Locus 1154

Sequence ID X_DroMel_CAF1
Location 3,445,967 – 3,446,063
Length 96
Max. P 0.638282
window1854 window1855

overview

Window 4

Location 3,445,967 – 3,446,063
Length 96
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 97.74
Mean single sequence MFE -21.82
Consensus MFE -19.85
Energy contribution -20.10
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -1.80
Structure conservation index 0.91
SVM decision value 0.18
SVM RNA-class probability 0.621346
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3445967 96 + 22224390
UUUUAAGACGACUUAACCGUUGACCCAGGCAUCCUGUUCAUUGCCUCGAGUCGUCGCCUCCGCUCUGAAGAACUUUCACAUCACUGCGCAUUAAUA
......((((((((...((.(((..((((...)))).))).))....)))))))).....(((..(((.(........).)))..)))........ ( -21.00)
>DroSec_CAF1 18184 96 + 1
UUUUAAGACGACUUAACCGUUGACCCAGGCAUCCUGUUCAUUGCCUCGAGUCGUCGCCUCCGCUCUGAAGAACUUUCACAUCACUGCGCAUUAAUA
......((((((((...((.(((..((((...)))).))).))....)))))))).....(((..(((.(........).)))..)))........ ( -21.00)
>DroEre_CAF1 20686 96 + 1
UUUUAAGACGACUUAACCAUUGACCCUGGCAUCCUGUUCAUUGCCUCGAGUCGUCGCCUGCGCUCUGAACAACUUUCACAUCACUGCGCAUUAAUA
......((((((((.............((((..........))))..))))))))...(((((..(((............)))..)))))...... ( -23.06)
>DroYak_CAF1 19459 96 + 1
UUUUAAGACGACUUAACCAUUGACCCAGGCAUCCUGUUCAUUGCCUCGAGUCGUCGCCUCCGCUCUGAAGAACUUUCACAUCACUGCGCAUUAAUA
......((((((((...((.(((..((((...)))).))).))....)))))))).....(((..(((.(........).)))..)))........ ( -22.20)
>consensus
UUUUAAGACGACUUAACCAUUGACCCAGGCAUCCUGUUCAUUGCCUCGAGUCGUCGCCUCCGCUCUGAAGAACUUUCACAUCACUGCGCAUUAAUA
......((((((((...((.(((..((((...)))).))).))....)))))))).....(((..(((.(........).)))..)))........ (-19.85 = -20.10 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 3,445,967 – 3,446,063
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 97.74
Mean single sequence MFE -28.88
Consensus MFE -25.77
Energy contribution -26.53
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.89
SVM decision value 0.22
SVM RNA-class probability 0.638282
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3445967 96 - 22224390
UAUUAAUGCGCAGUGAUGUGAAAGUUCUUCAGAGCGGAGGCGACGACUCGAGGCAAUGAACAGGAUGCCUGGGUCAACGGUUAAGUCGUCUUAAAA
........((((....))))...((((....)))).(((((((((((((.(((((..........)))))))))).........)))))))).... ( -29.20)
>DroSec_CAF1 18184 96 - 1
UAUUAAUGCGCAGUGAUGUGAAAGUUCUUCAGAGCGGAGGCGACGACUCGAGGCAAUGAACAGGAUGCCUGGGUCAACGGUUAAGUCGUCUUAAAA
........((((....))))...((((....)))).(((((((((((((.(((((..........)))))))))).........)))))))).... ( -29.20)
>DroEre_CAF1 20686 96 - 1
UAUUAAUGCGCAGUGAUGUGAAAGUUGUUCAGAGCGCAGGCGACGACUCGAGGCAAUGAACAGGAUGCCAGGGUCAAUGGUUAAGUCGUCUUAAAA
......(((((..(((............)))..)))))(((((((((((..((((..........)))).)))))..(.....)))))))...... ( -27.40)
>DroYak_CAF1 19459 96 - 1
UAUUAAUGCGCAGUGAUGUGAAAGUUCUUCAGAGCGGAGGCGACGACUCGAGGCAAUGAACAGGAUGCCUGGGUCAAUGGUUAAGUCGUCUUAAAA
........((((....))))...((((....)))).(((((((((((((.(((((..........))))))))))..(.....))))))))).... ( -29.70)
>consensus
UAUUAAUGCGCAGUGAUGUGAAAGUUCUUCAGAGCGGAGGCGACGACUCGAGGCAAUGAACAGGAUGCCUGGGUCAACGGUUAAGUCGUCUUAAAA
........((((....))))...((((....)))).(((((((((((((.(((((..........)))))))))).........)))))))).... (-25.77 = -26.53 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:38 2006