Locus 9782

Sequence ID dm3.chr3R
Location 8,956,886 – 8,956,939
Length 53
Max. P 0.991807
window13420 window13421

overview

Window 0

Location 8,956,886 – 8,956,939
Length 53
Sequences 6
Columns 66
Reading direction forward
Mean pairwise identity 62.54
Shannon entropy 0.69911
G+C content 0.42695
Mean single sequence MFE -14.67
Consensus MFE -9.31
Energy contribution -9.07
Covariance contribution -0.25
Combinations/Pair 1.56
Mean z-score -0.82
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.88
SVM RNA-class probability 0.972915
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8956886 53 + 27905053
UGCUCGACUCGGGGAGUCGAGUUUUAAAUUUAUCGAUCAAAGCUUAGAUUUUU-------------
.(((((((((...)))))))))............((((........))))...------------- ( -13.20, z-score =  -1.62, R)
>droSim1.chr3R 15054677 66 - 27517382
UGCUCGACUCGGGGAGUCGAGUUGGAAAUUUAUCGAUCAAAGCUUAGGGCUACCCCUUAGAUUUUU
.(((((((((...)))))))))....................((.((((....)))).))...... ( -18.00, z-score =  -0.72, R)
>droSec1.super_0 8080909 66 - 21120651
UGCUCGACUCGGGGAGUCGAGUUGGAAAUUUAUCGUUCAAAGCUUAGGGCUACCCCUUAGAUUUUU
.(((((((((...))))))))).(((((((((..((.....))..((((....))))))))))))) ( -18.50, z-score =  -0.90, R)
>droYak2.chr3R 13259513 53 + 28832112
UGCUCGACUUGGGGAGUCGAGUUGGAAAUUUAUCGAUCAGAUUUCCUAUUUUU-------------
.(((((((((...))))))))).((((((((.......)))))))).......------------- ( -17.10, z-score =  -2.72, R)
>droEre2.scaffold_4770 5060433 64 - 17746568
UGCUCGACUCGGGGAGUCGAGUUGGAAAUUUAUCGAUCAAAGCAUAGGGCU--CCCUUAGAUUUUU
.(((((((((...))))))))).(((((((((.............(((...--.)))))))))))) ( -16.71, z-score =  -0.58, R)
>droAna3.scaffold_13340 1510398 54 + 23697760
CAGUAGACGUUCUGACAUGGUUC----AUUUAUCGAUCACACACCGAAAUAGGUUUCG--------
(((........)))...(((((.----.......)))))...(((......)))....-------- (  -4.50, z-score =   1.65, R)
>consensus
UGCUCGACUCGGGGAGUCGAGUUGGAAAUUUAUCGAUCAAAGCUUAGAGCUACCCCUU________
.(((((((((...)))))))))............................................ ( -9.31 =  -9.07 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 8,956,886 – 8,956,939
Length 53
Sequences 6
Columns 66
Reading direction reverse
Mean pairwise identity 62.54
Shannon entropy 0.69911
G+C content 0.42695
Mean single sequence MFE -13.25
Consensus MFE -6.23
Energy contribution -7.73
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.50
SVM RNA-class probability 0.991807
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8956886 53 - 27905053
-------------AAAAAUCUAAGCUUUGAUCGAUAAAUUUAAAACUCGACUCCCCGAGUCGAGCA
-------------................................((((((((...)))))))).. ( -11.20, z-score =  -2.73, R)
>droSim1.chr3R 15054677 66 + 27517382
AAAAAUCUAAGGGGUAGCCCUAAGCUUUGAUCGAUAAAUUUCCAACUCGACUCCCCGAGUCGAGCA
..(((.((.((((....)))).)).))).................((((((((...)))))))).. ( -17.30, z-score =  -1.92, R)
>droSec1.super_0 8080909 66 + 21120651
AAAAAUCUAAGGGGUAGCCCUAAGCUUUGAACGAUAAAUUUCCAACUCGACUCCCCGAGUCGAGCA
..(((.((.((((....)))).)).))).................((((((((...)))))))).. ( -17.30, z-score =  -2.04, R)
>droYak2.chr3R 13259513 53 - 28832112
-------------AAAAAUAGGAAAUCUGAUCGAUAAAUUUCCAACUCGACUCCCCAAGUCGAGCA
-------------.......((((((...........))))))..(((((((.....))))))).. ( -13.20, z-score =  -3.46, R)
>droEre2.scaffold_4770 5060433 64 + 17746568
AAAAAUCUAAGGG--AGCCCUAUGCUUUGAUCGAUAAAUUUCCAACUCGACUCCCCGAGUCGAGCA
....(((....((--(((.....)))))....)))..........((((((((...)))))))).. ( -14.70, z-score =  -1.58, R)
>droAna3.scaffold_13340 1510398 54 - 23697760
--------CGAAACCUAUUUCGGUGUGUGAUCGAUAAAU----GAACCAUGUCAGAACGUCUACUG
--------(((((....)))))(((..((.((((((...----......)))).)).))..))).. (  -5.80, z-score =   1.14, R)
>consensus
________AAGGGAAAACCCUAAGCUUUGAUCGAUAAAUUUCCAACUCGACUCCCCGAGUCGAGCA
.............................................((((((((...)))))))).. ( -6.23 =  -7.73 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:11:02 2011