Locus 2603

Sequence ID 3L_DroMel_CAF1
Location 7,215,857 – 7,216,074
Length 217
Max. P 0.813329
window4072 window4073 window4074

overview

Window 2

Location 7,215,857 – 7,215,977
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -48.33
Consensus MFE -46.00
Energy contribution -45.90
Covariance contribution -0.10
Combinations/Pair 1.12
Mean z-score -1.70
Structure conservation index 0.95
SVM decision value 0.46
SVM RNA-class probability 0.744272
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7215857 120 + 23771897
AAGGAUCCGGCCCUGGCAAAGAGUCGAAUCUUCUUGGGCAACCUGCCGGUUUGCACGCGCGAGGAGCUGGUGAGCAUUUGCCAGCCAUAUGGCAAAGUGCUCGGUUCGAUGGUCCAGAAG
..(((((..((....)).....((((((((.....((....)).((((((((((....))))...))))))((((((((((((......)))).)))))))))))))))))))))..... ( -49.70)
>DroSim_CAF1 9367 120 + 1
AAGGACCCGGCCCUGGCCAAGAGUCGAAUCUUCUUGGGCAACCUGCCGGUUUGCACGCGCGAGGAGCUGGUGAGCAUUUGUCAGCCGUAUGGCAAAGUGCUUGGUUCGAUGGUCCAGAAG
..(((((.(((....)))....((((((((.....((....)).((((((((((....))))...))))))((((((((((((......)))).)))))))))))))))))))))..... ( -50.50)
>DroYak_CAF1 5258 120 + 1
AAGGAUCCGGCGCUUGCCAAGAGUCGUAUCUUCUUGGGCAACCUACCGGUUUGCACGCGCGAGGAGCUGGUGAGCAUUUGCCAGCCGUAUGGCAAGGUCCUUGGUUCGAUGGUCCAGAAA
..(((((..((((...(((((((.......)))))))((((((....)).))))..))))...((((..(.(..(.(((((((......))))))))..))..))))...)))))..... ( -44.80)
>consensus
AAGGAUCCGGCCCUGGCCAAGAGUCGAAUCUUCUUGGGCAACCUGCCGGUUUGCACGCGCGAGGAGCUGGUGAGCAUUUGCCAGCCGUAUGGCAAAGUGCUUGGUUCGAUGGUCCAGAAG
..(((((.(((....)))....((((((((.....((....)).((((((((((....))))...))))))((((((((((((......))))))).))))))))))))))))))..... (-46.00 = -45.90 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,215,977 – 7,216,074
Length 97
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 93.47
Mean single sequence MFE -29.17
Consensus MFE -24.25
Energy contribution -24.70
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.59
Structure conservation index 0.83
SVM decision value 0.64
SVM RNA-class probability 0.808355
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7215977 97 + 23771897
AACUACGGAUUCGUGCAGUUUGAAACGGAGGAGCUGGCCAAUAAAGCCGCCUCCGCCCUGCACAAGUCCACUUUUAAGCAAAACAUGCUCACCGUAC
...((((((((.((((((........((.((((.((((.......)))).)))).)))))))).))))).......((((.....))))....))). ( -32.30)
>DroSim_CAF1 9487 97 + 1
AACUAUGGAUUCGUGCAGUUUGAAACGGAGGAGCUGGCCAAUAAAGCCGCCUUCGCCCUGCACAAGUCCACCUUCAAGCAAAACAUGCUCACCGUAC
.....((((((.((((((........((.((((.((((.......)))).)))).)))))))).))))))......((((.....))))........ ( -28.80)
>DroYak_CAF1 5378 97 + 1
AACUACGGAUUCGUUCAGUUUGAAACGGAAGAGCUGGCCAAUAAAGCCGCCUCCGCCCUGCACAAGUCCACGUUCAAACAAAACGUCCUCACCGUAC
...(((((...((((..(((((((..(((.(((.((((.......)))).))).((...)).....)))...)))))))..))))......))))). ( -26.40)
>consensus
AACUACGGAUUCGUGCAGUUUGAAACGGAGGAGCUGGCCAAUAAAGCCGCCUCCGCCCUGCACAAGUCCACCUUCAAGCAAAACAUGCUCACCGUAC
......(((((.((((((........((.((((.((((.......)))).)))).)))))))).)))))............................ (-24.25 = -24.70 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,215,977 – 7,216,074
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -36.60
Consensus MFE -30.99
Energy contribution -31.33
Covariance contribution 0.34
Combinations/Pair 1.10
Mean z-score -2.48
Structure conservation index 0.85
SVM decision value 0.66
SVM RNA-class probability 0.813329
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7215977 97 - 23771897
GUACGGUGAGCAUGUUUUGCUUAAAAGUGGACUUGUGCAGGGCGGAGGCGGCUUUAUUGGCCAGCUCCUCCGUUUCAAACUGCACGAAUCCGUAGUU
.(((..((((((.....)))))).....(((.((((((((((((((((.((((.....))))....)))))))).....)))))))).))))))... ( -40.30)
>DroSim_CAF1 9487 97 - 1
GUACGGUGAGCAUGUUUUGCUUGAAGGUGGACUUGUGCAGGGCGAAGGCGGCUUUAUUGGCCAGCUCCUCCGUUUCAAACUGCACGAAUCCAUAGUU
...(..((((((.....))))))..)(((((.((((((((.((....))((((.....)))).................)))))))).))))).... ( -35.60)
>DroYak_CAF1 5378 97 - 1
GUACGGUGAGGACGUUUUGUUUGAACGUGGACUUGUGCAGGGCGGAGGCGGCUUUAUUGGCCAGCUCUUCCGUUUCAAACUGAACGAAUCCGUAGUU
.(((((......(((((.((((((((.((.(....).)).)((((((((((((.....)))).)))..)))))))))))).)))))...)))))... ( -33.90)
>consensus
GUACGGUGAGCAUGUUUUGCUUGAAAGUGGACUUGUGCAGGGCGGAGGCGGCUUUAUUGGCCAGCUCCUCCGUUUCAAACUGCACGAAUCCGUAGUU
..((..((((((.....))))))...))(((.((((((((((((((((.((((.....))))....)))))))).....)))))))).)))...... (-30.99 = -31.33 +   0.34)

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 10:37:14 2006