Locus 3409

Sequence ID 3R_DroMel_CAF1
Location 9,238,782 – 9,238,903
Length 121
Max. P 0.729681
window5471 window5472

overview

Window 1

Location 9,238,782 – 9,238,872
Length 90
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 82.25
Mean single sequence MFE -23.72
Consensus MFE -17.10
Energy contribution -18.88
Covariance contribution 1.78
Combinations/Pair 1.16
Mean z-score -1.87
Structure conservation index 0.72
SVM decision value 0.42
SVM RNA-class probability 0.729681
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9238782 90 + 27905053
AUAUU-----UUGGCCAAUUGGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAACAUAUACUAUUAAGUGGCGGAGGCAACUCCUAGACUCGUUU
.....-----..((((....)))).((((.(((((((((((...(((((.................))))))))))))))))))))......... ( -27.13)
>DroSec_CAF1 9706 90 + 1
AUAUU-----UUGGCCAAUUGGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAAGAUAUACUAUUAAGUGGCGGAGGCAACUCCUAGAUUCGUUU
.....-----..((((....)))).((((.(((((((((((...(((((.((.((.....)).)).))))))))))))))))))))......... ( -29.10)
>DroSim_CAF1 9489 90 + 1
AUAUU-----UUGGCCAAUUGGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAACAUAUACUAUUAACUGGCGGAGGCAACUCCUAGACUCGUUU
.....-----..((((....)))).((((.(((((((((((..............................)))))))))))))))......... ( -23.81)
>DroEre_CAF1 10256 89 + 1
AUAUU-----UUGGCCGAUUGGCUGUGGGCAGUUGUCGCUGAUUUCGCUCAAAUCAUAUACUAUUAAAU-GCGGAGACAACUCCCAGACUCGUUU
.....-----..((((....)))).((((.(((((((......(((((.....................-))))))))))))))))......... ( -22.80)
>DroYak_CAF1 9562 95 + 1
AUAUUUUUUUUUGGCCAAUUGGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAUCAUACACUAUUAAAUGGCGGAGACAACUCCCAGACUCGUUU
............((((....)))).((((.(((((((((((((((.....))))))..(.((((...)))).))))))))))))))......... ( -28.50)
>DroAna_CAF1 9947 73 + 1
AUAUU------UGGCCAAUUUGACGUGGGC----------------UCUUAAAUUACAUAUUAUUUACUGUCGCGGCCAACUCCCAUACUCGUUU
....(------(((((....(((((((((.----------------.................))))).)))).))))))............... ( -10.97)
>consensus
AUAUU_____UUGGCCAAUUGGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAACAUAUACUAUUAAAUGGCGGAGGCAACUCCCAGACUCGUUU
............((((....)))).((((.(((((((((((..............................)))))))))))))))......... (-17.10 = -18.88 +   1.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 9,238,797 – 9,238,903
Length 106
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 84.21
Mean single sequence MFE -31.29
Consensus MFE -23.19
Energy contribution -25.03
Covariance contribution 1.83
Combinations/Pair 1.17
Mean z-score -1.83
Structure conservation index 0.74
SVM decision value 0.05
SVM RNA-class probability 0.557193
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9238797 106 + 27905053
GGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAACAUAUACUAUUAAGUGGCGGAGGCAACUCCUAGACUCGUUUGGCUCUGGCAAAUUGCAGAGAAACAUGGCCA
(((((((((.(((((((((((...(((((.................)))))))))))))))))).............(((((........)))))...))))))). ( -36.03)
>DroSec_CAF1 9721 106 + 1
GGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAAGAUAUACUAUUAAGUGGCGGAGGCAACUCCUAGAUUCGUUUGGCUCUGGCAAAUUGCAGAGAAACAUGACCA
((.(.((((.(((((((((((...(((((.((.((.....)).)).)))))))))))))))))))).).((((.(..(((((........)))))..).)))))). ( -33.60)
>DroSim_CAF1 9504 106 + 1
GGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAACAUAUACUAUUAACUGGCGGAGGCAACUCCUAGACUCGUUUGGCUCUGGCAAAUUGCAGAGAAACAUGGCCA
(((((((((.(((((((((((..............................))))))))))))).............(((((........)))))...))))))). ( -32.71)
>DroEre_CAF1 10271 105 + 1
GGCUGUGGGCAGUUGUCGCUGAUUUCGCUCAAAUCAUAUACUAUUAAAU-GCGGAGACAACUCCCAGACUCGUUUGAAUCUGGCAAAUUGCAGAGAAACAUGGCCA
(((((((((.(((((((......(((((.....................-)))))))))))))))......((((...((((........)))).)))))))))). ( -30.10)
>DroYak_CAF1 9582 106 + 1
GGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAUCAUACACUAUUAAAUGGCGGAGACAACUCCCAGACUCGUUUGAGUCUGGCAAAUUGCAGAGAAACAUGGCCA
(((((((((.(((((((((((((((.....))))))..(.((((...)))).))))))))))))(((((((....)))))))((.....)).......))))))). ( -40.20)
>DroAna_CAF1 9961 89 + 1
UGACGUGGGC----------------UCUUAAAUUACAUAUUAUUUACUGUCGCGGCCAACUCCCAUACUCGUUUGCAUCUGGCAAAUUGCA-AUAAACAUGGCAA
...(((((.(----------------...(((((........)))))..))))))((((............((((((.....))))))....-.......)))).. ( -15.10)
>consensus
GGCUGUGGGCAGUUGUCUCUGAUUUCGCUCAAAACAUAUACUAUUAAAUGGCGGAGGCAACUCCCAGACUCGUUUGGCUCUGGCAAAUUGCAGAGAAACAUGGCCA
(((((((((.(((((((((((..............................))))))))))))))......((((..(((((........))))))))))))))). (-23.19 = -25.03 +   1.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:17 2006