Locus 2218

Sequence ID 3L_DroMel_CAF1
Location 6,114,955 – 6,115,071
Length 116
Max. P 0.977572
window3438 window3439

overview

Window 8

Location 6,114,955 – 6,115,047
Length 92
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 78.81
Mean single sequence MFE -26.86
Consensus MFE -20.15
Energy contribution -21.01
Covariance contribution 0.86
Combinations/Pair 1.30
Mean z-score -3.09
Structure conservation index 0.75
SVM decision value 1.79
SVM RNA-class probability 0.977572
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6114955 92 + 23771897
CCAGA-----CAACAAAAGCCAAUACC---------AAGCUCAGCCGACUAAGGCUGGGCUAUGUAUGCCCUACAAUACCACAAUACAUCGGGGCGUAUGCGUAAU
.....-----........((.......---------.(((((((((......)))))))))..(((((((((..................)))))))))))..... ( -29.97)
>DroSec_CAF1 20548 86 + 1
CCAGA-----CAACAAAAGCC---------------AAGCUCAGCCGACUAAGGCUGGGCUAUGUAUGCCCUACAAUACAGCAAUACAUCGGGGCGUAUGCGUAAU
.....-----........((.---------------.(((((((((......)))))))))..(((((((((..................)))))))))))..... ( -29.97)
>DroSim_CAF1 21230 86 + 1
CCAGA-----CAACAAAAGCC---------------AAGCUCAGCCGACUAAGGCUGGGCUAUGUAUGCCCUACAAUACAACAAUACAUCGGGGCGUAUGCGUAAU
.....-----........((.---------------.(((((((((......)))))))))..(((((((((..................)))))))))))..... ( -29.97)
>DroEre_CAF1 24201 92 + 1
CCAGA-----CAACAAAAGCCAAUACC---------AAGCUCAGUCGACUAUGGCUGAGCUAUGCAUGCCCUACAAUACCACAAUACAACUGGGCGUAUGCGUAAU
.....-----.................---------..((((((((......))))))))(((((((((((((.................)))).))))))))).. ( -26.83)
>DroYak_CAF1 23678 92 + 1
CCAGA-----CAACAAAAGCCAAUACC---------AAGCUCAGUCGACUAUGGCUCUACUAUGCAUGCCCUACAAUACCACAAUACAACUGGGCGUAUGCGUAAU
.....-----.......(((((.....---------...............)))))....(((((((((((((.................)))).))))))))).. ( -17.48)
>DroPer_CAF1 29213 95 + 1
GCAGAAGCGGCAACAACAGCCAAUAUCUGACACUUUCAGUUCAG-UGUCUGCGGUCGUGCUAU----GCCCUACAAUAAC-----CCAUC-GGGCGUAUGAGUAAU
(((((.(((((.......))).....((((.....))))....)-).)))))(.((((((...----((((.........-----.....-)))))))))).)... ( -26.94)
>consensus
CCAGA_____CAACAAAAGCCAAUACC_________AAGCUCAGCCGACUAAGGCUGGGCUAUGUAUGCCCUACAAUACCACAAUACAUCGGGGCGUAUGCGUAAU
......................................((((((((......))))))))((((((((((((...................))).))))))))).. (-20.15 = -21.01 +   0.86)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,114,977 – 6,115,071
Length 94
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 81.90
Mean single sequence MFE -32.14
Consensus MFE -23.37
Energy contribution -23.48
Covariance contribution 0.11
Combinations/Pair 1.23
Mean z-score -2.11
Structure conservation index 0.73
SVM decision value 0.69
SVM RNA-class probability 0.824967
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6114977 94 + 23771897
-----AAGCUCAGCCGACUAAGGCUGGGCUAUGUAUGCCCUACAAUACCACAAUACAUCGGGGCGUAUGCGUAAUGUCACUGCUGGUCAUUUUC-------GGGCA
-----.(((((((((......))))))))).....(((((...(((((((((..((((....(((....))).))))...)).)))).)))...-------))))) ( -33.70)
>DroSec_CAF1 20564 94 + 1
-----AAGCUCAGCCGACUAAGGCUGGGCUAUGUAUGCCCUACAAUACAGCAAUACAUCGGGGCGUAUGCGUAAUGUCACUGCUGGUCAUUUUC-------GGGCA
-----.(((((((((......))))))))).....(((((.......(((((..((((....(((....))).))))...))))).........-------))))) ( -35.59)
>DroSim_CAF1 21246 94 + 1
-----AAGCUCAGCCGACUAAGGCUGGGCUAUGUAUGCCCUACAAUACAACAAUACAUCGGGGCGUAUGCGUAAUGUCACUGCUGGUCAUUUUC-------GGGCA
-----.(((((((((......)))))))))..(((((((((..................))))))))).............(((.(.......)-------.))). ( -32.27)
>DroEre_CAF1 24223 94 + 1
-----AAGCUCAGUCGACUAUGGCUGAGCUAUGCAUGCCCUACAAUACCACAAUACAACUGGGCGUAUGCGUAAUGUCACUGCUGGUCAUUUUC-------GGGCA
-----..((((((((......))))))))(((((((((((((.................)))).)))))))))........(((.(.......)-------.))). ( -30.63)
>DroYak_CAF1 23700 94 + 1
-----AAGCUCAGUCGACUAUGGCUCUACUAUGCAUGCCCUACAAUACCACAAUACAACUGGGCGUAUGCGUAAUGUCACUGCUGGUCAUUUUC-------GGGCG
-----..((((((..(((((((((.....(((((((((((((.................)))).)))))))))..))))....)))))...)).-------)))). ( -24.23)
>DroAna_CAF1 28980 94 + 1
GAUGCGAGCUUCGCUAACAUCGGCUGGGCUAU----GCCCUACAAU--------ACAACGGGGCGUAUGCGUAAUGCCAUGUCAGGUCAUUUGCCGGGCUGGGCCA
((((..(((...)))..))))((((.((((((----(((((.....--------.....)))))))..(((.((((((......)).)))))))..)))).)))). ( -36.40)
>consensus
_____AAGCUCAGCCGACUAAGGCUGGGCUAUGUAUGCCCUACAAUACCACAAUACAACGGGGCGUAUGCGUAAUGUCACUGCUGGUCAUUUUC_______GGGCA
......(((((((((......)))))))))......((((......................(((....)))((((((......)).))))..........)))). (-23.37 = -23.48 +   0.11)

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 10:27:08 2006