Locus 3433

Sequence ID 2R_DroMel_CAF1
Location 11,587,297 – 11,587,402
Length 105
Max. P 0.997738
window5605 window5606

overview

Window 5

Location 11,587,297 – 11,587,402
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.33
Mean single sequence MFE -45.16
Consensus MFE -33.68
Energy contribution -33.56
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -4.01
Structure conservation index 0.75
SVM decision value 2.92
SVM RNA-class probability 0.997738
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11587297 105 + 20766785
GCCGCAACUUGUGGCUGCAACCGGAGAUGCGUGGUG--------G----CAUGGCGAUGGAGUGUUUGCUAGCU---GCAGGAUCUUCGCAAUGGAGUGGCAAAAGAAGUUGCGGCAAAA
((((((((((((.(((.((..(((((((.(...(..--------(----(.((((((........)))))))).---.).).)))))))...)).))).))).....))))))))).... ( -48.30)
>DroSec_CAF1 20860 108 + 1
GCCGCAACUUGUGGCUGCAACCGGAGAUGCGAGGUG--------G----CAUGGUGGUGGAGUGUUUGCUAGCUGCUGCAGGAUCUUCGCAAUGGAGUGGCAAAAGAAGUUACGGCAGAA
((((.(((((((.(((.((..(((((((.(...(..--------(----((.(.(((..((...))..))).))))..).).)))))))...)).))).))).....)))).)))).... ( -42.20)
>DroSim_CAF1 24147 108 + 1
GCCGCAACUUGUGGCUGCAACCGGAGAUGCGUGGUG--------G----CAUGGUGGUGGAGUGUUUGCUAGCUGCUGCAGGAUCUUCGCAAUGGAGUGGCAAAAGAAGUUGCGGCAAAA
((((((((((((.(((.((..(((((((.((..(..--------(----(.(((..(........)..)))))..)..).).)))))))...)).))).))).....))))))))).... ( -49.60)
>DroEre_CAF1 21712 102 + 1
GCCGCAACUUGCGGCUGCAACUGGAGAUGCGAGGCG---------------AGGAGGUGGAGUGUUUGCGGGCU---GCAGGAUCUUCGCAAUGGAGUGGCAAAGGAAGUUGCGGCAAAA
((((((((((.(.((..(..((.(.....).))(((---------------((((.(..(..((....))..).---.)....)))))))......)..))...).)))))))))).... ( -44.20)
>DroYak_CAF1 21634 117 + 1
GCCACAACUUGUGGCUGCAACUGGAGAUGCGAAGCGUGCAGGUGGUUGAGGGGGAGGUGGAGUGUUUGCUAGCU---GCAGGAUCUUCGCAAUGGAGUGGCAAAAGAAGUUGCGGCAAAA
(((.((((((.(.((..(..(......((((((((.(((((.((((.((.(...........).)).)))).))---))).)..)))))))..)..)..))...).)))))).))).... ( -41.50)
>consensus
GCCGCAACUUGUGGCUGCAACCGGAGAUGCGAGGUG________G____CAUGGAGGUGGAGUGUUUGCUAGCU___GCAGGAUCUUCGCAAUGGAGUGGCAAAAGAAGUUGCGGCAAAA
((((((((((.(.((..(..((..........))......................((((((..(((((........)))))..))))))......)..))...).)))))))))).... (-33.68 = -33.56 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,587,297 – 11,587,402
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.33
Mean single sequence MFE -30.18
Consensus MFE -23.74
Energy contribution -23.58
Covariance contribution -0.16
Combinations/Pair 1.12
Mean z-score -2.93
Structure conservation index 0.79
SVM decision value 2.46
SVM RNA-class probability 0.994259
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11587297 105 - 20766785
UUUUGCCGCAACUUCUUUUGCCACUCCAUUGCGAAGAUCCUGC---AGCUAGCAAACACUCCAUCGCCAUG----C--------CACCACGCAUCUCCGGUUGCAGCCACAAGUUGCGGC
....((((((((((.((((((.........))))))...((((---((((.((............)).(((----(--------......))))....))))))))....)))))))))) ( -31.10)
>DroSec_CAF1 20860 108 - 1
UUCUGCCGUAACUUCUUUUGCCACUCCAUUGCGAAGAUCCUGCAGCAGCUAGCAAACACUCCACCACCAUG----C--------CACCUCGCAUCUCCGGUUGCAGCCACAAGUUGCGGC
....((((((((((.((((((.........))))))...(((((((.....)).........(((...(((----(--------......))))....))))))))....)))))))))) ( -28.00)
>DroSim_CAF1 24147 108 - 1
UUUUGCCGCAACUUCUUUUGCCACUCCAUUGCGAAGAUCCUGCAGCAGCUAGCAAACACUCCACCACCAUG----C--------CACCACGCAUCUCCGGUUGCAGCCACAAGUUGCGGC
....((((((((((.((((((.........))))))...(((((((.....)).........(((...(((----(--------......))))....))))))))....)))))))))) ( -30.00)
>DroEre_CAF1 21712 102 - 1
UUUUGCCGCAACUUCCUUUGCCACUCCAUUGCGAAGAUCCUGC---AGCCCGCAAACACUCCACCUCCU---------------CGCCUCGCAUCUCCAGUUGCAGCCGCAAGUUGCGGC
....((((((((((.((((((.........))))))...((((---(((..(....)............---------------.((...)).......)))))))....)))))))))) ( -28.00)
>DroYak_CAF1 21634 117 - 1
UUUUGCCGCAACUUCUUUUGCCACUCCAUUGCGAAGAUCCUGC---AGCUAGCAAACACUCCACCUCCCCCUCAACCACCUGCACGCUUCGCAUCUCCAGUUGCAGCCACAAGUUGUGGC
....((((((((((...((((.(((....(((((((....(((---((...............................)))))..))))))).....))).))))....)))))))))) ( -33.78)
>consensus
UUUUGCCGCAACUUCUUUUGCCACUCCAUUGCGAAGAUCCUGC___AGCUAGCAAACACUCCACCACCAUG____C________CACCUCGCAUCUCCGGUUGCAGCCACAAGUUGCGGC
....((((((((((...((((.(((....(((((.(.....((....))..(....).............................).))))).....))).))))....)))))))))) (-23.74 = -23.58 +  -0.16)

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 10:55:26 2006