Locus 6402

Sequence ID 3R_DroMel_CAF1
Location 16,778,396 – 16,778,486
Length 90
Max. P 0.627479
window10441 window10442

overview

Window 1

Location 16,778,396 – 16,778,486
Length 90
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 92.35
Mean single sequence MFE -21.27
Consensus MFE -16.65
Energy contribution -18.65
Covariance contribution 2.00
Combinations/Pair 1.10
Mean z-score -1.73
Structure conservation index 0.78
SVM decision value 0.13
SVM RNA-class probability 0.598733
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16778396 90 + 27905053
GCGGACAAAUGCCAAUUUGGCAG---UAGCCGAAAAUAUCCAGCUAUACGAAGUCGAAUCAAAUUAUCGCACCGCUCGAUAAUGAGAAAUAAU
...(((...((((.....))))(---((((.(........).))))).....)))...((..(((((((.......)))))))..))...... ( -19.20)
>DroSec_CAF1 10767 89 + 1
GCGGAGAAAUGCCAAUUUGGCAG---UAGCCGAAAAUAUCCAGCUCUACGGAGUCGAAUCAAAUUAUCGCACCGCCCGAUAAUGAGAAAUAA-
.(((.....((((.....)))).---...)))........(.((((....)))).)..((..(((((((.......)))))))..)).....- ( -22.60)
>DroSim_CAF1 12455 90 + 1
GCGGACAAAUGCCAAUUUGGCAG---UAGCCGAAAAUAUCCAGCUCUACGGAGUCAAAUCAAAUUAUCGCACCGCCCGAUAAUGAGAAAUAAU
.(((.....((((.....)))).---...)))..........((((....))))....((..(((((((.......)))))))..))...... ( -22.20)
>DroEre_CAF1 6599 93 + 1
GCGGACAAACGCCAAAUUGGUAGUUAUAGCCGAAAAUAUCCAGCUCUACGGAGUCGAAUCAAAUUAUCGCACCGUCCGAUAAUGAGGAAUAAU
.(((...((((((.....))).)))....)))......(((.((((....))))........(((((((.......)))))))..)))..... ( -21.10)
>consensus
GCGGACAAAUGCCAAUUUGGCAG___UAGCCGAAAAUAUCCAGCUCUACGGAGUCGAAUCAAAUUAUCGCACCGCCCGAUAAUGAGAAAUAAU
.(((.....((((.....)))).......)))..........((((....))))....((..(((((((.......)))))))..))...... (-16.65 = -18.65 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 16,778,396 – 16,778,486
Length 90
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 92.35
Mean single sequence MFE -23.84
Consensus MFE -19.95
Energy contribution -19.70
Covariance contribution -0.25
Combinations/Pair 1.18
Mean z-score -1.57
Structure conservation index 0.84
SVM decision value 0.19
SVM RNA-class probability 0.627479
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16778396 90 - 27905053
AUUAUUUCUCAUUAUCGAGCGGUGCGAUAAUUUGAUUCGACUUCGUAUAGCUGGAUAUUUUCGGCUA---CUGCCAAAUUGGCAUUUGUCCGC
............((((.(((.((((((...............)))))).))).))))....((((..---.((((.....))))...).))). ( -23.16)
>DroSec_CAF1 10767 89 - 1
-UUAUUUCUCAUUAUCGGGCGGUGCGAUAAUUUGAUUCGACUCCGUAGAGCUGGAUAUUUUCGGCUA---CUGCCAAAUUGGCAUUUCUCCGC
-..............(((((((.((((.........))).).))))..(((((((....))))))).---.((((.....)))).....))). ( -23.90)
>DroSim_CAF1 12455 90 - 1
AUUAUUUCUCAUUAUCGGGCGGUGCGAUAAUUUGAUUUGACUCCGUAGAGCUGGAUAUUUUCGGCUA---CUGCCAAAUUGGCAUUUGUCCGC
...............((((((((((..(((((((....(....)(((((((((((....))))))).---)))))))))))))).))))))). ( -25.80)
>DroEre_CAF1 6599 93 - 1
AUUAUUCCUCAUUAUCGGACGGUGCGAUAAUUUGAUUCGACUCCGUAGAGCUGGAUAUUUUCGGCUAUAACUACCAAUUUGGCGUUUGUCCGC
...............(((((((.((((.........))).).))(((((((((((....)))))))....)))).............))))). ( -22.50)
>consensus
AUUAUUUCUCAUUAUCGGGCGGUGCGAUAAUUUGAUUCGACUCCGUAGAGCUGGAUAUUUUCGGCUA___CUGCCAAAUUGGCAUUUGUCCGC
...............(((((((.((((.........))).).))))..(((((((....))))))).....((((.....)))).....))). (-19.95 = -19.70 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:43 2006