Locus 4738

Sequence ID 2L_DroMel_CAF1
Location 13,558,164 – 13,558,283
Length 119
Max. P 0.820180
window7491 window7492

overview

Window 1

Location 13,558,164 – 13,558,254
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 90.74
Mean single sequence MFE -21.30
Consensus MFE -17.77
Energy contribution -18.15
Covariance contribution 0.38
Combinations/Pair 1.19
Mean z-score -1.80
Structure conservation index 0.83
SVM decision value 0.68
SVM RNA-class probability 0.820180
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13558164 90 - 22407834
AAAAAUAAGAUGGGAGGGCAAAAUAUUUCCUUCCUGACAGGCCGACAAGCCAACGAGAAUAAUUUUCGUUAAAGGUCGAAUUCUAUACCA
.......(((.(((((((.((....)).)))))))(((.(((......)))(((((((.....)))))))....)))....)))...... ( -22.00)
>DroSec_CAF1 19340 90 - 1
AAAAGUAAGAUGGGAGGGCAAAAUGUUUCCUUCCUGACAGGCCGACAAGCCAACGGGAACAAUUCUCGUUAAAGGUCAAAUUCUAUAGCA
.......(((.((((((((.....))..))))))((((.(((......)))(((((((.....)))))))....))))...)))...... ( -23.90)
>DroSim_CAF1 27004 90 - 1
AAAAGUAAGAUGGGAGGGCAAAAUGUUUCCUUCCUGACAGGCCGACAAGCCAACGGGAACAAUUCUCGUUAAAGGUCGAAUUCUAUACCA
....((((((.(((((((.((....)).)))))))(((.(((......)))(((((((.....)))))))....)))....))).))).. ( -24.80)
>DroYak_CAF1 17280 90 - 1
AAAAGUUAGACGAAAACGCAAAAUGUUUCCUUCCUGACAGGCCGACAAGCCAACGAGAACAAUACUCGGUAAAGGUCAAAUUGUAUACCA
....(((((..(.(((((.....))))).)...))))).((...(((((((..((((.......)))).....)))....))))...)). ( -14.50)
>consensus
AAAAGUAAGAUGGGAGGGCAAAAUGUUUCCUUCCUGACAGGCCGACAAGCCAACGAGAACAAUUCUCGUUAAAGGUCAAAUUCUAUACCA
...........(((((((.........)))))))((((.(((......)))(((((((.....)))))))....))))............ (-17.77 = -18.15 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 13,558,175 – 13,558,283
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 91.05
Mean single sequence MFE -30.91
Consensus MFE -24.36
Energy contribution -24.80
Covariance contribution 0.44
Combinations/Pair 1.16
Mean z-score -1.69
Structure conservation index 0.79
SVM decision value 0.27
SVM RNA-class probability 0.660301
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13558175 108 - 22407834
GCAGAGUGCAGCUUUUCGGCGAAGGGCAGAAAAAUAAGAUGGGAGGGCAAAAUAUUUCCUUCCUGACAGGCCGACAAGCCAACGAGAAUAAUUUUCGUUAAAGGUCGA
((.....)).(((((((...))))))).............(((((((.((....)).)))))))(((.(((......)))(((((((.....)))))))....))).. ( -28.70)
>DroSec_CAF1 19351 108 - 1
GCAGAGUGCAGCUUUUCGGCGAAGGGUAGAAAAGUAAGAUGGGAGGGCAAAAUGUUUCCUUCCUGACAGGCCGACAAGCCAACGGGAACAAUUCUCGUUAAAGGUCAA
((.....)).(((((((.((.....)).))))))).....((((((((.....))..))))))((((.(((......)))(((((((.....)))))))....)))). ( -32.10)
>DroSim_CAF1 27015 108 - 1
GCAGAGUGCAGCUUUUCGUCGAAGGGCAGAAAAGUAAGAUGGGAGGGCAAAAUGUUUCCUUCCUGACAGGCCGACAAGCCAACGGGAACAAUUCUCGUUAAAGGUCGA
((.....)).((((((((((....))).))))))).....(((((((.((....)).)))))))(((.(((......)))(((((((.....)))))))....))).. ( -35.60)
>DroYak_CAF1 17291 108 - 1
GCAGAGUGCAGCUUUUCGGUGAAGGAAAGAAAAGUUAGACGAAAACGCAAAAUGUUUCCUUCCUGACAGGCCGACAAGCCAACGAGAACAAUACUCGGUAAAGGUCAA
((.....)).((((.((((.((((((((.(...(((.......)))......).)))))))))))).)))).(((.......((((.......))))......))).. ( -27.22)
>consensus
GCAGAGUGCAGCUUUUCGGCGAAGGGCAGAAAAGUAAGAUGGGAGGGCAAAAUGUUUCCUUCCUGACAGGCCGACAAGCCAACGAGAACAAUUCUCGUUAAAGGUCAA
((.....)).(((((((..(....)...))))))).....(((((((.........)))))))((((.(((......)))(((((((.....)))))))....)))). (-24.36 = -24.80 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:54 2006