Locus 6116

Sequence ID 3L_DroMel_CAF1
Location 16,212,829 – 16,212,981
Length 152
Max. P 0.838693
window9826 window9827

overview

Window 6

Location 16,212,829 – 16,212,948
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.89
Mean single sequence MFE -41.90
Consensus MFE -31.80
Energy contribution -31.00
Covariance contribution -0.80
Combinations/Pair 1.25
Mean z-score -1.65
Structure conservation index 0.76
SVM decision value 0.17
SVM RNA-class probability 0.616567
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16212829 119 - 23771897
GGGAUGGGGACUCUUUAUGAGUCAGGGCGUGUUAAUUUGCUGCACGCGCCGUGC-UGAAAAGUUAAGACGGCGGAGGGGAUCAAGGAUGCGGUCAACUUGUUGCCAGUCCACCAAAUUGA
....(((.(((((.....))))).((((((.(((((((...(((((...)))))-....))))))).))(((((((..((((........))))..)))..)))).)))).)))...... ( -42.80)
>DroSec_CAF1 31584 119 - 1
GGAAUGGGGACUCUUUAUGGGGCAGGGCGUGUUAAUUUGCUGCACGCGCCGUGC-UGAAAAGUUAAGAUGGCGGAGGGGAUCAAGGAUGCGGUCAACUUGUUGCCAGUCCACCAAAUUGA
....(((((((((((.((..((((.(((((((((......)).))))))).)))-).....)).))))((((((((..((((........))))..)))..))))))))).)))...... ( -42.00)
>DroSim_CAF1 33427 119 - 1
GGAAUGGGGACUCUUUAUGGGGCAGGGCGUGUUAAUUUGCUGCACGCGCCGUGC-UGAAAAGUUAAGACGGCGGAGGGGAUCAAGGAUGCGGUCAACUUGUUGCCAGUCCACCAAAUUUA
....((((((((((....))(((((.((((((.........))))))(((((((-(....)))....))))).(((..((((........))))..))).)))))))))).)))...... ( -42.20)
>DroEre_CAF1 31068 120 - 1
GGGAUGGGGACUCUUUAUGAGGCAGGGCGUGUUAAUUUGUUGCACGCGCCGGGCAUGAAAAGUUAAGACGGCGGCGGGGAUCAAGGAGGUGGUCAACUUGUUGCCACUCCACCGCUUUAA
.((.((((((((.((((((.(((...((((((.........)))))))))...)))))).)))......((((((((((((((......)))))..))))))))).)))))))....... ( -45.00)
>DroYak_CAF1 68127 120 - 1
GGAAUGGGGACUCUUUAUGAGGCAGGGUGUGUUAAUUUGGUACACGCGCUGGGCAUGAAAAGUUAAGAUGGGGGAGGGGAUCAAGGAUCCGGUCAACUUGUUGCUACUCCACCGCUUUAA
........((((.((((((...(((.((((((.........)))))).)))..)))))).))))(((.(((.((((.(((((...)))))((.(((....))))).)))).))))))... ( -37.50)
>consensus
GGAAUGGGGACUCUUUAUGAGGCAGGGCGUGUUAAUUUGCUGCACGCGCCGUGC_UGAAAAGUUAAGACGGCGGAGGGGAUCAAGGAUGCGGUCAACUUGUUGCCAGUCCACCAAAUUAA
(((.(((.(((..........(((.(((((((((......)).))))))).))).....(((((..(((.(((..............))).))))))))))).))).))).......... (-31.80 = -31.00 +  -0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,212,869 – 16,212,981
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.05
Mean single sequence MFE -44.76
Consensus MFE -33.94
Energy contribution -34.26
Covariance contribution 0.32
Combinations/Pair 1.15
Mean z-score -1.98
Structure conservation index 0.76
SVM decision value 0.74
SVM RNA-class probability 0.838693
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16212869 112 - 23771897
AG-------CUUUCCCCACAUUUCCACCGUUUUGUUCCUCGGGAUGGGGACUCUUUAUGAGUCAGGGCGUGUUAAUUUGCUGCACGCGCCGUGC-UGAAAAGUUAAGACGGCGGAGGGGA
..-------...(((((.....(((.((((((((....((((.((((.(((((.....)))))...((((((.........)))))).)))).)-))).....)))))))).)))))))) ( -47.50)
>DroSec_CAF1 31624 119 - 1
AGCACCCAACUUUCCCCACACUUCCACCGUUUUGUUCCUCGGAAUGGGGACUCUUUAUGGGGCAGGGCGUGUUAAUUUGCUGCACGCGCCGUGC-UGAAAAGUUAAGAUGGCGGAGGGGA
....(((..(((.(((((....(((.((((((((.....))))))))))).......))))).)))((((((.........))))))(((((((-(....)))....)))))...))).. ( -44.00)
>DroSim_CAF1 33467 119 - 1
AGCACCCAACUUUCCCCACAUUUCCAACGUUUUGUUCCUCGGAAUGGGGACUCUUUAUGGGGCAGGGCGUGUUAAUUUGCUGCACGCGCCGUGC-UGAAAAGUUAAGACGGCGGAGGGGA
....(((..(((.(((((....(((..(((((((.....))))))).))).......))))).)))((((((.........))))))(((((((-(....)))....)))))...))).. ( -41.30)
>DroEre_CAF1 31108 119 - 1
AGCCCCCAGUUUUCCCCACAUCU-CCCCGUUUUGUUCUUCGGGAUGGGGACUCUUUAUGAGGCAGGGCGUGUUAAUUUGUUGCACGCGCCGGGCAUGAAAAGUUAAGACGGCGGCGGGGA
............(((((.....(-((((((((((.....)))))))))))(((.....)))((...((((((.........))))))((((..(.(((....))).).)))).))))))) ( -44.00)
>DroYak_CAF1 68167 120 - 1
AGCCCCCAACUUUCCCCACAUUUUCCCAGUUUUGUUCUAAGGAAUGGGGACUCUUUAUGAGGCAGGGUGUGUUAAUUUGGUACACGCGCUGGGCAUGAAAAGUUAAGAUGGGGGAGGGGA
...((((.....(((((.((((((((((.((((......)))).))))((((.((((((...(((.((((((.........)))))).)))..)))))).))))))))))))))))))). ( -47.00)
>consensus
AGCACCCAACUUUCCCCACAUUUCCACCGUUUUGUUCCUCGGAAUGGGGACUCUUUAUGAGGCAGGGCGUGUUAAUUUGCUGCACGCGCCGUGC_UGAAAAGUUAAGACGGCGGAGGGGA
............(((((.....(((.(((((((((((....))))...((((.((((....(((.(((((((((......)).))))))).))).)))).))))))))))).)))))))) (-33.94 = -34.26 +   0.32)

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 12:10:29 2006