Locus 1258

Sequence ID 3R_DroMel_CAF1
Location 3,773,082 – 3,773,197
Length 115
Max. P 0.512349
window2051

overview

Window 1

Location 3,773,082 – 3,773,197
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.82
Mean single sequence MFE -32.35
Consensus MFE -21.49
Energy contribution -23.68
Covariance contribution 2.19
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.66
SVM decision value -0.04
SVM RNA-class probability 0.512349
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3773082 115 + 27905053
AACAAUCAAGAGCAACUCGAGAGCGCC-CGACUGCAGUUC----GCCCAUCGCCAACGAGAGCGCCAGAAAUGCAUCGAGAGUGCAUUUGUUUGCGAUUACGCCAACAAAUUGCUGACAC
..........(((((.......(((((-(((.((((.(((----(((..(((....)))..).))..))).))))))).).)))).((((((.(((....))).)))))))))))..... ( -31.60)
>DroSec_CAF1 2596 120 + 1
AACAAUCAAGAGCAACUCGAGAGCGAACGGACUGCAGUUCGGACGCCCAACGCCAUCGAGAGCGCCAGAAAUGCAUCGGGAGUGCAUUUGUUUGCGAUUACGCCAACAAAUUGCUUACAC
.........(((((((((((..(((...((((....))))((....))..)))..))))).(((((.((......))..).)))).((((((.(((....))).)))))))))))).... ( -36.10)
>DroSim_CAF1 6240 120 + 1
AACAAUCAAGAGCAACUCGAGAGCGAACGGACUGCAGUUCGGAGGCCCAACGCCAUCGAGAGCGCCAGAAAUGCAUCGGGAGUGCAUUUGUUUGCGAUUACGCCAACAAAUUGCUUACAC
.........(((((((((((..(((...((((....))))((....))..)))..))))).(((((.((......))..).)))).((((((.(((....))).)))))))))))).... ( -36.10)
>DroYak_CAF1 4574 87 + 1
AACAAUUAAGAGCAACUCGAGAGA---------------------------------GAGAGCGCGAGAAAUGCAUCGGGAGUGCAUUUGUUUGCGAUUACGCCAACAAAUUGCUUACAC
.........(((((((((....))---------------------------------)....(((((((((((((.(....)))))))).))))))..............)))))).... ( -25.60)
>consensus
AACAAUCAAGAGCAACUCGAGAGCGAA_GGACUGCAGUUC____GCCCAACGCCAUCGAGAGCGCCAGAAAUGCAUCGGGAGUGCAUUUGUUUGCGAUUACGCCAACAAAUUGCUUACAC
.........(((((((((((..(((..(((((....))))).........)))..)))))........(((((((.(....))))))))(((.(((....))).)))...)))))).... (-21.49 = -23.68 +   2.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:51 2006