Locus 3890

Sequence ID	X_DroMel_CAF1
Location	10,393,152 – 10,393,249
Length	97
Max. P	0.762274

overview

Window 9

Location	10,393,152 – 10,393,249
Length	97
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	79.19
Mean single sequence MFE	-27.01
Consensus MFE	-16.21
Energy contribution	-16.57
Covariance contribution	0.36
Combinations/Pair	1.35
Mean z-score	-1.91
Structure conservation index	0.60
SVM decision value	0.51
SVM RNA-class probability	0.762274
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10393152 97 + 22224390
GGCUCCAAUAAGACAAAUAUGGGAG----------GGGCAUUCCAGAAGGAAUGCUGCUUUUACUUCCCAUUUCCAUUUCC-------AUUUGACCAAGCUGACAAAUUGGCUG
((.((.(((.........(((((((----------(((((((((....)))))))).......))))))))..........-------))).)))).(((..(....)..))). ( -27.32)
>DroSec_CAF1 37147 97 + 1
GGCUCCAAUAAGACAAAACUGGGAG----------GGGCAUUCCAGAAGGAAUGCUGCUUUUACUUCCCAUUUCCAUUUCC-------AUUUGACCAAGCUGACAAAUUGGCUA
((.((.(((..........((((((----------(((((((((....)))))))).......)))))))...........-------))).)))).(((..(....)..))). ( -25.41)
>DroEre_CAF1 41783 97 + 1
GGCUCCAAUAAGACAAAAAUGGGAG----------AGGCAUUCCAGAAGGAAUGCUGCUUUUACUUCCCAUUUUCAUUUCC-------AUUUGACCAAGUUGACAAAUUGGCUC
((.((.(((.(((..((((((((((----------.((((((((....))))))))........))))))))))..)))..-------))).)))).(((..(....)..))). ( -26.20)
>DroYak_CAF1 36865 97 + 1
GGCUCCAAUAAGACAAAAAUGGGAG----------GGGCAUUCCCGAAGGAAUGCUGCUUUUACUUCCCAUUUUCAUUUCC-------AUUUGACCAAGUUGACAAAUUGGCUC
((.((.(((.(((..((((((((((----------(((((((((....)))))))).......)))))))))))..)))..-------))).)))).(((..(....)..))). ( -28.41)
>DroAna_CAF1 31632 106 + 1
GGCUUUAAGAG----AGUGUGGGAGAGAAAGAGUAAGGUGCUUGAGAAGGAAUGUGACUUC----UCCCAUUUACUUUUCCUUCUGCUAUUUGGCCAAGUUGACAAAUUGUUUC
((((......(----((((..((((.(((.(((((((.((...((((((........))))----)).))))))))))))))))..).)))))))).................. ( -27.70)
>consensus
GGCUCCAAUAAGACAAAAAUGGGAG__________GGGCAUUCCAGAAGGAAUGCUGCUUUUACUUCCCAUUUCCAUUUCC_______AUUUGACCAAGUUGACAAAUUGGCUC
................(((((((((...........((((((((....))))))))........)))))))))........................((((((....)))))). (-16.21 = -16.57 +   0.36)

alignment

secondary structure

dotplot

Window 0

Location	10,393,152 – 10,393,249
Length	97
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	79.19
Mean single sequence MFE	-25.54
Consensus MFE	-16.50
Energy contribution	-18.98
Covariance contribution	2.48
Combinations/Pair	1.08
Mean z-score	-1.63
Structure conservation index	0.65
SVM decision value	0.11
SVM RNA-class probability	0.587782
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10393152 97 - 22224390
CAGCCAAUUUGUCAGCUUGGUCAAAU-------GGAAAUGGAAAUGGGAAGUAAAAGCAGCAUUCCUUCUGGAAUGCCC----------CUCCCAUAUUUGUCUUAUUGGAGCC
...(((((..(.(((((...((....-------.))...))..((((((.((....)).(((((((....)))))))..----------.))))))..))).)..))))).... ( -25.80)
>DroSec_CAF1 37147 97 - 1
UAGCCAAUUUGUCAGCUUGGUCAAAU-------GGAAAUGGAAAUGGGAAGUAAAAGCAGCAUUCCUUCUGGAAUGCCC----------CUCCCAGUUUUGUCUUAUUGGAGCC
...(((((..(.(((((...((....-------.))...))...(((((.((....)).(((((((....)))))))..----------.)))))...))).)..))))).... ( -24.80)
>DroEre_CAF1 41783 97 - 1
GAGCCAAUUUGUCAACUUGGUCAAAU-------GGAAAUGAAAAUGGGAAGUAAAAGCAGCAUUCCUUCUGGAAUGCCU----------CUCCCAUUUUUGUCUUAUUGGAGCC
(..((((((((.(......).)))))-------.((.(..(((((((((.((....)).(((((((....)))))))..----------.)))))))))..).))..)))..). ( -28.90)
>DroYak_CAF1 36865 97 - 1
GAGCCAAUUUGUCAACUUGGUCAAAU-------GGAAAUGAAAAUGGGAAGUAAAAGCAGCAUUCCUUCGGGAAUGCCC----------CUCCCAUUUUUGUCUUAUUGGAGCC
(..((((((((.(......).)))))-------.((.(..(((((((((.((....)).(((((((....)))))))..----------.)))))))))..).))..)))..). ( -31.70)
>DroAna_CAF1 31632 106 - 1
GAAACAAUUUGUCAACUUGGCCAAAUAGCAGAAGGAAAAGUAAAUGGGA----GAAGUCACAUUCCUUCUCAAGCACCUUACUCUUUCUCUCCCACACU----CUCUUAAAGCC
......(((((((.....)).)))))....((..(((((((((.((.((----((((........))))))...))..))))).))))..)).......----........... ( -16.50)
>consensus
GAGCCAAUUUGUCAACUUGGUCAAAU_______GGAAAUGAAAAUGGGAAGUAAAAGCAGCAUUCCUUCUGGAAUGCCC__________CUCCCAUUUUUGUCUUAUUGGAGCC
...((((((((.(......).))))............(..(((((((((..........(((((((....))))))).............)))))))))..)....)))).... (-16.50 = -18.98 +   2.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:06 2006