Locus 4105

Sequence ID 3R_DroMel_CAF1
Location 11,205,750 – 11,205,881
Length 131
Max. P 0.996829
window6572 window6573

overview

Window 2

Location 11,205,750 – 11,205,841
Length 91
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 85.53
Mean single sequence MFE -33.55
Consensus MFE -27.11
Energy contribution -25.98
Covariance contribution -1.13
Combinations/Pair 1.38
Mean z-score -2.25
Structure conservation index 0.81
SVM decision value 0.57
SVM RNA-class probability 0.784480
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11205750 91 + 27905053
GGCGUUUCGCAAAUGCCAAAGACUUCCGUUUGGUUCCGGCUAAAUGCUGUCAUGCAGCCGCCCACUA--GGGCGGGGCUCCACCAACACGAAU
((((((.....)))))).........((((((((...((((...(((......))).((((((....--))))))))))..))))).)))... ( -34.10)
>DroSec_CAF1 7800 81 + 1
GGCGUUUCGCAAAUGC----------CGUUUGGUUCCGGCUAAAUGCUGUCAUGCAGCCGCCCACUA--GGGCGGGGUACCACCAACACGAAU
((((((.....)))))----------)(((((((.((.......(((......))).((((((....--)))))))).))))..)))...... ( -30.80)
>DroSim_CAF1 8044 91 + 1
GGCGUUUCGCAAAUGCCAAAGACUUCCGUUUGGUUCCGGCUAAAUGCUGUCAUGCAGCCGCCCACUA--GGGCGGGGCACCACCAACACGAAU
((((((.....)))))).........((((((((..((((.....))))...(((..((((((....--)))))).)))..))))).)))... ( -34.50)
>DroEre_CAF1 12906 91 + 1
GGCGUUUCGCAAAUGCCAAAGACUUCCGUUUGGUUCCGGCUAAAUGCUGUCAUGCAACCGCCCACUA--GGGCGGGGCUCCACCAACACGAAU
((((((.....)))))).........((((((((...((((...(((......))).((((((....--))))))))))..))))).)))... ( -34.40)
>DroYak_CAF1 8210 91 + 1
GGCGUUUCGCAAAUGCCAAAGACUUCCGUUCGGUUCCGGCUAAAUGCUGUCAUGCAACCGCCCACUA--GGGCGGGGCUCCACCAACACGAAU
((((((.....))))))..........(((.(((...((((...(((......))).((((((....--))))))))))..))))))...... ( -31.70)
>DroAna_CAF1 8026 93 + 1
GGCGUACGGAAAAUAUCAAAGGCUUCGGGCUGGCUCCGGUUAAAUGCUGUCAUGCAAAUGCCCACCAAUGGGCGGGGCCAGACCAGCACAGCC
(((.....((.....))....(((..((.((((((((.......(((......)))...(((((....))))))))))))).)))))...))) ( -35.80)
>consensus
GGCGUUUCGCAAAUGCCAAAGACUUCCGUUUGGUUCCGGCUAAAUGCUGUCAUGCAACCGCCCACUA__GGGCGGGGCUCCACCAACACGAAU
((((((.....))))))..........((((((((.((((.....))))....((..((((((......)))))).))......))).))))) (-27.11 = -25.98 +  -1.13)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,205,776 – 11,205,881
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 95.71
Mean single sequence MFE -34.07
Consensus MFE -30.36
Energy contribution -31.04
Covariance contribution 0.68
Combinations/Pair 1.04
Mean z-score -2.14
Structure conservation index 0.89
SVM decision value 2.75
SVM RNA-class probability 0.996829
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11205776 105 + 27905053
CGUUUGGUUCCGGCUAAAUGCUGUCAUGCAGCCGCCCACUAGGGCGGGGCUCCACCAACACGAAUGCCGAAAGCAACAGCAACCACAACAACGCAUCAAAGGCGA
.(((((((....)))))))(((((..(((..((((((....))))))(((...............)))....))))))))...........(((.......))). ( -34.26)
>DroSec_CAF1 7816 105 + 1
CGUUUGGUUCCGGCUAAAUGCUGUCAUGCAGCCGCCCACUAGGGCGGGGUACCACCAACACGAAUGCCGAAAGCAACAGCAACCACAACAACGCAUGAAAGGCGA
.(((((((....)))))))(((.((((((..((((((....))))))(((..........((.....))...((....)).)))........))))))..))).. ( -34.10)
>DroSim_CAF1 8070 105 + 1
CGUUUGGUUCCGGCUAAAUGCUGUCAUGCAGCCGCCCACUAGGGCGGGGCACCACCAACACGAAUGCCGAAAGCAACAGCAACCACAACAACGCAUCAAAGGCGA
.(((((((....)))))))(((((..(((..((((((....))))))((((.............))))....))))))))...........(((.......))). ( -34.62)
>DroEre_CAF1 12932 105 + 1
CGUUUGGUUCCGGCUAAAUGCUGUCAUGCAACCGCCCACUAGGGCGGGGCUCCACCAACACGAAUUCCGAAAGCAAAAGCAUCCACAACAACGCAUCAAAGGCGA
((((((((...((((...(((......))).((((((....))))))))))..))))).)))..........((....))...........(((.......))). ( -31.40)
>DroYak_CAF1 8236 105 + 1
CGUUCGGUUCCGGCUAAAUGCUGUCAUGCAACCGCCCACUAGGGCGGGGCUCCACCAACACGAAUGCCGAUAGCAAGAGCAUCCACAACAACGCAUCAAAGGCGA
.(((.((.....(((...(((((((......((((((....))))))(((...............))))))))))..)))..))..)))..(((.......))). ( -35.96)
>consensus
CGUUUGGUUCCGGCUAAAUGCUGUCAUGCAGCCGCCCACUAGGGCGGGGCUCCACCAACACGAAUGCCGAAAGCAACAGCAACCACAACAACGCAUCAAAGGCGA
.(((((((....(((...((((.((......((((((....))))))(((...............))))).))))..))).)))).)))..(((.......))). (-30.36 = -31.04 +   0.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:14 2006