Locus 11208

Sequence ID	dm3.chr3R
Location	19,408,048 – 19,408,147
Length	99
Max. P	0.875083

overview

Window 3

Location	19,408,048 – 19,408,147
Length	99
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	88.89
Shannon entropy	0.17848
G+C content	0.48377
Mean single sequence MFE	-26.00
Consensus MFE	-23.81
Energy contribution	-23.75
Covariance contribution	-0.06
Combinations/Pair	1.12
Mean z-score	-1.42
Structure conservation index	0.92
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.81
SVM RNA-class probability	0.825221
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19408048 99 + 27905053
CCCGAUGGCCAGUUGGCCUAGUCAUUGAAGAACUGAACGAUAAAUGCUAAAAUGAGAGCUGCCACGUUCAGAAGUUCCAGAGGAAGCAGAGGUGGAGGA
.((...((((....))))...(((((......(((((((......(((........))).....)))))))...((((...)))).....))))).)). ( -24.50, z-score =  -0.40, R)
>droSim1.chr3R 19230910 89 + 27517382
CCCGAUGGCCAGUUGGCCUAGUCAUUGAAGAACUGAACGAUAAAUGCUAAAAUGAGAGCUGCCACGUUCAGAAGUUUCAGAGGAGGAGG----------
.(((((((((....))))..))).((((((..(((((((......(((........))).....)))))))...)))))).))......---------- ( -26.20, z-score =  -2.18, R)
>droSec1.super_0 19767167 93 + 21120651
CCCGAUGGCCAGUUGGCCUAGUCAUUGAAGAACUGAACGAUAAAUGCUAAAAUGAGAGCUGCCACGUUCAGAAGUUUCAGAGGAGGUGGAGGA------
.(((((((((....))))..))).((((((..(((((((......(((........))).....)))))))...)))))).))..........------ ( -26.20, z-score =  -1.49, R)
>droYak2.chr3R 20294191 93 + 28832112
CCUGAUGGCCAGUUGGCCUAGUCAUUGAAAAACUGGACGAUAAAUGCUAAAAUGAAAGCUGCCACGUUCAGUAGUUCCAGAGGAGGAGGAGCA------
..((((((((....))))..)))).......((((((((......(((........))).....)))))))).(((((.........))))).------ ( -27.10, z-score =  -1.60, R)
>consensus
CCCGAUGGCCAGUUGGCCUAGUCAUUGAAGAACUGAACGAUAAAUGCUAAAAUGAGAGCUGCCACGUUCAGAAGUUCCAGAGGAGGAGGAGGA______
.(((((((((....))))..))).((((((..(((((((......(((........))).....)))))))...)))))).))................ (-23.81 = -23.75 +  -0.06)

alignment

secondary structure

dotplot

Window 4

Location	19,408,048 – 19,408,147
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	88.89
Shannon entropy	0.17848
G+C content	0.48377
Mean single sequence MFE	-22.62
Consensus MFE	-21.09
Energy contribution	-20.90
Covariance contribution	-0.19
Combinations/Pair	1.10
Mean z-score	-1.49
Structure conservation index	0.93
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.02
SVM RNA-class probability	0.875083
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19408048 99 - 27905053
UCCUCCACCUCUGCUUCCUCUGGAACUUCUGAACGUGGCAGCUCUCAUUUUAGCAUUUAUCGUUCAGUUCUUCAAUGACUAGGCCAACUGGCCAUCGGG
....((............((..(((...((((((((((..(((........)))..))).)))))))...)))...))...((((....))))...)). ( -23.10, z-score =  -0.99, R)
>droSim1.chr3R 19230910 89 - 27517382
----------CCUCCUCCUCUGAAACUUCUGAACGUGGCAGCUCUCAUUUUAGCAUUUAUCGUUCAGUUCUUCAAUGACUAGGCCAACUGGCCAUCGGG
----------......((..((((....((((((((((..(((........)))..))).)))))))...)))).......((((....))))...)). ( -22.40, z-score =  -1.90, R)
>droSec1.super_0 19767167 93 - 21120651
------UCCUCCACCUCCUCUGAAACUUCUGAACGUGGCAGCUCUCAUUUUAGCAUUUAUCGUUCAGUUCUUCAAUGACUAGGCCAACUGGCCAUCGGG
------....((........((((....((((((((((..(((........)))..))).)))))))...)))).......((((....))))...)). ( -22.90, z-score =  -2.00, R)
>droYak2.chr3R 20294191 93 - 28832112
------UGCUCCUCCUCCUCUGGAACUACUGAACGUGGCAGCUUUCAUUUUAGCAUUUAUCGUCCAGUUUUUCAAUGACUAGGCCAACUGGCCAUCAGG
------.............((((((..((((.((((((..(((........)))..))).))).))))..)))........((((....))))..))). ( -22.10, z-score =  -1.06, R)
>consensus
______UCCUCCUCCUCCUCUGAAACUUCUGAACGUGGCAGCUCUCAUUUUAGCAUUUAUCGUUCAGUUCUUCAAUGACUAGGCCAACUGGCCAUCGGG
...................((((.....((((((((((..(((........)))..))).)))))))..............((((....)))).)))). (-21.09 = -20.90 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:38:29 2011