Locus 5603

Sequence ID 3L_DroMel_CAF1
Location 15,367,326 – 15,367,419
Length 93
Max. P 0.999356
window8858 window8859

overview

Window 8

Location 15,367,326 – 15,367,419
Length 93
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 88.22
Mean single sequence MFE -15.88
Consensus MFE -12.86
Energy contribution -12.70
Covariance contribution -0.16
Combinations/Pair 1.07
Mean z-score -1.39
Structure conservation index 0.81
SVM decision value -0.04
SVM RNA-class probability 0.513527
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15367326 93 + 23771897
UCGCU------------UUCUCCAAUUCUCCAUUUCACUGGCAUGACAUAUCCCACACCACAUCCCUUUACCCACCGGUUAACCUUUGGCUCUGGGCGGAAAUUU
.....------------...........(((.......(((..((........))..)))...(((.....(((..((....))..)))....))).)))..... ( -13.50)
>DroSec_CAF1 99032 93 + 1
UCGCU------------UUCUCCAAUUCUCCAUUUCACUGGCAUGACAUAUCCCACACCACAUCCCUUUACCCACCGGUUAACCUUUGGCUCUGGGCGGAAAUUU
.....------------...........(((.......(((..((........))..)))...(((.....(((..((....))..)))....))).)))..... ( -13.50)
>DroSim_CAF1 101093 93 + 1
UCGCU------------UUCUCCAAUUCUCCAUUUCACUGGCAUGACAUAUCCCACACCACAUCCCUUUACCCACCGGUUAACCUUUGGCUCUGGGCGGAAAUUU
.....------------...........(((.......(((..((........))..)))...(((.....(((..((....))..)))....))).)))..... ( -13.50)
>DroEre_CAF1 98834 105 + 1
UCUCAGUCUCAGUCGCUUUCUCCGAUUCUCCAUUUCUCUGGCAUGAUAUUUCCCACACCACAGCCUUUUACCCACCGGUUAACCUUUGGCUCUGGGCGGAAAUUU
.....(((..(((((.......)))))..(((......)))...)))((((((....(((.((((....(((....)))........)))).)))..)))))).. ( -19.00)
>DroYak_CAF1 102143 101 + 1
UCGCUUUCUCC----AAUUCUCCGUUUCUCCAUUUCUCCGGCAUGAUAUAUCCCACACCACAUCCCUUUAGCCACCGGUUAACCUUUGGCUCUGGGCGGAAAUUU
...........----.....((((...............((..((........))..))....(((...(((((..((....))..)))))..)))))))..... ( -19.90)
>consensus
UCGCU____________UUCUCCAAUUCUCCAUUUCACUGGCAUGACAUAUCCCACACCACAUCCCUUUACCCACCGGUUAACCUUUGGCUCUGGGCGGAAAUUU
............................(((........((..((........))..))....(((.....(((..((....))..)))....))).)))..... (-12.86 = -12.70 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,367,326 – 15,367,419
Length 93
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 88.22
Mean single sequence MFE -27.22
Consensus MFE -24.90
Energy contribution -24.70
Covariance contribution -0.20
Combinations/Pair 1.09
Mean z-score -2.56
Structure conservation index 0.91
SVM decision value 3.54
SVM RNA-class probability 0.999356
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15367326 93 - 23771897
AAAUUUCCGCCCAGAGCCAAAGGUUAACCGGUGGGUAAAGGGAUGUGGUGUGGGAUAUGUCAUGCCAGUGAAAUGGAGAAUUGGAGAA------------AGCGA
...(((((((((..(.(((..((....))..))).)...)))...((((((((......))))))))......)))))).........------------..... ( -25.50)
>DroSec_CAF1 99032 93 - 1
AAAUUUCCGCCCAGAGCCAAAGGUUAACCGGUGGGUAAAGGGAUGUGGUGUGGGAUAUGUCAUGCCAGUGAAAUGGAGAAUUGGAGAA------------AGCGA
...(((((((((..(.(((..((....))..))).)...)))...((((((((......))))))))......)))))).........------------..... ( -25.50)
>DroSim_CAF1 101093 93 - 1
AAAUUUCCGCCCAGAGCCAAAGGUUAACCGGUGGGUAAAGGGAUGUGGUGUGGGAUAUGUCAUGCCAGUGAAAUGGAGAAUUGGAGAA------------AGCGA
...(((((((((..(.(((..((....))..))).)...)))...((((((((......))))))))......)))))).........------------..... ( -25.50)
>DroEre_CAF1 98834 105 - 1
AAAUUUCCGCCCAGAGCCAAAGGUUAACCGGUGGGUAAAAGGCUGUGGUGUGGGAAAUAUCAUGCCAGAGAAAUGGAGAAUCGGAGAAAGCGACUGAGACUGAGA
...((((((((((.((((.....((.(((....))).)).)))).))).)))))))...((...(((......)))((..((((.........))))..)))).. ( -27.60)
>DroYak_CAF1 102143 101 - 1
AAAUUUCCGCCCAGAGCCAAAGGUUAACCGGUGGCUAAAGGGAUGUGGUGUGGGAUAUAUCAUGCCGGAGAAAUGGAGAAACGGAGAAUU----GGAGAAAGCGA
...(((((((((..(((((..((....))..)))))...))).(.((((((((......)))))))).)............))))))...----........... ( -32.00)
>consensus
AAAUUUCCGCCCAGAGCCAAAGGUUAACCGGUGGGUAAAGGGAUGUGGUGUGGGAUAUGUCAUGCCAGUGAAAUGGAGAAUUGGAGAA____________AGCGA
...(((((((((..(.(((..((....))..))).)...)))...((((((((......))))))))..............)))))).................. (-24.90 = -24.70 +  -0.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:27 2006