Locus 4270

Sequence ID dm3.chr2R
Location 11,791,795 – 11,791,846
Length 51
Max. P 0.861156
window5852 window5853

overview

Window 2

Location 11,791,795 – 11,791,846
Length 51
Sequences 5
Columns 52
Reading direction forward
Mean pairwise identity 95.74
Shannon entropy 0.06990
G+C content 0.53688
Mean single sequence MFE -14.68
Consensus MFE -14.66
Energy contribution -14.50
Covariance contribution -0.16
Combinations/Pair 1.07
Mean z-score -1.25
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.861156
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11791795 51 + 21146708
-CUGUUGUUGUCCACGGAUUGGACGACUCUACGGCUCUGUGGCUUUGGCAAA
-((((.((((((((.....))))))))...)))).......((....))... ( -14.90, z-score =  -1.55, R)
>droSim1.chr2R_random 2479822 51 + 2996586
-CUGUUGUUGUCCACGGAUUGGACGACUCUACGGCUCUGUGGCUUUGGCAAA
-((((.((((((((.....))))))))...)))).......((....))... ( -14.90, z-score =  -1.55, R)
>droSec1.super_1 9287638 51 + 14215200
-CUGUUGUUGUCCACGGAUUGGACGACUCUACGGCUCUGUGGCUUUGGCAAA
-((((.((((((((.....))))))))...)))).......((....))... ( -14.90, z-score =  -1.55, R)
>droYak2.chr2R 3948281 52 - 21139217
CUGGUUGUUGUCCACGGAUUGGACGACUCUACGGCUCUGUGGCUUUGGCAAA
......((((((((.....)))))))).(((.((((....)))).))).... ( -14.60, z-score =  -1.08, R)
>droEre2.scaffold_4845 8522729 52 - 22589142
CUGGUUGUUGUCCACGGAUUGGACGGCUCUACGGCUCUGUGGCUUUGGCAAA
......((((((((.....)))))))).(((.((((....)))).))).... ( -14.10, z-score =  -0.49, R)
>consensus
_CUGUUGUUGUCCACGGAUUGGACGACUCUACGGCUCUGUGGCUUUGGCAAA
......((((((((.....)))))))).(((.((((....)))).))).... (-14.66 = -14.50 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 11,791,795 – 11,791,846
Length 51
Sequences 5
Columns 52
Reading direction reverse
Mean pairwise identity 95.74
Shannon entropy 0.06990
G+C content 0.53688
Mean single sequence MFE -8.90
Consensus MFE -8.46
Energy contribution -8.66
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.10
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.545514
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11791795 51 - 21146708
UUUGCCAAAGCCACAGAGCCGUAGAGUCGUCCAAUCCGUGGACAACAACAG-
(((((....((......)).)))))((.(((((.....))))).)).....- (  -9.10, z-score =  -1.16, R)
>droSim1.chr2R_random 2479822 51 - 2996586
UUUGCCAAAGCCACAGAGCCGUAGAGUCGUCCAAUCCGUGGACAACAACAG-
(((((....((......)).)))))((.(((((.....))))).)).....- (  -9.10, z-score =  -1.16, R)
>droSec1.super_1 9287638 51 - 14215200
UUUGCCAAAGCCACAGAGCCGUAGAGUCGUCCAAUCCGUGGACAACAACAG-
(((((....((......)).)))))((.(((((.....))))).)).....- (  -9.10, z-score =  -1.16, R)
>droYak2.chr2R 3948281 52 + 21139217
UUUGCCAAAGCCACAGAGCCGUAGAGUCGUCCAAUCCGUGGACAACAACCAG
(((((....((......)).)))))((.(((((.....))))).))...... (  -9.10, z-score =  -1.25, R)
>droEre2.scaffold_4845 8522729 52 + 22589142
UUUGCCAAAGCCACAGAGCCGUAGAGCCGUCCAAUCCGUGGACAACAACCAG
(((((....((......)).)))))...(((((.....)))))......... (  -8.10, z-score =  -0.77, R)
>consensus
UUUGCCAAAGCCACAGAGCCGUAGAGUCGUCCAAUCCGUGGACAACAACAG_
(((((....((......)).)))))((.(((((.....))))).))...... ( -8.46 =  -8.66 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:25:57 2011