Locus 8646

Sequence ID 3L_DroMel_CAF1
Location 22,447,435 – 22,447,563
Length 128
Max. P 0.982000
window14168 window14169 window14170 window14171

overview

Window 8

Location 22,447,435 – 22,447,540
Length 105
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -20.66
Consensus MFE -19.58
Energy contribution -19.36
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.49
Structure conservation index 0.95
SVM decision value -0.03
SVM RNA-class probability 0.517430
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22447435 105 + 23771897
GAACUUUUCAGUUGGCUUUCUUCUGCUCCGGUGUCCCCCGCAACUCCUUUUUUUGAGCCAGAGCGGCACAACAAUUUUGCCGCAACUUUUUUGCCUGCAUUGUUU
..........((.(((.....((((((((((......)))..............))).))))((((((.........)))))).........))).))....... ( -24.13)
>DroEre_CAF1 3073 105 + 1
GAACUUUUCAGUUGGCUUUCUUCUGCUCCAAUGUCCCCCGCACCACCUUUUUUUCAGCCAGAGCGGCACAACAAUUUUGCCGCAACUUUUUUGCCUGCAUUGUUU
((((..(.(((((((((..............(((.....))).............)))))).((((((.........))))))...........))).)..)))) ( -19.13)
>DroYak_CAF1 2439 105 + 1
AAACUUUUCAGUUGGCUUUCUUCUACUCCAAUGUCCCCCGCACCUCCUUUUUUUCAGCCAGAGCGGCACAACAAUUUUGCCGCAACUUUUUUGCCUGCAUUGUUU
((((..(.(((((((((..............(((.....))).............)))))).((((((.........))))))...........))).)..)))) ( -18.73)
>consensus
GAACUUUUCAGUUGGCUUUCUUCUGCUCCAAUGUCCCCCGCACCUCCUUUUUUUCAGCCAGAGCGGCACAACAAUUUUGCCGCAACUUUUUUGCCUGCAUUGUUU
((((..(.(((((((((..............(((.....))).............)))))).((((((.........))))))...........))).)..)))) (-19.58 = -19.36 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,447,435 – 22,447,540
Length 105
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -26.25
Consensus MFE -23.33
Energy contribution -22.89
Covariance contribution -0.44
Combinations/Pair 1.09
Mean z-score -1.82
Structure conservation index 0.89
SVM decision value 0.06
SVM RNA-class probability 0.562780
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22447435 105 - 23771897
AAACAAUGCAGGCAAAAAAGUUGCGGCAAAAUUGUUGUGCCGCUCUGGCUCAAAAAAAGGAGUUGCGGGGGACACCGGAGCAGAAGAAAGCCAACUGAAAAGUUC
..........(((......(..((((((....))))))..)((((((((((........))).....(....).)))))))........)))((((....)))). ( -29.10)
>DroEre_CAF1 3073 105 - 1
AAACAAUGCAGGCAAAAAAGUUGCGGCAAAAUUGUUGUGCCGCUCUGGCUGAAAAAAAGGUGGUGCGGGGGACAUUGGAGCAGAAGAAAGCCAACUGAAAAGUUC
..........(((.......((((..(((...((((.(.((((.(((.((.......)).))).))))).)))))))..))))......)))((((....)))). ( -26.52)
>DroYak_CAF1 2439 105 - 1
AAACAAUGCAGGCAAAAAAGUUGCGGCAAAAUUGUUGUGCCGCUCUGGCUGAAAAAAAGGAGGUGCGGGGGACAUUGGAGUAGAAGAAAGCCAACUGAAAAGUUU
..........(((.......((((..(((...((((.(.((((.((..((.......))..)).))))).)))))))..))))......)))((((....)))). ( -23.12)
>consensus
AAACAAUGCAGGCAAAAAAGUUGCGGCAAAAUUGUUGUGCCGCUCUGGCUGAAAAAAAGGAGGUGCGGGGGACAUUGGAGCAGAAGAAAGCCAACUGAAAAGUUC
..........(((......(..((((((....))))))..)((((((((...............)).(....)..))))))........)))((((....)))). (-23.33 = -22.89 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,447,472 – 22,447,563
Length 91
Sequences 3
Columns 91
Reading direction forward
Mean pairwise identity 97.07
Mean single sequence MFE -22.93
Consensus MFE -21.53
Energy contribution -21.87
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.94
SVM decision value 0.05
SVM RNA-class probability 0.559013
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22447472 91 + 23771897
CCGCAACUCCUUUUUUUGAGCCAGAGCGGCACAACAAUUUUGCCGCAACUUUUUUGCCUGCAUUGUUUUUGACUGCAACGCUCCGGCCGGC
...............(((.(((.(((((((((((.(((..(((.((((.....))))..)))..))).)))..)))..))))).)))))). ( -24.70)
>DroEre_CAF1 3110 91 + 1
CCGCACCACCUUUUUUUCAGCCAGAGCGGCACAACAAUUUUGCCGCAACUUUUUUGCCUGCAUUGUUUUUGACUGCAACGCUCCGGCCGGC
................((.(((.(((((((((((.(((..(((.((((.....))))..)))..))).)))..)))..))))).))).)). ( -24.40)
>DroYak_CAF1 2476 91 + 1
CCGCACCUCCUUUUUUUCAGCCAGAGCGGCACAACAAUUUUGCCGCAACUUUUUUGCCUGCAUUGUUUUUGACUGCAACGCUCCGACCGGC
...................(((.(((((((((((.(((..(((.((((.....))))..)))..))).)))..)))..))))).....))) ( -19.70)
>consensus
CCGCACCUCCUUUUUUUCAGCCAGAGCGGCACAACAAUUUUGCCGCAACUUUUUUGCCUGCAUUGUUUUUGACUGCAACGCUCCGGCCGGC
...................(((.(((((((((((.(((..(((.((((.....))))..)))..))).)))..)))..))))).))).... (-21.53 = -21.87 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,447,472 – 22,447,563
Length 91
Sequences 3
Columns 91
Reading direction reverse
Mean pairwise identity 97.07
Mean single sequence MFE -30.73
Consensus MFE -30.29
Energy contribution -30.40
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.63
Structure conservation index 0.99
SVM decision value 1.90
SVM RNA-class probability 0.982000
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22447472 91 - 23771897
GCCGGCCGGAGCGUUGCAGUCAAAAACAAUGCAGGCAAAAAAGUUGCGGCAAAAUUGUUGUGCCGCUCUGGCUCAAAAAAAGGAGUUGCGG
.((((((((((((..((((.(((......(((..((((.....)))).)))...)))))))..)))))))))((........))....))) ( -30.10)
>DroEre_CAF1 3110 91 - 1
GCCGGCCGGAGCGUUGCAGUCAAAAACAAUGCAGGCAAAAAAGUUGCGGCAAAAUUGUUGUGCCGCUCUGGCUGAAAAAAAGGUGGUGCGG
..(((((((((((..((((.(((......(((..((((.....)))).)))...)))))))..)))))))))))................. ( -32.40)
>DroYak_CAF1 2476 91 - 1
GCCGGUCGGAGCGUUGCAGUCAAAAACAAUGCAGGCAAAAAAGUUGCGGCAAAAUUGUUGUGCCGCUCUGGCUGAAAAAAAGGAGGUGCGG
..(((((((((((..((((.(((......(((..((((.....)))).)))...)))))))..)))))))))))................. ( -29.70)
>consensus
GCCGGCCGGAGCGUUGCAGUCAAAAACAAUGCAGGCAAAAAAGUUGCGGCAAAAUUGUUGUGCCGCUCUGGCUGAAAAAAAGGAGGUGCGG
..(((((((((((..((((.(((......(((..((((.....)))).)))...)))))))..)))))))))))................. (-30.29 = -30.40 +   0.11)

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 13:21:17 2006