Locus 8579

Sequence ID dm3.chr3RHet
Location 1,009,803 – 1,009,891
Length 88
Max. P 0.953965
window11783 window11784

overview

Window 3

Location 1,009,803 – 1,009,891
Length 88
Sequences 5
Columns 88
Reading direction forward
Mean pairwise identity 74.09
Shannon entropy 0.47485
G+C content 0.54188
Mean single sequence MFE -24.58
Consensus MFE -14.80
Energy contribution -17.08
Covariance contribution 2.28
Combinations/Pair 1.23
Mean z-score -1.81
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.60
SVM RNA-class probability 0.953965
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1009803 88 + 2517507
CCAGUUGGUCACUUCAGCUAUAGUCACCGAUCGUGGACACCACCUGAUCCCGAUCCGCACUCUGCACCACACCGCCGCUGCAGAGGCG
......(((.(((........))).)))(((((.(((((.....)).))))))))(((.(((((((.(........).)))))))))) ( -29.30, z-score =  -2.55, R)
>droEre2.scaffold_4784 24019961 88 + 25762168
CCAGUUGGUCACCUGAACUAUAGUCACCGAUCGUGGCCACCACCUGGUCCCGAUCCGCACUCUGUACCACACCACAGCUACAGAGGCG
......(((.((..........)).)))(((((.(((((.....))))).)))))(((.(((((((.(........).)))))))))) ( -27.70, z-score =  -1.97, R)
>droSec1.super_6 17490 88 + 4358794
CUACUUGGUCACUUCAGCUAUAGUCACCGAUCGUGGCCACCACCUGGUCCUGAUCCGCACUCUCUACCACACCACAGCUACAUAGGCG
......(((.(((........))).)))(((((.(((((.....))))).))))).....................(((.....))). ( -18.60, z-score =  -0.52, R)
>droSim1.chr2h_random 1477450 88 + 3178526
CCUGUUGGUCACUUCAGUUAUAGUCACCGAUCGUGGCCACCACCUGGUCCCGAUCCGCACUCUGUACCACACCGCAGCUACAGAGGCG
......(((.(((........))).)))(((((.(((((.....))))).)))))(((.(((((((.(........).)))))))))) ( -30.50, z-score =  -2.79, R)
>droVir3.scaffold_12916 38087 84 + 114074
----UUUGUUAGUUUUGCUAUAGUCCUCUCAUAUAGGCAAAAUUCUAUUAAGAUCGGAGCACUAUAUCAUAUAGCUGCCAUAGCAACG
----..........(((((((..(((..((..(((((......)))))...))..)))((((((((...))))).))).))))))).. ( -16.80, z-score =  -1.23, R)
>consensus
CCAGUUGGUCACUUCAGCUAUAGUCACCGAUCGUGGCCACCACCUGGUCCCGAUCCGCACUCUGUACCACACCGCAGCUACAGAGGCG
......(((.(((........))).)))(((((.(((((.....))))).))))).((.(((((((.(........).))))))))). (-14.80 = -17.08 +   2.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 1,009,803 – 1,009,891
Length 88
Sequences 5
Columns 88
Reading direction reverse
Mean pairwise identity 74.09
Shannon entropy 0.47485
G+C content 0.54188
Mean single sequence MFE -30.00
Consensus MFE -18.26
Energy contribution -19.86
Covariance contribution 1.60
Combinations/Pair 1.30
Mean z-score -1.24
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.749671
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1009803 88 - 2517507
CGCCUCUGCAGCGGCGGUGUGGUGCAGAGUGCGGAUCGGGAUCAGGUGGUGUCCACGAUCGGUGACUAUAGCUGAAGUGACCAACUGG
((((((((((.((......)).))))))).)))(((((((((........)))).)))))(((.(((........))).)))...... ( -36.20, z-score =  -1.63, R)
>droEre2.scaffold_4784 24019961 88 - 25762168
CGCCUCUGUAGCUGUGGUGUGGUACAGAGUGCGGAUCGGGACCAGGUGGUGGCCACGAUCGGUGACUAUAGUUCAGGUGACCAACUGG
((((((((((.(........).))))))).)))(((((((.(((.....))))).)))))(((.(((........))).)))...... ( -35.70, z-score =  -1.61, R)
>droSec1.super_6 17490 88 - 4358794
CGCCUAUGUAGCUGUGGUGUGGUAGAGAGUGCGGAUCAGGACCAGGUGGUGGCCACGAUCGGUGACUAUAGCUGAAGUGACCAAGUAG
(((.....((((((((((...........(((.((((.((.(((.....)))))..)))).)))))))))))))..)))......... ( -22.20, z-score =   1.06, R)
>droSim1.chr2h_random 1477450 88 - 3178526
CGCCUCUGUAGCUGCGGUGUGGUACAGAGUGCGGAUCGGGACCAGGUGGUGGCCACGAUCGGUGACUAUAACUGAAGUGACCAACAGG
((((((((((.(........).))))))).)))(((((((.(((.....))))).)))))(((.(((........))).)))...... ( -35.70, z-score =  -2.05, R)
>droVir3.scaffold_12916 38087 84 - 114074
CGUUGCUAUGGCAGCUAUAUGAUAUAGUGCUCCGAUCUUAAUAGAAUUUUGCCUAUAUGAGAGGACUAUAGCAAAACUAACAAA----
..(((((((((..((((((...))))))..(((..(((((((((........)))).)))))))))))))))))..........---- ( -20.20, z-score =  -1.98, R)
>consensus
CGCCUCUGUAGCUGCGGUGUGGUACAGAGUGCGGAUCGGGACCAGGUGGUGGCCACGAUCGGUGACUAUAGCUGAAGUGACCAACUGG
((((((((((.(........).))))))).)))((((((((((....)))..)).)))))(((.(((........))).)))...... (-18.26 = -19.86 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:48:13 2011