Locus 1135

Sequence ID 3R_DroMel_CAF1
Location 3,398,232 – 3,398,346
Length 114
Max. P 0.795917
window1865

overview

Window 5

Location 3,398,232 – 3,398,346
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.02
Mean single sequence MFE -53.60
Consensus MFE -50.51
Energy contribution -50.08
Covariance contribution -0.44
Combinations/Pair 1.11
Mean z-score -1.59
Structure conservation index 0.94
SVM decision value 0.60
SVM RNA-class probability 0.795917
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3398232 114 + 27905053
GGCGGGCGAGUGCUGCUGGGCCUG------GGCCUGCGUUUGCUUCAUGCAGCUCUUCUUGGUCAGAGUGCCGCACUGAUUGCCCAUCACCUGGAGGGCGUGUGGCGGCGGCAUUUGCAC
.....((((((((((((.((((.(------(((.(((((.......))))))))).....)))).....(((((((.....((((..(....)..))))))))))))))))))))))).. ( -53.70)
>DroSim_CAF1 7186 114 + 1
GGCGGGCGAGUGCUGCUGGGCCUG------GGCCUGCGUUUGCUUCAUGCAGCUCUUCUUGGUCAGGGUGCCGCACUGAUUGCCCAUCACUUGGAGGGCGUGUGGCGGCGGCAUUUGCAC
.....((((((((((((.((((.(------(((.(((((.......))))))))).....)))).....(((((((.....((((..(....)..))))))))))))))))))))))).. ( -53.70)
>DroEre_CAF1 5514 120 + 1
GGCGGGCGAGUGCUGCUGGGCCUGGGCCUGGGCCUGGGUUUGCUUCAUGCAGCUCUUCUUGGUCAGUGUGCCGCACUGAUUGCCCAUCACCUGGAGGGCGUGUGGCGGCGGCAUUUGCAC
.....(((((((((((((((((..(((....)))..)))))(((.(((((..((((...(((((((((.....))))))....)))......)))).))))).))))))))))))))).. ( -60.70)
>DroYak_CAF1 10886 114 + 1
GGCGGGUGAGUGCUGCUGGGUUUG------GGCCUGCGUUUGCUUCAUGCAGCUCUUUUUGGUCAGAGUGCCGCACUGAUUGCCCAUCACUUGGAGGGCGUGUGGCGGCGGCAUUUGCAC
.....(..(((((((((((((...------.)))).....(((.....)))(((((........)))))(((((((.....((((..(....)..))))))))))))))))))))..).. ( -46.30)
>consensus
GGCGGGCGAGUGCUGCUGGGCCUG______GGCCUGCGUUUGCUUCAUGCAGCUCUUCUUGGUCAGAGUGCCGCACUGAUUGCCCAUCACCUGGAGGGCGUGUGGCGGCGGCAUUUGCAC
.....(((((((((((((((((........))))).....(((.....)))(((((........)))))(((((((.....((((..(....)..))))))))))))))))))))))).. (-50.51 = -50.08 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:55 2006