Locus 8680

Sequence ID 3L_DroMel_CAF1
Location 22,510,698 – 22,510,866
Length 168
Max. P 0.996964
window14226 window14227 window14228

overview

Window 6

Location 22,510,698 – 22,510,805
Length 107
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 94.26
Mean single sequence MFE -33.02
Consensus MFE -31.35
Energy contribution -31.60
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.95
SVM decision value 1.41
SVM RNA-class probability 0.951489
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22510698 107 - 23771897
CAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUAGUAACAAGUAA------------CGAGCGCCCAGCGCCAUAAACUUAAAUCACGAUUAAAAGUGUGAUUAUCCUUGUGG
..(((((((.(.(.(((.(((((((((...))))))(((.......)))..------------))))))))))))))).........(((((((........))))))).......... ( -32.80)
>DroSec_CAF1 18756 119 - 1
CAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUAGUAACAAGUAACGGAAAACUAAACGAGCGCCCAGCGCCAUAAACUUAAAUCACGAUUAAAAGUGUGAUUAUCCUUGUGG
..(((((((.(.(.(((.(((((((((...))))))..........(((........)))...))))))))))))))).........(((((((........))))))).......... ( -33.10)
>DroSim_CAF1 19194 119 - 1
CAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUAGUAACAAGUAACAGAAAACUAAACGAGCGCCCAGCGCCAUAAACUUAAAUCACGAUUAAAAGUGUGAUUAUCCUUGUGG
..(((((((.(.(.(((.(((((((((...))))))..........(((........)))...))))))))))))))).........(((((((........))))))).......... ( -33.10)
>DroEre_CAF1 20835 119 - 1
CAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAAGUAGUAACAAGUAACAGAAAACUAAACGAGCGCCCAGCGCCAUAAACUUAAAUCACGAUUAAAAGUGUGAUUAUCCUUGUGG
..(((((((.(.(.(((.(((((((((...))))))..........(((........)))...))))))))))))))).........(((((((........))))))).......... ( -33.10)
>consensus
CAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUAGUAACAAGUAACAGAAAACUAAACGAGCGCCCAGCGCCAUAAACUUAAAUCACGAUUAAAAGUGUGAUUAUCCUUGUGG
..(((((((.(.(.(((.(((((((((...))))))(((.......)))..............))))))))))))))).........(((((((........))))))).......... (-31.35 = -31.60 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 22,510,738 – 22,510,844
Length 106
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 92.09
Mean single sequence MFE -36.88
Consensus MFE -35.32
Energy contribution -35.38
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.77
Structure conservation index 0.96
SVM decision value 2.78
SVM RNA-class probability 0.996964
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22510738 106 - 23771897
GUCGAUAGAGCCGUGAGAAAGGAAUUGAAAAAAUCAUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUAGUAACAAGUAA------------CGAGCGCCCAGCGCCA
.........(((((((.................))))))).(((((((.(.(.(((.(((((((((...))))))(((.......)))..------------))))))))))))))). ( -37.43)
>DroSec_CAF1 18796 118 - 1
UCCGAGAGAGCCGUGAGAAAGGAAUUGAAAAAAUCAUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUAGUAACAAGUAACGGAAAACUAAACGAGCGCCCAGCGCCA
.........(((((((.................))))))).(((((((.(.(.(((.(((((((((...))))))..........(((........)))...))))))))))))))). ( -37.73)
>DroSim_CAF1 19234 118 - 1
UCCGAUAGAGCCGUGAGAAAGGAAUUGAAAAAAUCAUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUAGUAACAAGUAACAGAAAACUAAACGAGCGCCCAGCGCCA
.........(((((((.................))))))).(((((((.(.(.(((.(((((((((...))))))..........(((........)))...))))))))))))))). ( -37.73)
>DroEre_CAF1 20875 118 - 1
UCCGAUGGAGCCGUGAGAAAGGAAUUGAAAAAAUCGUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAAGUAGUAACAAGUAACAGAAAACUAAACGAGCGCCCAGCGCCA
(((...)))(((((((.................))))))).(((((((.(.(.(((.(((((((((...))))))..........(((........)))...))))))))))))))). ( -34.63)
>consensus
UCCGAUAGAGCCGUGAGAAAGGAAUUGAAAAAAUCAUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUAGUAACAAGUAACAGAAAACUAAACGAGCGCCCAGCGCCA
.........(((((((.................))))))).(((((((.(.(.(((.(((((((((...))))))(((.......)))..............))))))))))))))). (-35.32 = -35.38 +   0.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,510,765 – 22,510,866
Length 101
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 92.27
Mean single sequence MFE -35.32
Consensus MFE -32.23
Energy contribution -32.73
Covariance contribution 0.50
Combinations/Pair 1.12
Mean z-score -2.03
Structure conservation index 0.91
SVM decision value 1.45
SVM RNA-class probability 0.955389
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22510765 101 - 23771897
C-----CCUUGACCGACGAAGGACGGAGUCGAUAGAGCCGUGAGAAAGGAAUUGAAAAAAUCAUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUA
.-----(((((....((((.((((((.(((......(((((((.................))))))).)))((........)).))))))))))..)))))..... ( -32.13)
>DroSec_CAF1 18835 101 - 1
C-----CCUCGUCCUGCGAAGGACGGAUCCGAGAGAGCCGUGAGAAAGGAAUUGAAAAAAUCAUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUA
.-----((((((..(((((.(((((((((((((.(.(((((((.................)))))))...).)).)).)))...)))))))))))))))))..... ( -36.83)
>DroSim_CAF1 19273 101 - 1
C-----CCUCGUCCUGCGAAGGACGGAUCCGAUAGAGCCGUGAGAAAGGAAUUGAAAAAAUCAUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUA
.-----((((((..(((((.(((((((((((.(((.(((((((.................))))))).....))))).)))...)))))))))))))))))..... ( -36.53)
>DroEre_CAF1 20914 106 - 1
CUCGUUCCUCGUCCGCCGAAGGACGGAUCCGAUGGAGCCGUGAGAAAGGAAUUGAAAAAAUCGUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAAGUA
....((((((((....(((.((((((...((((....((........)).))))......(((..((....))..)))......)))))))))..))))))))... ( -35.80)
>consensus
C_____CCUCGUCCGGCGAAGGACGGAUCCGAUAGAGCCGUGAGAAAGGAAUUGAAAAAAUCAUGGCAGGCGCUGCGAGAUGCAUCGUCCUCGUAACGAGGAACUA
......((((((..(((((.((((((..........(((((((.................)))))))....((........)).)))))))))))))))))..... (-32.23 = -32.73 +   0.50)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:10 2006