Locus 11314

Sequence ID dm3.chr3R
Location 20,283,081 – 20,283,132
Length 51
Max. P 0.953336
window15561 window15562

overview

Window 1

Location 20,283,081 – 20,283,132
Length 51
Sequences 4
Columns 52
Reading direction forward
Mean pairwise identity 90.29
Shannon entropy 0.15602
G+C content 0.53658
Mean single sequence MFE -17.40
Consensus MFE -14.57
Energy contribution -14.82
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.724856
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20283081 51 + 27905053
AGAUAC-AGGACCUUUCUCGCUCUCUUCGAGUGGCAGGUCCUUUGGCAUGAU
.(.((.-(((((((...((((((.....)))))).))))))).)).)..... ( -17.10, z-score =  -1.73, R)
>droSec1.super_0 20619669 52 + 21120651
AGAUACCAGGACCUUUCUCGCUCUCUUCGAGUGGCAGAUCCCUUGGCAUGCU
.....(((((...(((.((((((.....)))))).)))...)))))...... ( -12.20, z-score =   0.20, R)
>droYak2.chr3R 2612094 51 - 28832112
AGAUAC-AGGACCUUGCUCGCUCUCUUCGAGUGGCAGGUCCUUUCGCAUGCU
.((...-(((((((.((.(((((.....)))))))))))))).))....... ( -21.70, z-score =  -3.25, R)
>droEre2.scaffold_4820 2693859 51 - 10470090
AGGUAC-AGGACCUUUAUCGCUCUCUUCGAGUGGCAGGUCCUACGGCAUGCU
..((..-(((((((...((((((.....)))))).)))))))...))..... ( -18.60, z-score =  -2.20, R)
>consensus
AGAUAC_AGGACCUUUCUCGCUCUCUUCGAGUGGCAGGUCCUUUGGCAUGCU
........((((((...((((((.....)))))).))))))........... (-14.57 = -14.82 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,283,081 – 20,283,132
Length 51
Sequences 4
Columns 52
Reading direction reverse
Mean pairwise identity 90.29
Shannon entropy 0.15602
G+C content 0.53658
Mean single sequence MFE -17.00
Consensus MFE -15.30
Energy contribution -14.92
Covariance contribution -0.38
Combinations/Pair 1.14
Mean z-score -2.09
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.59
SVM RNA-class probability 0.953336
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20283081 51 - 27905053
AUCAUGCCAAAGGACCUGCCACUCGAAGAGAGCGAGAAAGGUCCU-GUAUCU
...((((...(((((((....((((.......))))..)))))))-)))).. ( -15.90, z-score =  -2.22, R)
>droSec1.super_0 20619669 52 - 21120651
AGCAUGCCAAGGGAUCUGCCACUCGAAGAGAGCGAGAAAGGUCCUGGUAUCU
((.((((((..((((((....((((.......))))..)))))))))))))) ( -17.30, z-score =  -1.44, R)
>droYak2.chr3R 2612094 51 + 28832112
AGCAUGCGAAAGGACCUGCCACUCGAAGAGAGCGAGCAAGGUCCU-GUAUCU
((.((((...((((((((((.(((.....))).).)).)))))))-)))))) ( -19.20, z-score =  -2.66, R)
>droEre2.scaffold_4820 2693859 51 + 10470090
AGCAUGCCGUAGGACCUGCCACUCGAAGAGAGCGAUAAAGGUCCU-GUACCU
.........((((((((..(.(((.....))).)....)))))))-)..... ( -15.60, z-score =  -2.02, R)
>consensus
AGCAUGCCAAAGGACCUGCCACUCGAAGAGAGCGAGAAAGGUCCU_GUAUCU
....(((...(((((((..(.(((.....))).)....))))))).)))... (-15.30 = -14.92 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:40:41 2011