Locus 6738

Sequence ID 2L_DroMel_CAF1
Location 18,835,886 – 18,836,045
Length 159
Max. P 0.948356
window10764 window10765

overview

Window 4

Location 18,835,886 – 18,836,005
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.43
Mean single sequence MFE -33.90
Consensus MFE -32.06
Energy contribution -31.73
Covariance contribution -0.33
Combinations/Pair 1.09
Mean z-score -2.37
Structure conservation index 0.95
SVM decision value 1.38
SVM RNA-class probability 0.948356
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18835886 119 + 22407834
UUUCAGCGAGUGGACGCUU-AAAAGCUUUUUUAAUUAAUUCCGGGACCGUAACUAGAUACUCCAUGAGGGACAUUUCGUCUUUCAGAGUGUUCAGAUACAUGCGCUGAAUGUUCCUGAUA
.(((((((.(((...(((.-...)))...............((....))...((..((((((..((((((((.....))))))))))))))..))...))).)))))))........... ( -32.80)
>DroSec_CAF1 1801 120 + 1
UUUCAGCGAGUGGAUGCUCUAUAAGCUUUUUUAAUUAAUUCCGGGACCGUAACUAGAUACUCGAUAAGAGACAUUUCGUCUUUCAGAGUGUUUAGAUACAUGCGCUGAACGUUCCUGAUA
.((((((((((....)))).....((................(....)(((.((((((((((....((((((.....))))))..)))))))))).)))..))))))))........... ( -34.00)
>DroSim_CAF1 42 119 + 1
UUUCAGCGAGUGGACGCUC-AUAAGCUUUUUUAAUUAAUUCCGGGACCGUAACUAAAUACUCGAUAAGAGACAUUUCGUCUUUCAGAGUGUUUAGAUACAUGCGCUGAACGUUCCUGAUA
.((((((((((....))))-....((................(....)(((.((((((((((....((((((.....))))))..)))))))))).)))..))))))))........... ( -34.90)
>consensus
UUUCAGCGAGUGGACGCUC_AUAAGCUUUUUUAAUUAAUUCCGGGACCGUAACUAGAUACUCGAUAAGAGACAUUUCGUCUUUCAGAGUGUUUAGAUACAUGCGCUGAACGUUCCUGAUA
.((((((((((....)))).....((................(....)(((.((((((((((....((((((.....))))))..)))))))))).)))..))))))))........... (-32.06 = -31.73 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,835,925 – 18,836,045
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -31.37
Consensus MFE -27.09
Energy contribution -27.10
Covariance contribution 0.01
Combinations/Pair 1.09
Mean z-score -1.69
Structure conservation index 0.86
SVM decision value 0.26
SVM RNA-class probability 0.658059
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18835925 120 + 22407834
CCGGGACCGUAACUAGAUACUCCAUGAGGGACAUUUCGUCUUUCAGAGUGUUCAGAUACAUGCGCUGAAUGUUCCUGAUAACCGGAUCAAUUACUUUGUUAAUAUCUGCAUCAGUAGGAC
((((............((((((..((((((((.....))))))))))))))((((..((((.......))))..))))...))))...................(((((....))))).. ( -31.70)
>DroSec_CAF1 1841 105 + 1
CCGGGACCGUAACUAGAUACUCGAUAAGAGACAUUUCGUCUUUCAGAGUGUUUAGAUACAUGCGCUGAACGUUCCUGAUAACCGGGUCAAUUACUUUGUUAAUGU---------------
.(((((..(((.((((((((((....((((((.....))))))..)))))))))).)))..(((.....)))))))).((((..(((.....)))..))))....--------------- ( -30.50)
>DroSim_CAF1 81 120 + 1
CCGGGACCGUAACUAAAUACUCGAUAAGAGACAUUUCGUCUUUCAGAGUGUUUAGAUACAUGCGCUGAACGUUCCUGAUAACCGGGUCAAUUACUUUGUUAAUGUCUGCAUAACUAGGAC
((((....(((.((((((((((....((((((.....))))))..)))))))))).)))..(((.....))).........))))........(((.((((.((....)))))).))).. ( -31.90)
>consensus
CCGGGACCGUAACUAGAUACUCGAUAAGAGACAUUUCGUCUUUCAGAGUGUUUAGAUACAUGCGCUGAACGUUCCUGAUAACCGGGUCAAUUACUUUGUUAAUGUCUGCAU_A_UAGGAC
.(((((..(((.((((((((((....((((((.....))))))..)))))))))).)))..(((.....)))))))).((((..(((.....)))..))))................... (-27.09 = -27.10 +   0.01)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:52 2006