCGGGCGAUUUUUCGCCAGUGGCAAAAGAAAGAAAAACAAAAAACGUAUUUACCUCAAAUUAAACAUUAUUAUGCCAGGGGAGGCUGGUCAUUUGAGGGCA
...((.((.(((((....))))).)).)).............................((((((((....(((....)))((((......))))..))))))))... ( -26.90)
>DroEre_CAF1 17630 103 + 1
CUCGCAGCGGGCGAUUUUUCGCCAGUGGCGAAA----GAAAAACAAAAAACGUAUUUACCUCAAAUUAAACAUUAUUAUGCCAGGGGAGGCUGGUCAUUUGAGGGCA
.((((.((.(((((....))))).)).))))..----.....................((((((((....(((....)))((((......))))..))))))))... ( -30.10)
>DroYak_CAF1 18034 107 + 1
CUCGCAGCGGGCGAUUUUUCGCCAGUGGCGAAAGAAAGAAAAACAAAAAACGUAUUUACCUCAAAUUAAACAUUAUUAUGCCAGGGGAGGCUGGUCAUUUGAGGGCA
.((((.((.(((((....))))).)).))))...........................((((((((....(((....)))((((......))))..))))))))... ( -30.10)
>consensus
CUCGCAGCGGGCGAUUUUUCGCCAGUGGCAAAAGAAAGAAAAACAAAAAACGUAUUUACCUCAAAUUAAACAUUAUUAUGCCAGGGGAGGCUGGUCAUUUGAGGGCA
...((.((.(((((....))))).)).)).............................((((((((....(((....)))((((......))))..))))))))... (-26.90 = -26.90 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	3,898,171 – 3,898,278
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	97.57
Mean single sequence MFE	-25.34
Consensus MFE	-25.58
Energy contribution	-25.34
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-1.51
Structure conservation index	1.01
SVM decision value	1.75
SVM RNA-class probability	0.975299
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3898171 107 - 22224390
UACCCUCAAAUGACCAGCCUCCCCUGGCAUAAUAAUGUUUAAUUUGAGGUAAAUACGUUUUUUGUUUUUCUUUCUUUUGCCACUGGCGAAAAAUCGCCCGCUGCGAG
...((((((((.....(((......))).(((......)))))))))))...........................((((..(.(((((....))))).)..)))). ( -24.50)
>DroSec_CAF1 15541 107 - 1
UGCCCUCAAAUGACCAGCCUCCCCUGGCAUAAUAAUGUUUAAUUUGAGGUAAAUACGUUUUUUGUUUUUCUUUCUUUUGCCACUGGCGAAAAAUCGCCCGCUGCGAG
...((((((((.....(((......))).(((......)))))))))))...........................((((..(.(((((....))))).)..)))). ( -24.50)
>DroSim_CAF1 12677 107 - 1
UGCCCUCAAAUGACCAGCCUCCCCUGGCAUAAUAAUGUUUAAUUUGAGGUAAAUACGUUUUUUGUUUUUCUUUCUUUUGCCACUGGCGAAAAAUCGCCCGCUGCGAG
...((((((((.....(((......))).(((......)))))))))))...........................((((..(.(((((....))))).)..)))). ( -24.50)
>DroEre_CAF1 17630 103 - 1
UGCCCUCAAAUGACCAGCCUCCCCUGGCAUAAUAAUGUUUAAUUUGAGGUAAAUACGUUUUUUGUUUUUC----UUUCGCCACUGGCGAAAAAUCGCCCGCUGCGAG
...((((((((.....(((......))).(((......))))))))))).....................----..((((..(.(((((....))))).)..)))). ( -26.60)
>DroYak_CAF1 18034 107 - 1
UGCCCUCAAAUGACCAGCCUCCCCUGGCAUAAUAAUGUUUAAUUUGAGGUAAAUACGUUUUUUGUUUUUCUUUCUUUCGCCACUGGCGAAAAAUCGCCCGCUGCGAG
...((((((((.....(((......))).(((......)))))))))))...........................((((..(.(((((....))))).)..)))). ( -26.60)
>consensus
UGCCCUCAAAUGACCAGCCUCCCCUGGCAUAAUAAUGUUUAAUUUGAGGUAAAUACGUUUUUUGUUUUUCUUUCUUUUGCCACUGGCGAAAAAUCGCCCGCUGCGAG
...((((((((.....(((......))).(((......)))))))))))...........................((((..(.(((((....))))).)..)))). (-25.58 = -25.34 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:15 2006