Locus 1030

Sequence ID 3R_DroMel_CAF1
Location 3,219,473 – 3,219,573
Length 100
Max. P 0.980760
window1668 window1669

overview

Window 8

Location 3,219,473 – 3,219,573
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 97.70
Mean single sequence MFE -30.43
Consensus MFE -29.03
Energy contribution -29.27
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.26
Structure conservation index 0.95
SVM decision value 0.48
SVM RNA-class probability 0.752892
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3219473 100 + 27905053
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGCAUUU
.........((((((.(((((.((....))......(((((((((....))).......)))))).))))).((((.((.....)))))).))))))... ( -32.11)
>DroSec_CAF1 44194 100 + 1
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGCAUUU
.........((((((.(((((.((....))......(((((((((....))).......)))))).))))).((((.((.....)))))).))))))... ( -32.11)
>DroSim_CAF1 45556 100 + 1
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGCAUUU
.........((((((.(((((.((....))......(((((((((....))).......)))))).))))).((((.((.....)))))).))))))... ( -32.11)
>DroEre_CAF1 38521 98 + 1
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGCAGCUUUGGGCCCCCACUCGCAU--
.......((.((((..(((((.((....))......(((((((((....))).......)))))).))))).((((........))))))))..))..-- ( -26.21)
>DroYak_CAF1 28846 100 + 1
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGGAUUG
.(((((((..(((((..((((((...((................))...))))))......(((((((((.....)))))))))...)))))))))))). ( -29.59)
>consensus
AAGUUUGGCUGUGGGACGAGCAGCAAACGUAACAUAUUGACACAGUAAACUGCUUAGAUUGUCAAAGUUCGAGGGGAGCUUUGGGCCCCCACCCGCAUUU
.........((((((.(((((.((....))......(((((((((....))).......)))))).))))).((((.((.....)))))).))))))... (-29.03 = -29.27 +   0.24) 

alignment

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secondary structure

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dotplot

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Window 9

Location 3,219,473 – 3,219,573
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 97.70
Mean single sequence MFE -28.55
Consensus MFE -28.31
Energy contribution -28.35
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.58
Structure conservation index 0.99
SVM decision value 1.87
SVM RNA-class probability 0.980760
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3219473 100 - 27905053
AAAUGCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. ( -29.11)
>DroSec_CAF1 44194 100 - 1
AAAUGCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. ( -29.11)
>DroSim_CAF1 45556 100 - 1
AAAUGCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. ( -29.11)
>DroEre_CAF1 38521 98 - 1
--AUGCGAGUGGGGGCCCAAAGCUGCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
--..(((((..(((((........)))).(((((..(((((......((((....)))).......))))).))))))..)))))............... ( -26.22)
>DroYak_CAF1 28846 100 - 1
CAAUCCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. ( -29.21)
>consensus
AAAUGCGGGUGGGGGCCCAAAGCUCCCCUCGAACUUUGACAAUCUAAGCAGUUUACUGUGUCAAUAUGUUACGUUUGCUGCUCGUCCCACAGCCAAACUU
.....((((.((((((.....))))))))))(((.(((((.......((((....)))))))))...)))..((((((((.........))).))))).. (-28.31 = -28.35 +   0.04) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:48 2006