Locus 4923

Sequence ID 3L_DroMel_CAF1
Location 13,677,613 – 13,677,805
Length 192
Max. P 0.998970
window7778 window7779

overview

Window 8

Location 13,677,613 – 13,677,727
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.70
Mean single sequence MFE -31.56
Consensus MFE -29.14
Energy contribution -29.42
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.13
Structure conservation index 0.92
SVM decision value 0.10
SVM RNA-class probability 0.581112
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13677613 114 + 23771897
CACUCGAAUAUA------CUUUGCCGUUACAACUGUUUACUCGCUUUUGGCUUUUCAAUAAUUUACGUUACAUACGUGUGGGCGUGGCCUGUCGUCCCAGGUGCCCACAGUUGGAUGGCA
............------...(((((((.(((((((......((.....))............(((((.....))))).((((...(((((......))))))))))))))))))))))) ( -34.80)
>DroSec_CAF1 84918 114 + 1
CACUCGAAUAUA------CUUUGCCGUUACAACUAUUUACUCCCUUUUGGCUUUUCAAUAAUUUACGUUACAUACGUGUGGGCGUGGCAUGUCGUCCCAGGUGCCCAAAGUUGGAUGGCA
............------...(((((((.(((((....((.(((..((((....)))).....(((((.....))))).))).))(((((.(......).)))))...)))))))))))) ( -28.10)
>DroSim_CAF1 95512 114 + 1
CACUCGAAUAUA------CUUUGCCGUUACAACUGUUUACUCGCUUUUGGCUUUUCAAUAAUUUACGUUACAUACGUGUGGGCGUGGCAUGUCGUCCCAGGUGCCCACAGUUGGAUGGCA
............------...(((((((.(((((((...(((((..((((....))))......((((.....))))))))).(.(((((.(......).)))))))))))))))))))) ( -30.80)
>DroEre_CAF1 90178 120 + 1
CACUCGAAUAUACUCGUACUUUGCCGUUACAACUGUUUACUCGCUUUUGGCUUUUCAAUAAUUUACGUUACAUACGUGUGGGCGUGGUCUGUCGUCCCAGGUGCCCACAGUUGGAUGGCA
....(((......))).....(((((((.(((((((......((.....))............(((((.....))))).(((((...((((......))))))))))))))))))))))) ( -32.00)
>DroYak_CAF1 93684 114 + 1
CACUCGAAUAUA------CUUUGUCGUUACAACUGUUUACUCGCUUUUGGCUUUUCAAUAAUUUACGUUACAUACGUGUGGGCGUGGCCUGUCGUCCCAGGUGCCCACAGUUGGAUGGCA
............------...(((((((.(((((((......((.....))............(((((.....))))).((((...(((((......))))))))))))))))))))))) ( -32.10)
>consensus
CACUCGAAUAUA______CUUUGCCGUUACAACUGUUUACUCGCUUUUGGCUUUUCAAUAAUUUACGUUACAUACGUGUGGGCGUGGCCUGUCGUCCCAGGUGCCCACAGUUGGAUGGCA
.....................(((((((.(((((((...........................(((((.....))))).((((...(((((......))))))))))))))))))))))) (-29.14 = -29.42 +   0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,677,687 – 13,677,805
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 97.97
Mean single sequence MFE -36.72
Consensus MFE -34.06
Energy contribution -34.50
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.44
Structure conservation index 0.93
SVM decision value 3.31
SVM RNA-class probability 0.998970
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13677687 118 + 23771897
GGCGUGGCCUGUCGUCCCAGGUGCCCACAGUUGGAUGGCACUUGUGUGUAUAAAUAAGUAAUAAAUACGCUUAGUUGCAUCAAAAAGUGCCACUAACCGAAAAAUAGUUGGCCAACCA
(((((((((((......))))...)))).(((((.((((((((..(((((....(((((.........)))))..)))))....))))))))))))).............)))..... ( -38.50)
>DroSec_CAF1 84992 118 + 1
GGCGUGGCAUGUCGUCCCAGGUGCCCAAAGUUGGAUGGCACUUGUGUGUAUAAAUAAGUAAUAAAUACGCUUAGUUGCAUCAAAAAGUGCCACUAACCGAAAAAUAGUUGGCCAACCC
((((.(((((.(......).))))))...(((((.((((((((..(((((....(((((.........)))))..)))))....))))))))))))).............)))..... ( -35.80)
>DroSim_CAF1 95586 118 + 1
GGCGUGGCAUGUCGUCCCAGGUGCCCACAGUUGGAUGGCACUUGUGUGUAUAAAUAAGUAAUAAAUACGCUUAGUUGCAUCAAAAAGUGCCACUAACCGAAAAAUAGUUGGCCAACCC
((((((((((.(......).))).)))).(((((.((((((((..(((((....(((((.........)))))..)))))....))))))))))))).............)))..... ( -36.80)
>DroEre_CAF1 90258 118 + 1
GGCGUGGUCUGUCGUCCCAGGUGCCCACAGUUGGAUGGCACUUCUGUGUAUAAAUAAGUAAUAAAUACGCUUAGUUGCAUCAAAAAGUGCCACUAACCGAAAAAUAGUUGGCCAACCC
(((((((((((......))))...)))).(((((.((((((((..(((((....(((((.........)))))..)))))....))))))))))))).............)))..... ( -35.10)
>DroYak_CAF1 93758 118 + 1
GGCGUGGCCUGUCGUCCCAGGUGCCCACAGUUGGAUGGCACUUCUGUGUAUAAAUAAGUAAUAAAUACGCUUAGUUGCAUCAAAAAGUGCCACUAACCGAAAAAUAGUUGGCCAACCC
(((((((((((......))))...)))).(((((.((((((((..(((((....(((((.........)))))..)))))....))))))))))))).............)))..... ( -37.40)
>consensus
GGCGUGGCCUGUCGUCCCAGGUGCCCACAGUUGGAUGGCACUUGUGUGUAUAAAUAAGUAAUAAAUACGCUUAGUUGCAUCAAAAAGUGCCACUAACCGAAAAAUAGUUGGCCAACCC
(((((((((((......))))...)))).(((((.((((((((..(((((....(((((.........)))))..)))))....))))))))))))).............)))..... (-34.06 = -34.50 +   0.44)

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 11:37:11 2006