Locus 4995

Sequence ID 3R_DroMel_CAF1
Location 13,153,772 – 13,153,926
Length 154
Max. P 0.806959
window8167 window8168

overview

Window 7

Location 13,153,772 – 13,153,886
Length 114
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 93.07
Mean single sequence MFE -28.92
Consensus MFE -24.80
Energy contribution -24.32
Covariance contribution -0.48
Combinations/Pair 1.18
Mean z-score -1.32
Structure conservation index 0.86
SVM decision value 0.30
SVM RNA-class probability 0.677917
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13153772 114 + 27905053
UCCGCCGUCAAAUUCCCCCUAAUGAGGGUCAGUCUGCGAGUGCACACUGUACCAAAGAACUACAGCUUUGGACAGAACACAUGAGCAAUCCUUCAACAAGGAUAUUCAGUUUCA
..(((((.((.(((..((((....))))..))).)))).)))....((((.((((((........))))))))))......((((..((((((....)))))).))))...... ( -29.30)
>DroSec_CAF1 183141 114 + 1
UCCGCCGUCAAAUUUUUCCUAAUGAGGGUCAGUCUGCGAGUGCACACUGUACCAAAGAACUACAGCUUUGGACAGAACACAUGAGCCAUCCUUCAACAAGGAUAUUCGGUUUCA
...((((...(((...((((..((((((.......((..(((....((((.((((((........))))))))))....)))..))...))))))...)))).))))))).... ( -29.10)
>DroSim_CAF1 168421 114 + 1
UCCGCCGUCAAAUUCCUCCUAAUGAGGGUCAGUCUGCGAGUGCACACUGUACCAAAUAUCUACAGAGUUGGACAGAACACAUGAGCCAUCCUUCAACAAGGAUAUUCAGUUUCA
......(((.((((((((.....)))(((((((.(((....))).)))).)))...........))))).))).(((.((.((((..((((((....)))))).))))))))). ( -29.00)
>DroEre_CAF1 174266 114 + 1
UCCGCCGUCAAAUUCCCCCUAAUGAGGGUCAGCCUGCGAGUGCACACUGUCCUAAAGAACUACAGCUUUGGACAGAACACAUGAGCAAUCCUUCAACAAGGAUAUUCAGUUUCA
..(((((.((..((..((((....))))..))..)))).)))....((((((.((((........))))))))))......((((..((((((....)))))).))))...... ( -27.20)
>DroYak_CAF1 181869 114 + 1
UCCGCCGUCAAAUGCCCCCUAAUGAGGGUCAGUCUGCGAGUGCACACUGUCCUAAAGAGCUACAGCUUUGCACGGAACACAUGGGCAAUCCUUCAACAAGGAUAUUCAGUUUCU
............(((((........(((.((((.(((....))).)))).)))..(((((....))))).............)))))((((((....))))))........... ( -30.00)
>consensus
UCCGCCGUCAAAUUCCCCCUAAUGAGGGUCAGUCUGCGAGUGCACACUGUACCAAAGAACUACAGCUUUGGACAGAACACAUGAGCAAUCCUUCAACAAGGAUAUUCAGUUUCA
..(((((.((.(((..((((....))))..))).)))).)))....((((.((((((........))))))))))......((((..((((((....)))))).))))...... (-24.80 = -24.32 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,153,807 – 13,153,926
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 86.89
Mean single sequence MFE -31.86
Consensus MFE -21.96
Energy contribution -22.60
Covariance contribution 0.64
Combinations/Pair 1.18
Mean z-score -2.32
Structure conservation index 0.69
SVM decision value 0.64
SVM RNA-class probability 0.806959
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13153807 119 + 27905053
GCGAGUGCACACUGUACCAAAGAACUACAGCUUUGGACAGAACACAUGAGCAAUCCUUCAACAAGGAUAUUCAGUUUCAUGUAUAAAGACGUCAUUACAAUUUGUGAAAGUGAAUGCAU
((..(((....((((.((((((........))))))))))....)))..)).((((((....))))))(((((.(((((((((............)))).....))))).))))).... ( -29.70)
>DroSec_CAF1 183176 119 + 1
GCGAGUGCACACUGUACCAAAGAACUACAGCUUUGGACAGAACACAUGAGCCAUCCUUCAACAAGGAUAUUCGGUUUCAUGUGGAAAGACGCCAUUACAAUUUGUGAAAGUGAAUGCAU
....(((((..((((.((((((........))))))))))..((((((((((((((((....))))))....)).))))))))......(((..((((.....))))..)))..))))) ( -36.60)
>DroSim_CAF1 168456 119 + 1
GCGAGUGCACACUGUACCAAAUAUCUACAGAGUUGGACAGAACACAUGAGCCAUCCUUCAACAAGGAUAUUCAGUUUCAUGUAGAAAGACUCUAUUACAAUUUGUGCAAGUGAAUGCAU
....(((((((((((((.((((......((((((..((((((.((.((((..((((((....)))))).))))))))).))).....))))))......)))))))).))))..))))) ( -29.90)
>DroEre_CAF1 174301 112 + 1
GCGAGUGCACACUGUCCUAAAGAACUACAGCUUUGGACAGAACACAUGAGCAAUCCUUCAACAAGGAUAUUCAGUUUCAUGCACCAAGCCGCCAUUACAAUUUGUGGAGGUC-------
..(.(((((..((((((.((((........))))))))))......((((..((((((....)))))).))))......))))))..(((.((((........)))).))).------- ( -32.80)
>DroYak_CAF1 181904 119 + 1
GCGAGUGCACACUGUCCUAAAGAGCUACAGCUUUGCACGGAACACAUGGGCAAUCCUUCAACAAGGAUAUUCAGUUUCUUGUAUCAGGCAGCCAUGACAAUUUGUAAAAGUGAAUGCAU
....(((((((((.(((...(((((....)))))....)))...(((((.(...(((...(((((((........)))))))...)))..))))))............))))..))))) ( -30.30)
>consensus
GCGAGUGCACACUGUACCAAAGAACUACAGCUUUGGACAGAACACAUGAGCAAUCCUUCAACAAGGAUAUUCAGUUUCAUGUAGAAAGACGCCAUUACAAUUUGUGAAAGUGAAUGCAU
((..(((....((((.((((((........))))))))))....)))..)).((((((....))))))(((((.(((((((.....................))))))).))))).... (-21.96 = -22.60 +   0.64)

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 11:43:51 2006