Locus 969

Sequence ID 2R_DroMel_CAF1
Location 4,115,281 – 4,115,378
Length 97
Max. P 0.843533
window1724 window1725

overview

Window 4

Location 4,115,281 – 4,115,378
Length 97
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 88.59
Mean single sequence MFE -27.03
Consensus MFE -19.76
Energy contribution -20.70
Covariance contribution 0.94
Combinations/Pair 1.16
Mean z-score -2.22
Structure conservation index 0.73
SVM decision value 0.76
SVM RNA-class probability 0.843533
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4115281 97 + 20766785
UAAAAGUCCCACACCCCAUAAAUCAUUGUCCAAGUGGAAGUGGAAA-AUACUUGUCGGACGAUGAUUUGGCUGGAAUGGCUACCGAAUAAUGCCAGGU
........((...((...(((((((((((((....(.(((((....-.))))).).)))))))))))))...))..((((...........)))))). ( -27.60)
>DroSim_CAF1 28391 97 + 1
UAAAAGUCCCACGCCCCAUAAAUCAUUGUCCAAGUGGAAGUGGAAA-AUACUUGUCGGACGAUGAUUUGGCUGGAAUGGCUACCGAAUAAUGCCGGGU
....(((((((.(((....((((((((((((....(.(((((....-.))))).).))))))))))))))))))...)))).(((........))).. ( -30.10)
>DroEre_CAF1 5953 97 + 1
UAAA-AACCCACACCCCAUAAAUCAUUGUCCACGUAGCAGUAGAAAACUACUUGUCGCUCGGUUAUUUGGCUAGUAUGGCUACCGAACAAUGGCAGUU
....-.................(((((((....(..(((((((....)))).)))..)(((((.....((((.....))))))))))))))))..... ( -20.70)
>DroYak_CAF1 12419 98 + 1
UAAAAAACCCACUCCCCAUAAAUCAUUGUCCAAGUAGAAGUAGAAAAAUACUUGUCGGACGAUGAUUUGGCUGGAAUGGCUACCGAAUAAUGCCAGGU
......(((...(((...(((((((((((((....(.(((((......))))).).)))))))))))))...))).((((...........))))))) ( -29.70)
>consensus
UAAAAAACCCACACCCCAUAAAUCAUUGUCCAAGUAGAAGUAGAAA_AUACUUGUCGGACGAUGAUUUGGCUGGAAUGGCUACCGAAUAAUGCCAGGU
........(((.(((...(((((((((((((....(.(((((......))))).).)))))))))))))...))).)))................... (-19.76 = -20.70 +   0.94)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,115,281 – 4,115,378
Length 97
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 88.59
Mean single sequence MFE -25.94
Consensus MFE -19.50
Energy contribution -21.75
Covariance contribution 2.25
Combinations/Pair 1.10
Mean z-score -1.61
Structure conservation index 0.75
SVM decision value 0.21
SVM RNA-class probability 0.633760
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4115281 97 - 20766785
ACCUGGCAUUAUUCGGUAGCCAUUCCAGCCAAAUCAUCGUCCGACAAGUAU-UUUCCACUUCCACUUGGACAAUGAUUUAUGGGGUGUGGGACUUUUA
.((((((...........)))((((((...(((((((.((((((.((((..-.....))))....)))))).))))))).))))))..)))....... ( -25.30)
>DroSim_CAF1 28391 97 - 1
ACCCGGCAUUAUUCGGUAGCCAUUCCAGCCAAAUCAUCGUCCGACAAGUAU-UUUCCACUUCCACUUGGACAAUGAUUUAUGGGGCGUGGGACUUUUA
.((((((...........))).(((((...(((((((.((((((.((((..-.....))))....)))))).))))))).)))))...)))....... ( -26.50)
>DroEre_CAF1 5953 97 - 1
AACUGCCAUUGUUCGGUAGCCAUACUAGCCAAAUAACCGAGCGACAAGUAGUUUUCUACUGCUACGUGGACAAUGAUUUAUGGGGUGUGGGUU-UUUA
((((((..(((((((((..................)))))))))...)))))).(((((.((..((((((......))))))..)))))))..-.... ( -23.87)
>DroYak_CAF1 12419 98 - 1
ACCUGGCAUUAUUCGGUAGCCAUUCCAGCCAAAUCAUCGUCCGACAAGUAUUUUUCUACUUCUACUUGGACAAUGAUUUAUGGGGAGUGGGUUUUUUA
..((((......))))...(((((((....(((((((.((((((.(((((......)))))....)))))).)))))))....)))))))........ ( -28.10)
>consensus
ACCUGGCAUUAUUCGGUAGCCAUUCCAGCCAAAUCAUCGUCCGACAAGUAU_UUUCCACUUCCACUUGGACAAUGAUUUAUGGGGUGUGGGACUUUUA
..((((......))))...(((((((....(((((((.((((((.(((((......)))))....)))))).)))))))....)))))))........ (-19.50 = -21.75 +   2.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:01 2006