Locus 660

Sequence ID X_DroMel_CAF1
Location 1,849,413 – 1,849,548
Length 135
Max. P 0.752113
window1061 window1062 window1063

overview

Window 1

Location 1,849,413 – 1,849,514
Length 101
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 86.30
Mean single sequence MFE -43.35
Consensus MFE -32.90
Energy contribution -34.40
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.76
SVM decision value 0.05
SVM RNA-class probability 0.560300
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1849413 101 + 22224390
AUCCAAGGCCAGCAGUGUUGUUGCGGCAGCUGCCGAGCUAGAGGCAGCAACAACCACGGCAGCGCUGGCCACGUCCUCCGCCACGGAGGCUUCUGCAGCGG
..((..(((((((...(((((((.((..((((((........)))))).....)).))))))))))))))..(.((((((...))))))).........)) ( -46.50)
>DroSec_CAF1 50946 101 + 1
AUCCAAGGCCAGCAGUGUUGUUGCGGCAGCUGCCGAGCUAGAGGCAGCAACAACUACGGCAGCGCUGGCCACGGCCUCGGCCACGGAGGCUUCUGCAGCGG
.(((..(((((((..((((((.(..(..((((((........))))))..)..).))))))..)))))))..(((....)))..))).(((.....))).. ( -47.30)
>DroEre_CAF1 52276 101 + 1
AUCCAAGGCCAGCAGUGUUGUUGCGGCAACUGCGGAACUAGAGGCAGCAACUGCCACCGGAUCGCUGGCCACGGCCUCGGCCACGGAGGCUUCUGCAGCGG
.(((..(((((((.(((((((....))))).)).((.(..(.(((((...))))).)..).)))))))))..(((....)))..))).(((.....))).. ( -42.30)
>DroYak_CAF1 42182 86 + 1
AUCCAAGGCCAGCAGUGUUGUUGCGGCAGCUGCCGAUCUAGAGGCAGCCAC---------------GGCCACGGCCUCGGCCACGGAGGCAACUGCAGCGG
..((.(((((.((((.....))))(((.((((((........))))))...---------------.)))..))))).))((.((.((....)).).).)) ( -37.30)
>consensus
AUCCAAGGCCAGCAGUGUUGUUGCGGCAGCUGCCGAGCUAGAGGCAGCAACAACCACGGCAGCGCUGGCCACGGCCUCGGCCACGGAGGCUUCUGCAGCGG
.(((..(((((((..(((((...)))))((((((........))))))...............)))))))..(((....)))..))).((....))..... (-32.90 = -34.40 +   1.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,849,439 – 1,849,548
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 84.56
Mean single sequence MFE -46.35
Consensus MFE -35.40
Energy contribution -35.77
Covariance contribution 0.37
Combinations/Pair 1.09
Mean z-score -1.75
Structure conservation index 0.76
SVM decision value 0.48
SVM RNA-class probability 0.752113
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1849439 109 + 22224390
CAGCUGCCGAGCUAGAGGCAGCAACAACCACGGCAGCGCUGGCCACGUCCUCCGCCACGGAGGCUUCUGCAGCGGACAGCUAUCCUGCCGUACAGCAGAACGGCGGCCA
..((((((........)))))).........(((..(((((.....(.((((((...)))))))((((((.((((.(((.....)))))))...)))))))))))))). ( -48.80)
>DroSec_CAF1 50972 109 + 1
CAGCUGCCGAGCUAGAGGCAGCAACAACUACGGCAGCGCUGGCCACGGCCUCGGCCACGGAGGCUUCUGCAGCGGACAGCUAUCCCGCCGUACAGCAGAACGGCGGCCA
..(((((((.((.....))((......)).)))))))...((((..(((....)))..(((((((((((...)))).)))).))).(((((........))))))))). ( -46.80)
>DroEre_CAF1 52302 109 + 1
CAACUGCGGAACUAGAGGCAGCAACUGCCACCGGAUCGCUGGCCACGGCCUCGGCCACGGAGGCUUCUGCAGCGGACAGCUAUACCGCCGUGCAGCAGAACGGUGGCCA
.....((((..(..(.(((((...))))).)..).)))).(((((((((....))).((....((.(((((((((.........))))..))))).))..)))))))). ( -45.30)
>DroYak_CAF1 42208 94 + 1
CAGCUGCCGAUCUAGAGGCAGCCAC---------------GGCCACGGCCUCGGCCACGGAGGCAACUGCAGCGGACAGCUAUGCCGCCGUGCAGCAGAAUGGCGGCCA
..(((((((.(((.(((((.((...---------------.))....))))).(((((((.((((...((........))..)))).)))))..))))).))))))).. ( -44.50)
>consensus
CAGCUGCCGAGCUAGAGGCAGCAACAACCACGGCAGCGCUGGCCACGGCCUCGGCCACGGAGGCUUCUGCAGCGGACAGCUAUCCCGCCGUACAGCAGAACGGCGGCCA
..((((((........))))))..................((((...(((((.......)))))......(((.....))).....(((((........))))))))). (-35.40 = -35.77 +   0.37)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,849,439 – 1,849,548
Length 109
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 84.56
Mean single sequence MFE -51.30
Consensus MFE -42.58
Energy contribution -43.20
Covariance contribution 0.62
Combinations/Pair 1.10
Mean z-score -1.61
Structure conservation index 0.83
SVM decision value 0.35
SVM RNA-class probability 0.702185
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1849439 109 - 22224390
UGGCCGCCGUUCUGCUGUACGGCAGGAUAGCUGUCCGCUGCAGAAGCCUCCGUGGCGGAGGACGUGGCCAGCGCUGCCGUGGUUGUUGCUGCCUCUAGCUCGGCAGCUG
(((((((..((((((.(((((((......)))))..)).))))))(((((((...)))))).))))))))..(((((((.(((((..(....)..)))))))))))).. ( -53.30)
>DroSec_CAF1 50972 109 - 1
UGGCCGCCGUUCUGCUGUACGGCGGGAUAGCUGUCCGCUGCAGAAGCCUCCGUGGCCGAGGCCGUGGCCAGCGCUGCCGUAGUUGUUGCUGCCUCUAGCUCGGCAGCUG
(((((((..((((((.(((((((......)))))..)).))))))(((((.......))))).)))))))..(((((((.(((((..(....)..)))))))))))).. ( -52.80)
>DroEre_CAF1 52302 109 - 1
UGGCCACCGUUCUGCUGCACGGCGGUAUAGCUGUCCGCUGCAGAAGCCUCCGUGGCCGAGGCCGUGGCCAGCGAUCCGGUGGCAGUUGCUGCCUCUAGUUCCGCAGUUG
(((((((..((((((.(((((((......)))))..)).))))))(((((.......))))).)))))))(((..(..(.(((((...))))).)..)...)))..... ( -50.50)
>DroYak_CAF1 42208 94 - 1
UGGCCGCCAUUCUGCUGCACGGCGGCAUAGCUGUCCGCUGCAGUUGCCUCCGUGGCCGAGGCCGUGGCC---------------GUGGCUGCCUCUAGAUCGGCAGCUG
.((((((......(((((((((((((...)))).))).)))))).(((((.......))))).))))))---------------..(((((((........))))))). ( -48.60)
>consensus
UGGCCGCCGUUCUGCUGCACGGCGGGAUAGCUGUCCGCUGCAGAAGCCUCCGUGGCCGAGGCCGUGGCCAGCGCUGCCGUGGUUGUUGCUGCCUCUAGCUCGGCAGCUG
(((((((..((((((.(((((((......)))))..)).))))))(((((.......))))).))))))).................((((((........)))))).. (-42.58 = -43.20 +   0.62)

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 09:50:31 2006