Locus 9619

Sequence ID 3R_DroMel_CAF1
Location 25,404,817 – 25,404,913
Length 96
Max. P 0.999480
window15373 window15374

overview

Window 3

Location 25,404,817 – 25,404,913
Length 96
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 70.41
Mean single sequence MFE -26.91
Consensus MFE -12.99
Energy contribution -15.00
Covariance contribution 2.01
Combinations/Pair 1.09
Mean z-score -3.62
Structure conservation index 0.48
SVM decision value 3.64
SVM RNA-class probability 0.999480
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25404817 96 + 27905053
CUAAUGAUUUUGCUCGUUG----UUAUAUG-----AUAUGCCACAUAUAUACAUAUGUACAUAUGUGGUUCCACUAGGAAGAUCUCCAAAUUGACGAGCAAAUUC
.....((.(((((((((((----......(-----((..(((((((((.(((....))).)))))))))(((....)))..))).......))))))))))).)) ( -31.12)
>DroSim_CAF1 89180 84 + 1
CUAAUGAUUUGGCUCGUUG----UUAUAUG-----AUAUGCCGCAUAU------------AUAGGUGGUUCCACUCGGAACAUCUCCAAAUUGACGAGCAAAUUC
.....((((((.((((((.----.((((((-----........)))))------------)..((..(((((....)))))....)).....)))))))))))). ( -23.50)
>DroYak_CAF1 96244 92 + 1
CUGCUCAUCU-GCAUGCUGCAUCAAAUACGAAACUCUAGGCUACAGAU------------AGAGGUUGUUCCACUCGGAACAUCUCCAAAUUGAUGAGCAAAUUC
.(((((((((-((.....)))........((..(((((..(....).)------------))))..((((((....))))))))........))))))))..... ( -26.10)
>consensus
CUAAUGAUUU_GCUCGUUG____UUAUAUG_____AUAUGCCACAUAU____________AUAGGUGGUUCCACUCGGAACAUCUCCAAAUUGACGAGCAAAUUC
...........(((((((.....................(((((.(((((((....))))))).))))).......(((.....))).....)))))))...... (-12.99 = -15.00 +   2.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 25,404,817 – 25,404,913
Length 96
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 70.41
Mean single sequence MFE -26.85
Consensus MFE -10.65
Energy contribution -13.77
Covariance contribution 3.11
Combinations/Pair 1.03
Mean z-score -3.10
Structure conservation index 0.40
SVM decision value 0.48
SVM RNA-class probability 0.753440
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25404817 96 - 27905053
GAAUUUGCUCGUCAAUUUGGAGAUCUUCCUAGUGGAACCACAUAUGUACAUAUGUAUAUAUGUGGCAUAU-----CAUAUAA----CAACGAGCAAAAUCAUUAG
((.(((((((((.......((....((((....))))((((((((((((....))))))))))))....)-----)......----..))))))))).))..... ( -33.46)
>DroSim_CAF1 89180 84 - 1
GAAUUUGCUCGUCAAUUUGGAGAUGUUCCGAGUGGAACCACCUAU------------AUAUGCGGCAUAU-----CAUAUAA----CAACGAGCCAAAUCAUUAG
((.((.((((((.....((..(((((.(((.(((....)))....------------.....))).))))-----).))...----..)))))).)).))..... ( -18.40)
>DroYak_CAF1 96244 92 - 1
GAAUUUGCUCAUCAAUUUGGAGAUGUUCCGAGUGGAACAACCUCU------------AUCUGUAGCCUAGAGUUUCGUAUUUGAUGCAGCAUGC-AGAUGAGCAG
.....((((((((....(((((.((((((....))))))..))))------------)..(((.((...((((.....))))...)).)))...-.)))))))). ( -28.70)
>consensus
GAAUUUGCUCGUCAAUUUGGAGAUGUUCCGAGUGGAACCACCUAU____________AUAUGUGGCAUAU_____CAUAUAA____CAACGAGC_AAAUCAUUAG
..(((((((((((.((((((((...)))))))).)).((((.(((((((....))))))).))))........................))))).))))...... (-10.65 = -13.77 +   3.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:23 2006