Locus 3972

Sequence ID 3L_DroMel_CAF1
Location 11,547,104 – 11,547,257
Length 153
Max. P 0.854718
window6189 window6190 window6191

overview

Window 9

Location 11,547,104 – 11,547,223
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 93.56
Mean single sequence MFE -35.77
Consensus MFE -29.21
Energy contribution -29.43
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -2.21
Structure conservation index 0.82
SVM decision value 0.13
SVM RNA-class probability 0.598996
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11547104 119 + 23771897
GUUUUGUAGUCCCUGGACCGUGUUUCAUCCAUAUCCUGUUCAAUAGGCGCCUUUUGCGGACUAUUAAAGUCUUUGAAAGGUGCUGCAUUCAUGUCCUGUUUAAUGGACGCCUUUUUCGC
....(((.(((....)))...........................(((((((((((.(((((.....))))).)))))))))))))).....((((........))))........... ( -29.70)
>DroSec_CAF1 45653 119 + 1
GUUUUGUAGUCCCUGGACGGUGUUUCAUCCAUAUCCUGUUGAAUAGGCACCUUUUGCGGACUAUUAAUGCCUUUGAAAGGUGCUGCAUUCAUGUCCUGUCGAAUGGGCGCCUUUUUCGC
((...(((((((.(..(.(((((((.((.((........)).))))))))).)..).)))))))....))....((((((((((.(((((..........))))))))))))))).... ( -35.90)
>DroSim_CAF1 44070 119 + 1
GUUUUGUAGUCCCUGGACUGUGUUUCAUCCAUAUCCUGUUGAAUGGGCACCUUUUGGGGACUAUUAAAGUCUUUGAAAGGUGCUGCAUUCAUGUCCUGUUUAAUGGGCGUCUUUUUCGC
......(((((....)))))....................((((((((((((((..((((((.....))))))..))))))))).)))))((((((........))))))......... ( -41.70)
>consensus
GUUUUGUAGUCCCUGGACCGUGUUUCAUCCAUAUCCUGUUGAAUAGGCACCUUUUGCGGACUAUUAAAGUCUUUGAAAGGUGCUGCAUUCAUGUCCUGUUUAAUGGGCGCCUUUUUCGC
........(((....))).(((.................(((((.((((((((((..((((.......))))..))))))))))..)))))(((((........))))).......))) (-29.21 = -29.43 +   0.23)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,547,143 – 11,547,257
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 91.23
Mean single sequence MFE -37.40
Consensus MFE -30.73
Energy contribution -30.40
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -2.69
Structure conservation index 0.82
SVM decision value 0.80
SVM RNA-class probability 0.854718
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11547143 114 + 23771897
UCAAUAGGCGCCUUUUGCGGACUAUUAAAGUCUUUGAAAGGUGCUGCAUUCAUGUCCUGUUUAAUGGACGCCUUUUUCGCAGUUUUGAAUUGCGGUCCCUCUGGGGGUUUUUUC
......(((((((((((.(((((.....))))).)))))))))))........((((........)))).......(((((((.....)))))))((((....))))....... ( -37.10)
>DroSec_CAF1 45692 114 + 1
UGAAUAGGCACCUUUUGCGGACUAUUAAUGCCUUUGAAAGGUGCUGCAUUCAUGUCCUGUCGAAUGGGCGCCUUUUUCGCAGUUUUGAAGUGCUGAGCCUCUGGUGGUUUUUUC
......((((((((((..((.(.......)))...))))))))))(((((((....(((.((((.((....))..)))))))...)).))))).(((((......))))).... ( -31.80)
>DroSim_CAF1 44109 114 + 1
UGAAUGGGCACCUUUUGGGGACUAUUAAAGUCUUUGAAAGGUGCUGCAUUCAUGUCCUGUUUAAUGGGCGUCUUUUUCGCAGUUUUGAAGUGCGGACCCUCUGGUGGUUUUUUC
.((((((((((((((..((((((.....))))))..))))))))).)))))((((((........))))))......((((.(.....).))))(((((....).))))..... ( -43.30)
>consensus
UGAAUAGGCACCUUUUGCGGACUAUUAAAGUCUUUGAAAGGUGCUGCAUUCAUGUCCUGUUUAAUGGGCGCCUUUUUCGCAGUUUUGAAGUGCGGACCCUCUGGUGGUUUUUUC
......((((((((((..((((.......))))..))))))))))(((((((.((((........))))((.......)).....)))).)))....((......))....... (-30.73 = -30.40 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,547,143 – 11,547,257
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 91.23
Mean single sequence MFE -26.80
Consensus MFE -20.71
Energy contribution -20.93
Covariance contribution 0.23
Combinations/Pair 1.08
Mean z-score -2.14
Structure conservation index 0.77
SVM decision value -0.04
SVM RNA-class probability 0.510884
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11547143 114 - 23771897
GAAAAAACCCCCAGAGGGACCGCAAUUCAAAACUGCGAAAAAGGCGUCCAUUAAACAGGACAUGAAUGCAGCACCUUUCAAAGACUUUAAUAGUCCGCAAAAGGCGCCUAUUGA
.......(((.....)))...(((.((((.....((.......))((((........)))).))))))).((.(((((....((((.....))))....))))).))....... ( -27.30)
>DroSec_CAF1 45692 114 - 1
GAAAAAACCACCAGAGGCUCAGCACUUCAAAACUGCGAAAAAGGCGCCCAUUCGACAGGACAUGAAUGCAGCACCUUUCAAAGGCAUUAAUAGUCCGCAAAAGGUGCCUAUUCA
(((..................(((.((((...(((((((...(....)..)))).)))....))))))).((((((((....(((.......)))....))))))))...))). ( -25.10)
>DroSim_CAF1 44109 114 - 1
GAAAAAACCACCAGAGGGUCCGCACUUCAAAACUGCGAAAAAGACGCCCAUUAAACAGGACAUGAAUGCAGCACCUUUCAAAGACUUUAAUAGUCCCCAAAAGGUGCCCAUUCA
.......((......))((((.............(((.......)))..........)))).((((((..((((((((....((((.....))))....)))))))).)))))) ( -28.00)
>consensus
GAAAAAACCACCAGAGGGUCCGCACUUCAAAACUGCGAAAAAGGCGCCCAUUAAACAGGACAUGAAUGCAGCACCUUUCAAAGACUUUAAUAGUCCGCAAAAGGUGCCUAUUCA
.......((......))....(((.((((.....(((.......)))((........))...))))))).((((((((....((((.....))))....))))))))....... (-20.71 = -20.93 +   0.23)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:25 2006