Locus 6418

Sequence ID 2R_DroMel_CAF1
Location 20,057,694 – 20,057,865
Length 171
Max. P 0.528535
window10243 window10244

overview

Window 3

Location 20,057,694 – 20,057,801
Length 107
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 79.82
Mean single sequence MFE -29.32
Consensus MFE -11.35
Energy contribution -12.16
Covariance contribution 0.81
Combinations/Pair 1.17
Mean z-score -2.04
Structure conservation index 0.39
SVM decision value -0.01
SVM RNA-class probability 0.528355
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20057694 107 + 20766785
AGAUUAAUUGGCGGAGCAAUGCAACGCGGCGUAUGAGUGAUGCGGAAUUUGAAAUUCCAUUGGU---AUUAAGGGUAUUUCAGAAAAUAGAAAUAUUUGUGAAAUUCCCA
..((((((..(((..((...))..))).((((.......))))(((((.....)))))))))))---.....(((.((((((..(((((....))))).)))))).))). ( -27.10)
>DroSec_CAF1 17293 92 + 1
CGAUUAAUUGGCGGAGCAGUGCAACGCGGCCAA------------------ACAUUCCAUUGUUUGGCUUAGGGGUAUUUCAGAAAAUAGAAAUAUUUCUGAAAUUCCCA
..........(((..((...))..)))((((((------------------(((......)))))))))..((((.((((((((((.((....)))))))))))))))). ( -35.40)
>DroSim_CAF1 17758 110 + 1
CGAUUAAUUGGCGGAGCAGUGCAACGCGGCGUAUGAGUGAUGCGGAAUUUGAAAUUCCAUUGGCUGGCUUAGGGGUAUUUCAGAAAAUAGUAAUAUUUUUGAAAUUCCCA
.............((((((((((.(((.........))).)))(((((.....)))))....))).)))).((((.((((((((((.((....)))))))))))))))). ( -30.70)
>DroEre_CAF1 17766 110 + 1
AGAUUAAUUGGUGGACCAGUGCAACGUCGCGUAUGAGUGAUGCGGAAUUUGAAAUUCCAUUCGUUAGCUUAGGGUUACUUCGGAAAGUAUAAGCCUUUGUGAAAUUCCCA
......(((((....)))))((..((((((......)))))).(((((.....)))))........))...(((....((((.((((.......)))).))))...))). ( -27.20)
>DroYak_CAF1 17815 109 + 1
AGAUUAAUUGGUGGAGCAGUGCAACGCCGCGUAUGAGUGAUGCGGAAUUUGAAAUUCCAUUUGUUAGCUAAGGG-UAUUUCAGAAAGUAUGAGCAUUUGUAGAAUUCCCA
((.(((((..((((((.....(((..((((((.......))))))...)))...))))))..)))))))..(((-.(((..(.(((((....)).))).)..))).))). ( -26.20)
>consensus
AGAUUAAUUGGCGGAGCAGUGCAACGCGGCGUAUGAGUGAUGCGGAAUUUGAAAUUCCAUUGGUUAGCUUAGGGGUAUUUCAGAAAAUAGAAAUAUUUGUGAAAUUCCCA
............(((((........))..(((((.....)))))...........)))..............(((.((((((.(((((....)).))).)))))).))). (-11.35 = -12.16 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,057,761 – 20,057,865
Length 104
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 77.03
Mean single sequence MFE -23.43
Consensus MFE -9.05
Energy contribution -9.89
Covariance contribution 0.84
Combinations/Pair 1.21
Mean z-score -1.83
Structure conservation index 0.39
SVM decision value -0.01
SVM RNA-class probability 0.528535
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20057761 104 + 20766785
AAGGGUAUUUCAGAAAAUAGAAAUAUUUGUGAAAUUCCCAUUCCCUGG---------GAACAACUUAUUAAGUAGUGCAUGAGUCUGGCACAAGAACUAGGAAUUUUAAUCUU
..(((.((((((..(((((....))))).)))))).)))....(((((---------.....(((.....))).((((.........)))).....)))))............ ( -25.40)
>DroSec_CAF1 17345 105 + 1
AGGGGUAUUUCAGAAAAUAGAAAUAUUUCUGAAAUUCCCAUUCCCUGU--------AUAACAACUUAUUAAGUAAUGCAUGAGUCUGACACAAGAACAAGGAAUUCUAAUCUU
.((((.((((((((((.((....))))))))))))))))(((((.(((--------.......(((((..(....)..)))))(((......)))))).)))))......... ( -25.90)
>DroSim_CAF1 17828 105 + 1
AGGGGUAUUUCAGAAAAUAGUAAUAUUUUUGAAAUUCCCAUUCCCUGU--------ACAACAACUUAUUAAGUAAUGCAUGAGUCUGACACAAGAACAAGGAAUUCUAAUCUU
.((((.((((((((((.((....))))))))))))))))(((((.(((--------.......(((((..(....)..)))))(((......)))))).)))))......... ( -22.80)
>DroEre_CAF1 17836 113 + 1
AGGGUUACUUCGGAAAGUAUAAGCCUUUGUGAAAUUCCCAUUCGCUGUAUCAGAUUAUAACAACUUAUUAAGUAAUGCAUGAGUAUGGCUCAAGUACUAGGAAUGCCCGUCUA
.((((...(((....(((((.((((...(((((.......))))).................((((((..(....)..))))))..))))...))))).)))..))))..... ( -21.50)
>DroYak_CAF1 17885 112 + 1
AGGG-UAUUUCAGAAAGUAUGAGCAUUUGUAGAAUUCCCAUAUCUGGCAUCAGAUUAUAAAAACUUAUUAAGUAAUGCAUGAGUACAGUUCAAAUACCAAGGAUUCAAGUCCA
..((-(((((..(((.((((..(((((.((((.........(((((....))))).........)))).....)))))....))))..))))))))))..((((....)))). ( -21.57)
>consensus
AGGGGUAUUUCAGAAAAUAGAAAUAUUUGUGAAAUUCCCAUUCCCUGU________AUAACAACUUAUUAAGUAAUGCAUGAGUCUGGCACAAGAACAAGGAAUUCUAAUCUU
..(((.((((((.(((((....)).))).)))))).)))(((((.(((..............((((((..........))))))...........))).)))))......... ( -9.05 =  -9.89 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:33 2006