Locus 4668

Sequence ID 3R_DroMel_CAF1
Location 12,318,834 – 12,318,994
Length 160
Max. P 0.882490
window7661 window7662 window7663

overview

Window 1

Location 12,318,834 – 12,318,954
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -33.60
Consensus MFE -32.89
Energy contribution -33.33
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.69
Structure conservation index 0.98
SVM decision value 0.46
SVM RNA-class probability 0.744984
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12318834 120 + 27905053
ACAAAUUGUCGCUGUUGUUUUUUAUUUGGGCAUGCAAAUUUUUUCGCACACUCUGAGAACCGAAAACGGAAAAGUGCCAGGAAAACACAAUUGGAAAAUCACCGCACAGCGACGUGCGGA
.(....(((((((((((((((((.....(((((.......((((((.......))))))(((....)))....))))).)))))))).....((.......))..)))))))))....). ( -29.50)
>DroSec_CAF1 10087 120 + 1
ACAAAUUGUCGCUGUUGUUUUUUAUUUGGGCAUGCAAAUUUUUUCGCACACUCUGAGAACCGAAAACGGAAAGGUGCCCGGGAAAAACAAUUGGAAAAUCACCGCACAGCGACGUGCGGA
........((.(.((((((((((...(((((((.......((((((.......))))))(((....)))....))))))).)))))))))).)))......((((((......)))))). ( -35.70)
>DroSim_CAF1 6186 120 + 1
ACAAAUUGUCGCUGUUGUUUUUUAUUUGGGCAUGCAAAUUUUUUCGCACACUCUGAGAACCGAAAACGGAAAAGUGCCCGGGAAAAACAAUUGGAAAAUCACCGCACAGCGACGUGCGGA
........((.(.((((((((((...(((((((.......((((((.......))))))(((....)))....))))))).)))))))))).)))......((((((......)))))). ( -35.60)
>consensus
ACAAAUUGUCGCUGUUGUUUUUUAUUUGGGCAUGCAAAUUUUUUCGCACACUCUGAGAACCGAAAACGGAAAAGUGCCCGGGAAAAACAAUUGGAAAAUCACCGCACAGCGACGUGCGGA
........((.(.((((((((((...(((((((.......((((((.......))))))(((....)))....))))))).)))))))))).)))......((((((......)))))). (-32.89 = -33.33 +   0.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,318,834 – 12,318,954
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -34.53
Consensus MFE -32.87
Energy contribution -33.87
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.95
SVM decision value 0.92
SVM RNA-class probability 0.882490
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12318834 120 - 27905053
UCCGCACGUCGCUGUGCGGUGAUUUUCCAAUUGUGUUUUCCUGGCACUUUUCCGUUUUCGGUUCUCAGAGUGUGCGAAAAAAUUUGCAUGCCCAAAUAAAAAACAACAGCGACAAUUUGU
.......((((((((..((.......)).....((((((...((((((((.(((....))).....)))))(((((((....)))))))))).......))))))))))))))....... ( -31.60)
>DroSec_CAF1 10087 120 - 1
UCCGCACGUCGCUGUGCGGUGAUUUUCCAAUUGUUUUUCCCGGGCACCUUUCCGUUUUCGGUUCUCAGAGUGUGCGAAAAAAUUUGCAUGCCCAAAUAAAAAACAACAGCGACAAUUUGU
.......((((((((..((.......))...(((((((...((((......(((....)))..........(((((((....))))))))))).....)))))))))))))))....... ( -35.00)
>DroSim_CAF1 6186 120 - 1
UCCGCACGUCGCUGUGCGGUGAUUUUCCAAUUGUUUUUCCCGGGCACUUUUCCGUUUUCGGUUCUCAGAGUGUGCGAAAAAAUUUGCAUGCCCAAAUAAAAAACAACAGCGACAAUUUGU
.......((((((((..((.......))...(((((((...(((((((((.(((....))).....)))))(((((((....))))))))))).....)))))))))))))))....... ( -37.00)
>consensus
UCCGCACGUCGCUGUGCGGUGAUUUUCCAAUUGUUUUUCCCGGGCACUUUUCCGUUUUCGGUUCUCAGAGUGUGCGAAAAAAUUUGCAUGCCCAAAUAAAAAACAACAGCGACAAUUUGU
.......((((((((..((.......))...(((((((...(((((((((.(((....))).....)))))(((((((....))))))))))).....)))))))))))))))....... (-32.87 = -33.87 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,318,874 – 12,318,994
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -39.33
Consensus MFE -37.57
Energy contribution -37.47
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.87
Structure conservation index 0.96
SVM decision value 0.60
SVM RNA-class probability 0.795175
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12318874 120 + 27905053
UUUUCGCACACUCUGAGAACCGAAAACGGAAAAGUGCCAGGAAAACACAAUUGGAAAAUCACCGCACAGCGACGUGCGGACCAAAUUGUGGGGCUCCCAAGGGGGCGGCAUUUGUGGCAA
.....((.(((........(((....)))..(((((((.......(((((((((.......((((((......)))))).)).)))))))..(((((....))))))))))))))))).. ( -44.40)
>DroSec_CAF1 10127 119 + 1
UUUUCGCACACUCUGAGAACCGAAAACGGAAAGGUGCCCGGGAAAAACAAUUGGAAAAUCACCGCACAGCGACGUGCGGACCAAAUUGUGGGGCUCUCAAGG-GGCGGCAUUUGUGGCAA
..........((((((((.(((....)))......((((.(.((.....(((....)))..((((((......))))))......)).).)))))))).)))-)((.((....)).)).. ( -35.90)
>DroSim_CAF1 6226 120 + 1
UUUUCGCACACUCUGAGAACCGAAAACGGAAAAGUGCCCGGGAAAAACAAUUGGAAAAUCACCGCACAGCGACGUGCGGACCAAAUUGUGGGGCUCUCAAGGGGGCGGCAUUUGUGGCAA
.....((.(((........(((....)))..(((((((........((((((((.......((((((......)))))).)).))))))...(((((....))))))))))))))))).. ( -37.70)
>consensus
UUUUCGCACACUCUGAGAACCGAAAACGGAAAAGUGCCCGGGAAAAACAAUUGGAAAAUCACCGCACAGCGACGUGCGGACCAAAUUGUGGGGCUCUCAAGGGGGCGGCAUUUGUGGCAA
.....((.(((........(((....)))..(((((((........((((((((.......((((((......)))))).)).))))))...(((((....))))))))))))))))).. (-37.57 = -37.47 +  -0.11)

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 11:35:56 2006