Locus 2572

Sequence ID 3L_DroMel_CAF1
Location 7,190,106 – 7,190,294
Length 188
Max. P 0.780574
window3989 window3990 window3991

overview

Window 9

Location 7,190,106 – 7,190,226
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -35.77
Consensus MFE -29.58
Energy contribution -29.82
Covariance contribution 0.25
Combinations/Pair 1.09
Mean z-score -2.11
Structure conservation index 0.83
SVM decision value 0.32
SVM RNA-class probability 0.686251
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7190106 120 - 23771897
UGGACCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCCAACGGGGGAAUUGGUUAAAAGGAGGAGCAAUGGAGGCUGGUGGAUUGAUAGGGGGUGGC
..((((((...(((((((.....(((....))).((((((((((......)))))))))))))))))....)))))).........(((.......)))..................... ( -33.80)
>DroSec_CAF1 3562 120 - 1
UGGACCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCCAACCGGGGAAUUGCUUAAAAGGAGGAGCAAUGGAGGCUGGUGGAUUGAUAGGGGGUGGC
....(((....(((((..(..(.........((.((((((((((......))))))))))))(((((...(((((((........))))))).....))))))..)..)).)))..))). ( -38.80)
>DroEre_CAF1 3478 119 - 1
UGGAGCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCUAGCCGGGGAAUUGGUUAAAAGAAGGAGCGAUGGAGGCUGGUGGAUUGAUAGGG-GUGGC
....((....((((.(...((..(((........((((((((((......))))))))))(((((.....((((.((........)).))))...))))))))..))...).))-)).)) ( -35.10)
>DroYak_CAF1 479 120 - 1
UGGACCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCCAACCGGGGAAUUGGUUAAAAGAAGGAGCCAUGGAAGCUGGUGGAUUGAUAGGGGGUGGC
....(((....(((((..(..(.........((.((((((((((......))))))))))))(((((.....(((((.........)))))......))))))..)..)).)))..))). ( -35.40)
>consensus
UGGACCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCCAACCGGGGAAUUGGUUAAAAGAAGGAGCAAUGGAGGCUGGUGGAUUGAUAGGGGGUGGC
....(((....(((((..(..(.........((.((((((((((......))))))))))))(((((...((((.((........)).)))).....))))))..)..)).)))..))). (-29.58 = -29.82 +   0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,190,146 – 7,190,254
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.38
Mean single sequence MFE -30.12
Consensus MFE -25.80
Energy contribution -25.93
Covariance contribution 0.13
Combinations/Pair 1.08
Mean z-score -1.46
Structure conservation index 0.86
SVM decision value 0.14
SVM RNA-class probability 0.604212
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7190146 108 - 23771897
GCCAGA------------GAAGCAGCAGAAAUUAUCAACUUGGACCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCCAACGGGGGAAUUGGUUAAA
((....------------...))...................((((((...(((((((.....(((....))).((((((((((......)))))))))))))))))....))))))... ( -32.40)
>DroSec_CAF1 3602 108 - 1
GCCAGA------------GAAGCAGCAGAAAUUAUCAACUUGGACCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCCAACCGGGGAAUUGCUUAAA
......------------.((((((.........(((((..((........)).)))))..(((.......((.((((((((((......))))))))))))....)))..))))))... ( -27.10)
>DroEre_CAF1 3517 120 - 1
GCCAGUGAAACAGCAGCAGAAGCAGCAGAAAUUAUCAACUUGGAGCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCUAGCCGGGGAAUUGGUUAAA
((((((......((.((....)).))............(((((((((......)))).................((((((((((......))))))))))...)))))..)))))).... ( -31.90)
>DroYak_CAF1 519 114 - 1
GCCAGAGAAACA------GAAGCAGCAGAAAUUAUCAACUUGGACCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCCAACCGGGGAAUUGGUUAAA
............------........................((((((...(((((((.....(((....))).((((((((((......))))))))))))).))))...))))))... ( -29.10)
>consensus
GCCAGA____________GAAGCAGCAGAAAUUAUCAACUUGGACCGAAAACCCGUUGAGACUCAUAAAAAUGUGCCACUUAGCAGGGAAGUUGGGUGGCCAACCGGGGAAUUGGUUAAA
..........................................((((((...(((((((.....(((....))).((((((((((......)))))))))))))).)))...))))))... (-25.80 = -25.93 +   0.13)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,190,186 – 7,190,294
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.67
Mean single sequence MFE -28.70
Consensus MFE -26.16
Energy contribution -26.16
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.91
SVM decision value 0.56
SVM RNA-class probability 0.780574
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7190186 108 + 23771897
AGUGGCACAUUUUUAUGAGUCUCAACGGGUUUUCGGUCCAAGUUGAUAAUUUCUGCUGCUUC------------UCUGGCGCUUCUGUAGUUGUUAUCAUUUUGCAUGUGCUGCGCAUUU
.(..((((((.....((((.((.....))..))))...((((.(((((((..((((((((..------------...)))).....))))..))))))).)))).))))))..)...... ( -28.40)
>DroSec_CAF1 3642 108 + 1
AGUGGCACAUUUUUAUGAGUCUCAACGGGUUUUCGGUCCAAGUUGAUAAUUUCUGCUGCUUC------------UCUGGCGCUUCUGUAGUUGUUAUCAUUUUGCAUGUGCUGCGCAUUU
.(..((((((.....((((.((.....))..))))...((((.(((((((..((((((((..------------...)))).....))))..))))))).)))).))))))..)...... ( -28.40)
>DroEre_CAF1 3557 120 + 1
AGUGGCACAUUUUUAUGAGUCUCAACGGGUUUUCGCUCCAAGUUGAUAAUUUCUGCUGCUUCUGCUGCUGUUUCACUGGCGCUUCUGUAGUUGUUAUCAUUUUGCAUGUGCUCCGCAUUU
.(..((((((................((((....))))((((.(((((((....(((((....((.(((........)))))....))))).))))))).)))).))))))..)...... ( -29.70)
>DroYak_CAF1 559 114 + 1
AGUGGCACAUUUUUAUGAGUCUCAACGGGUUUUCGGUCCAAGUUGAUAAUUUCUGCUGCUUC------UGUUUCUCUGGCGCUUCUGUAGUUGUUAUCAUUUUGCAUGUGCUGCGCAUUU
.(..((((((.....((((.((.....))..))))...((((.(((((((..((((.((.((------.........)).))....))))..))))))).)))).))))))..)...... ( -28.30)
>consensus
AGUGGCACAUUUUUAUGAGUCUCAACGGGUUUUCGGUCCAAGUUGAUAAUUUCUGCUGCUUC____________UCUGGCGCUUCUGUAGUUGUUAUCAUUUUGCAUGUGCUGCGCAUUU
.(..((((((.....((((.((.....))..))))...((((.(((((((..((((((((.................)))).....))))..))))))).)))).))))))..)...... (-26.16 = -26.16 +  -0.00)

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 10:35:57 2006