Locus 7194

Sequence ID 3R_DroMel_CAF1
Location 18,962,633 – 18,962,723
Length 90
Max. P 0.998970
window11643 window11644

overview

Window 3

Location 18,962,633 – 18,962,723
Length 90
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 78.85
Mean single sequence MFE -35.20
Consensus MFE -23.93
Energy contribution -23.68
Covariance contribution -0.25
Combinations/Pair 1.21
Mean z-score -3.01
Structure conservation index 0.68
SVM decision value 3.31
SVM RNA-class probability 0.998970
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18962633 90 + 27905053
GGAGCUCGAUCUUGGA----------------------------GCUUGAAGCUGGCAGUUGGAGUAGCCAAGAGUCAGGUAAGAGCCGAGUUCGGGCCGGGUCUUAAAUGAUAAGCG
.(.((((((.(((((.----------------------------.((((...(((((..((((.....))))..))))).))))..))))).)))))))..(((......)))..... ( -33.00)
>DroSec_CAF1 74004 90 + 1
GGAGCUCGAGCUUGGA----------------------------GCUUGGAUCUGGUGGUUGGAGUAGCCAAGAGUCAGGUAAGAGCCAAGUUCGGGCCGGGUCUUAAAUGAUAAGCG
.(.((((((((((((.----------------------------.(((..(((((((..((((.....))))..))))))))))..)))))))))))))..(((......)))..... ( -34.30)
>DroSim_CAF1 75608 90 + 1
GGAGCUCGAGCUUGGA----------------------------GCUGGCAGUUGGCGGUUGGAGUAGCCAAGAGUCAGGUAAGAGCCAAGUUCGGGCCGGGUCUUAAAUGAUAAGCG
.(.((((((((((((.----------------------------.((.((...((((..((((.....))))..)))).)).))..)))))))))))))..(((......)))..... ( -35.20)
>DroYak_CAF1 76553 118 + 1
GGAGCUCAAGCUUGGAGCUUGGAGCUGGCAGUUGGAAGUUGGCAGUUGGAAGUUGGCAGUUGGAGAGGCCAAGAGUCAGGUAAGAGUUGAGUUCGGGCCGGGUCUUAAAUGAUAAGCG
.((((((((.(((...((((((..(((((..(..(..((..((........))..))..)..)....))).))..))))))..)))))))))))..((...(((......)))..)). ( -38.30)
>consensus
GGAGCUCGAGCUUGGA____________________________GCUGGAAGCUGGCAGUUGGAGUAGCCAAGAGUCAGGUAAGAGCCAAGUUCGGGCCGGGUCUUAAAUGAUAAGCG
.(.((((((((((((..............................(((..(.(((((..((((.....))))..))))).)..))))))))))))))))..(((......)))..... (-23.93 = -23.68 +  -0.25)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 18,962,633 – 18,962,723
Length 90
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 78.85
Mean single sequence MFE -20.20
Consensus MFE -14.48
Energy contribution -14.72
Covariance contribution 0.25
Combinations/Pair 1.10
Mean z-score -1.72
Structure conservation index 0.72
SVM decision value 0.52
SVM RNA-class probability 0.767507
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18962633 90 - 27905053
CGCUUAUCAUUUAAGACCCGGCCCGAACUCGGCUCUUACCUGACUCUUGGCUACUCCAACUGCCAGCUUCAAGC----------------------------UCCAAGAUCGAGCUCC
.((...(((..(((((.((((.......)))).)))))..)))....((((..........))))))....(((----------------------------((.......))))).. ( -21.10)
>DroSec_CAF1 74004 90 - 1
CGCUUAUCAUUUAAGACCCGGCCCGAACUUGGCUCUUACCUGACUCUUGGCUACUCCAACCACCAGAUCCAAGC----------------------------UCCAAGCUCGAGCUCC
..((((.....))))....(((.(((.(((((..(((..(((....((((.....))))....)))....))).----------------------------.))))).))).))).. ( -18.90)
>DroSim_CAF1 75608 90 - 1
CGCUUAUCAUUUAAGACCCGGCCCGAACUUGGCUCUUACCUGACUCUUGGCUACUCCAACCGCCAACUGCCAGC----------------------------UCCAAGCUCGAGCUCC
..((((.....))))....(((.(((.(((((.......(((.(..(((((..........)))))..).))).----------------------------.))))).))).))).. ( -20.90)
>DroYak_CAF1 76553 118 - 1
CGCUUAUCAUUUAAGACCCGGCCCGAACUCAACUCUUACCUGACUCUUGGCCUCUCCAACUGCCAACUUCCAACUGCCAACUUCCAACUGCCAGCUCCAAGCUCCAAGCUUGAGCUCC
..((((.....))))....(((...........((......))...(((((..........))))).........)))..............(((((.((((.....))))))))).. ( -19.90)
>consensus
CGCUUAUCAUUUAAGACCCGGCCCGAACUCGGCUCUUACCUGACUCUUGGCUACUCCAACCGCCAACUUCAAGC____________________________UCCAAGCUCGAGCUCC
.((((.(((..(((((.((((.......)))).)))))..)))...(((((..........))))).............................................))))... (-14.48 = -14.72 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:51 2006