Locus 4279

Sequence ID 3R_DroMel_CAF1
Location 11,405,046 – 11,405,154
Length 108
Max. P 0.898466
window6955 window6956

overview

Window 5

Location 11,405,046 – 11,405,154
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.53
Mean single sequence MFE -36.80
Consensus MFE -28.50
Energy contribution -29.70
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.77
SVM decision value 1.00
SVM RNA-class probability 0.898466
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11405046 108 + 27905053
CGGGAUGUUAAUUUCUUGGACAAGCCUAAGCCGAUCCGCGUCGGCUUAAUGUCGAUUACACAAUCGACUUGUAGG------------GAACCGGCUUGCCUCCGUCUUGUUUGAACUGCA
(((((((..........((.(((((((((((((((....)))))))))..(((((((....))))))).......------------.....))))))))..)))))))........... ( -35.80)
>DroSec_CAF1 152697 108 + 1
CGGGAUGCUAAUUUCUUGGACAAGCCUAAGCCGAUCCGCGUCGGCUUAAUGUCGAUUACACAAUCGACUUGUAGG------------GUACCGGCUUGGUUCCGUCUUAUUUGAACUGCA
((((((.((((....)))).(((((((((((((((....)))))))))..(((((((....))))))).......------------.....))))))))))))................ ( -36.40)
>DroSim_CAF1 144174 108 + 1
CGGGAUGCUAAUUUCUUGGACAAGCCUAAGCCGAUCCGCGUCGGCUUAAUGUCGAUUACACAAUCGACUUGUAGG------------GUACCGGCUUGGCUCCGUCUUGUUUGAACUGCA
.(..((....))..)(..((((((.(..((((((.(((.((.(.((((..(((((((....)))))))...))))------------.)))))).))))))..).))))))..)...... ( -36.70)
>DroEre_CAF1 140655 89 + 1
CGGGAUGCUAAUUUCUUGGACAAGCCUAAGCCGAUCCACGUCGGCUUAAUGUCGAUUACACAAUCGACUGGCUGGC-------------------------------UGUUUGAACUGCA
.(..((....))..)(..((((.((((((((((((....)))))))))..(((((((....))))))).....)))-------------------------------))))..)...... ( -31.80)
>DroYak_CAF1 144079 120 + 1
CGGGAUGCUAAUUUCUUGGACAAGCCUAAGCCGAUCCACGUCGGCUUAAUGUCGAUUACACAAUCGACUGGCAGGCUACGAGCUUGGGUGCCGGCUUGGCUCCGACUUGUUUGAACUGCA
.((..((((((....)))).))..))(((((((((....)))))))))..(((((((....)))))))..((((...(((((.(((((.(((.....))))))))))))).....)))). ( -43.30)
>consensus
CGGGAUGCUAAUUUCUUGGACAAGCCUAAGCCGAUCCGCGUCGGCUUAAUGUCGAUUACACAAUCGACUUGUAGG____________GUACCGGCUUGGCUCCGUCUUGUUUGAACUGCA
(((((........)))))..(((((((((((((((....)))))))))..(((((((....)))))))........................))))))...................... (-28.50 = -29.70 +   1.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,405,046 – 11,405,154
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.53
Mean single sequence MFE -34.74
Consensus MFE -26.46
Energy contribution -28.46
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.76
SVM decision value 0.81
SVM RNA-class probability 0.856735
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11405046 108 - 27905053
UGCAGUUCAAACAAGACGGAGGCAAGCCGGUUC------------CCUACAAGUCGAUUGUGUAAUCGACAUUAAGCCGACGCGGAUCGGCUUAGGCUUGUCCAAGAAAUUAACAUCCCG
................(((.((((((((.....------------.......(((((((....)))))))..((((((((......)))))))))))))))).((....))......))) ( -34.90)
>DroSec_CAF1 152697 108 - 1
UGCAGUUCAAAUAAGACGGAACCAAGCCGGUAC------------CCUACAAGUCGAUUGUGUAAUCGACAUUAAGCCGACGCGGAUCGGCUUAGGCUUGUCCAAGAAAUUAGCAUCCCG
(((.(((.......)))(((..((((((.....------------.......(((((((....)))))))..((((((((......))))))))))))))))).........)))..... ( -35.00)
>DroSim_CAF1 144174 108 - 1
UGCAGUUCAAACAAGACGGAGCCAAGCCGGUAC------------CCUACAAGUCGAUUGUGUAAUCGACAUUAAGCCGACGCGGAUCGGCUUAGGCUUGUCCAAGAAAUUAGCAUCCCG
(((...........((((.((((((((((((.(------------(......(((((((....))))))).....((....)))))))))))).)))))))).((....)).)))..... ( -35.30)
>DroEre_CAF1 140655 89 - 1
UGCAGUUCAAACA-------------------------------GCCAGCCAGUCGAUUGUGUAAUCGACAUUAAGCCGACGUGGAUCGGCUUAGGCUUGUCCAAGAAAUUAGCAUCCCG
(((((((......-------------------------------((.((((.(((((((....)))))))..((((((((......)))))))))))).))......)))).)))..... ( -29.10)
>DroYak_CAF1 144079 120 - 1
UGCAGUUCAAACAAGUCGGAGCCAAGCCGGCACCCAAGCUCGUAGCCUGCCAGUCGAUUGUGUAAUCGACAUUAAGCCGACGUGGAUCGGCUUAGGCUUGUCCAAGAAAUUAGCAUCCCG
(((..............(((..((((((((((.....((.....)).)))).(((((((....)))))))..((((((((......)))))))))))))))))((....)).)))..... ( -39.40)
>consensus
UGCAGUUCAAACAAGACGGAGCCAAGCCGGUAC____________CCUACAAGUCGAUUGUGUAAUCGACAUUAAGCCGACGCGGAUCGGCUUAGGCUUGUCCAAGAAAUUAGCAUCCCG
(((..............(((..((((((........................(((((((....)))))))..((((((((......)))))))))))))))))((....)).)))..... (-26.46 = -28.46 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:27 2006