Locus 3936

Sequence ID 2R_DroMel_CAF1
Location 12,989,079 – 12,989,189
Length 110
Max. P 0.990939
window6354 window6355

overview

Window 4

Location 12,989,079 – 12,989,189
Length 110
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 92.39
Mean single sequence MFE -23.04
Consensus MFE -20.28
Energy contribution -20.92
Covariance contribution 0.64
Combinations/Pair 1.12
Mean z-score -1.77
Structure conservation index 0.88
SVM decision value 1.84
SVM RNA-class probability 0.979570
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12989079 110 + 20766785
UGACGCUGGAUAAAGCAAAGUAAUUAACCCAAAAUUUCGUUUCCUCAAUUGUUCAAAAAUGAGUCGUCUGCUUUGUCCAGUUGUCUCCAUUAAUUAUACACUGAACUA-AC
.((((((((((((((((((....))..................((((.((......)).)))).....)))))))))))).)))).......................-.. ( -24.50)
>DroSec_CAF1 3623 110 + 1
UGACGCUGGAUAAAGCAAAGUAGUUUACCCAACUUUUCGUUUCCACAAUUGUUCAACAAUGAGUCGUCUGCUUUGUCCAGUUGUCUCCAUUAAUUAUACACUGAACUA-AC
.((((((((((((((((((((.(......).))))).((.(((....((((.....))))))).))...))))))))))).)))).......................-.. ( -24.40)
>DroSim_CAF1 3551 111 + 1
UGACGCUGGACGAAGCAAAGUAGUUUACCCAACUUUUCGUUUCCACAAUUGUUCAACAAUGAGUCGUCUGCUUUGUCCAGUUGUCUCCAUUAAUUAUACACUGAACUAAAC
.((((((((((((((((((((.(......).))))).((.(((....((((.....))))))).))...))))))))))).)))).......................... ( -26.00)
>DroEre_CAF1 3645 110 + 1
UGACACCGGACAAAGCAAAGUAGUUUACCUAACUUUUCGUUUCCACAAUUGUUCAACAAUGAGUCGUCUGCCUUGUCCAGAUGUCUCCAUUAAUUAUGCACUGAACUA-AC
.......(((....(.(((((((.....)).))))).)...)))......(((((.....(((.((((((.......)))))).)))(((.....)))...)))))..-.. ( -19.30)
>DroYak_CAF1 3624 110 + 1
UGACGACGGACAAAGCAAAGUAGUUUACCUAACUUUUCGUUUCCACAAUUGUUCAACAAUGAGUCGUCUGCUUUGUCCAGAUGUCCACAUUAAUUAUACACUGAACUA-AU
.((((.(((((((((((....((((.....))))...((.(((....((((.....))))))).))..)))))))))).).)))).......................-.. ( -21.00)
>consensus
UGACGCUGGACAAAGCAAAGUAGUUUACCCAACUUUUCGUUUCCACAAUUGUUCAACAAUGAGUCGUCUGCUUUGUCCAGUUGUCUCCAUUAAUUAUACACUGAACUA_AC
.((((((((((((((((..(.((((.....))))...)............(((((....)))).)...)))))))))))).)))).......................... (-20.28 = -20.92 +   0.64)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,989,079 – 12,989,189
Length 110
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 92.39
Mean single sequence MFE -29.36
Consensus MFE -24.92
Energy contribution -26.52
Covariance contribution 1.60
Combinations/Pair 1.07
Mean z-score -2.12
Structure conservation index 0.85
SVM decision value 2.24
SVM RNA-class probability 0.990939
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12989079 110 - 20766785
GU-UAGUUCAGUGUAUAAUUAAUGGAGACAACUGGACAAAGCAGACGACUCAUUUUUGAACAAUUGAGGAAACGAAAUUUUGGGUUAAUUACUUUGCUUUAUCCAGCGUCA
((-(((((........)))))))...(((..(((((.((((((((.((((((.........((((..(....)..)))).))))))......)))))))).))))).))). ( -24.40)
>DroSec_CAF1 3623 110 - 1
GU-UAGUUCAGUGUAUAAUUAAUGGAGACAACUGGACAAAGCAGACGACUCAUUGUUGAACAAUUGUGGAAACGAAAAGUUGGGUAAACUACUUUGCUUUAUCCAGCGUCA
((-(((((........)))))))...(((..(((((.((((((((((((.....))))..(((((.((....))...)))))..........)))))))).))))).))). ( -29.30)
>DroSim_CAF1 3551 111 - 1
GUUUAGUUCAGUGUAUAAUUAAUGGAGACAACUGGACAAAGCAGACGACUCAUUGUUGAACAAUUGUGGAAACGAAAAGUUGGGUAAACUACUUUGCUUCGUCCAGCGUCA
......((((.((......)).))))(((..((((((.(((((((((((.....))))..(((((.((....))...)))))..........))))))).)))))).))). ( -30.50)
>DroEre_CAF1 3645 110 - 1
GU-UAGUUCAGUGCAUAAUUAAUGGAGACAUCUGGACAAGGCAGACGACUCAUUGUUGAACAAUUGUGGAAACGAAAAGUUAGGUAAACUACUUUGCUUUGUCCGGUGUCA
((-(((((........)))))))...((((.((((((((((((((((((.....)))).....((((....))))..((((.....))))..)))))))))))))))))). ( -34.00)
>DroYak_CAF1 3624 110 - 1
AU-UAGUUCAGUGUAUAAUUAAUGUGGACAUCUGGACAAAGCAGACGACUCAUUGUUGAACAAUUGUGGAAACGAAAAGUUAGGUAAACUACUUUGCUUUGUCCGUCGUCA
..-..(((((((((...((....))..))).))))))......(((((((((....)))........(((.....(((((.(((((...))))).))))).))))))))). ( -28.60)
>consensus
GU_UAGUUCAGUGUAUAAUUAAUGGAGACAACUGGACAAAGCAGACGACUCAUUGUUGAACAAUUGUGGAAACGAAAAGUUGGGUAAACUACUUUGCUUUGUCCAGCGUCA
..........................(((..((((((((((((((((((.....))))..(((((.((....))...)))))..........)))))))))))))).))). (-24.92 = -26.52 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:44 2006