Locus 2078

Sequence ID 3L_DroMel_CAF1
Location 5,705,565 – 5,705,693
Length 128
Max. P 0.951524
window3240 window3241

overview

Window 0

Location 5,705,565 – 5,705,668
Length 103
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 91.63
Mean single sequence MFE -22.04
Consensus MFE -18.10
Energy contribution -18.50
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.82
SVM decision value 1.41
SVM RNA-class probability 0.951524
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5705565 103 - 23771897
CUUCAGGAGGUCAUCCUCCUGA-------CACCAACCUCCCUCCACCUUCCUCCUCGUGAUCAUACCAACGAUUUUCGGGCACUGCACUUACUUGCUCCGCGGUCUUUAG
..((((((((....))))))))-------.(((.....................(((.((((........))))..)))((...(((......)))...)))))...... ( -23.70)
>DroSec_CAF1 79336 100 - 1
CUUCAGGAGGUCAUCCUCCUGC-------CACCAACCUCCCUCCACCUUCCUCC---UGAUCAUACCAACGAUUUUCGGGCACUGCACUUACUUGCUCCGCGGUCUUUAG
...(((((((....))))))).-------.(((...................((---.((((........))))...))((...(((......)))...)))))...... ( -21.30)
>DroSim_CAF1 78708 100 - 1
CUUCAGGAGGUCAUCCUCCUGC-------CACCAACCUCCCUCCACCUUCCUCC---UGAUCAUACCAACGAUUUUCGGGCACUGCACUUACUUGCUCCGCGGUCUUUAG
...(((((((....))))))).-------.(((...................((---.((((........))))...))((...(((......)))...)))))...... ( -21.30)
>DroEre_CAF1 81580 100 - 1
CUUCAGGAGGUCAUCCUCCAGC-------CGCCAACCUCCCUCCACCUUCCUCC---UGAUCAUAACAACGAUUUUCGGGCACUGCACUUACUUGCUCCGCGGUCUUUAG
.....(((((....))))).((-------(((.................(((..---.((((........))))...)))....(((......)))...)))))...... ( -22.30)
>DroYak_CAF1 82328 107 - 1
CUUCAGGAGGUCAUCCUCCUGCCUUGUGCCUCCAACCUCCCUCCACCUUCCUCC---AGAUCAUACAAACGUGUUUCGGACGAUGCACUUACUUGCUCCGCGGUCUUUAG
...(((((((....)))))))......(((.....................(((---.((..((((....)))).)))))((..(((......)))..)).)))...... ( -21.60)
>consensus
CUUCAGGAGGUCAUCCUCCUGC_______CACCAACCUCCCUCCACCUUCCUCC___UGAUCAUACCAACGAUUUUCGGGCACUGCACUUACUUGCUCCGCGGUCUUUAG
...(((((((....))))))).....................................((((.......((.....)).((...(((......)))...))))))..... (-18.10 = -18.50 +   0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,705,601 – 5,705,693
Length 92
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 85.71
Mean single sequence MFE -16.32
Consensus MFE -12.47
Energy contribution -12.80
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.76
SVM decision value 0.40
SVM RNA-class probability 0.721097
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5705601 92 - 23771897
GUUGUCCCCAUUCCAAGUUUUCCAGCUUCAGGAGGUCAUCCUCCUGA-------CACCAACCUCCCUCCACCUUCCUCCUCGUGAUCAUACCAACGAUU
((((...........(((......)))((((((((....))))))))-------...))))..................((((..........)))).. ( -17.90)
>DroEre_CAF1 81616 89 - 1
GUUGUCCCCAUUCCCAGUUGUCCAGCUUCAGGAGGUCAUCCUCCAGC-------CGCCAACCUCCCUCCACCUUCCUCC---UGAUCAUAACAACGAUU
................(((((......((((((((............-------....................)))))---))).....))))).... ( -16.95)
>DroYak_CAF1 82364 96 - 1
GUUGUCCCCAUUCCCAGUUUUCCAGCUUCAGGAGGUCAUCCUCCUGCCUUGUGCCUCCAACCUCCCUCCACCUUCCUCC---AGAUCAUACAAACGUGU
((((....(((....(((......))).(((((((....)))))))....)))....))))..................---.....((((....)))) ( -14.10)
>consensus
GUUGUCCCCAUUCCCAGUUUUCCAGCUUCAGGAGGUCAUCCUCCUGC_______CACCAACCUCCCUCCACCUUCCUCC___UGAUCAUACCAACGAUU
((((...........((((....)))).(((((((....)))))))...........))))...................................... (-12.47 = -12.80 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:55 2006