Locus 11396

Sequence ID dm3.chr3R
Location 20,824,924 – 20,825,030
Length 106
Max. P 0.923598
window15662 window15663

overview

Window 2

Location 20,824,924 – 20,825,030
Length 106
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 85.26
Shannon entropy 0.23620
G+C content 0.47398
Mean single sequence MFE -38.55
Consensus MFE -28.12
Energy contribution -29.43
Covariance contribution 1.31
Combinations/Pair 1.14
Mean z-score -1.91
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.715594
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20824924 106 + 27905053
GCAGAAUAAUUACCGCAACAAGUUGCUGCUUGCUCUCUUGAUGGCUGCUGCUCCUGCUAGUUGCAACUGUUGGUAGUUGCUAGUUGCAAGUUGGCAAGCAGCAAUA
((.(........).)).....(((((((((((((..((((.((((.((((((...((.(((....))))).)))))).))))....))))..))))))))))))). ( -41.20, z-score =  -1.97, R)
>droSec1.super_33 86216 106 + 478481
GCAGAAUAAUUACCGCAACAAGUUGCUGCUUGCUCUCCUGAUGGCUGCUGCUCCUGCUAGUUGCAACUCUUAGUAGUUGCUAGUUGCAAGUUGGCAAGCAGCAACA
((.(........).)).....(((((((((((((..(.((.((((.((((((..(((.....)))......)))))).))))....)).)..))))))))))))). ( -39.10, z-score =  -1.58, R)
>droYak2.chr3R 3158472 97 - 28832112
GCAGAAUAAUUACCGCAACAAGUUGCUGCUUGCUUUCCUGAUGGUUGCAAC-------AGUUGCUA--GUUGCUAGUUGGUAGUUGCUCGUUGGCAAGCAGCAACA
((.(........).)).....(((((((((((((.....(((((..(((((-------....((((--(...))))).....))))))))))))))))))))))). ( -34.20, z-score =  -1.28, R)
>droEre2.scaffold_4820 3241954 96 - 10470090
GCAGAAUAAUUACCGCAACAAGUUGCUGCUUGCUCUCCUGAUGGCUGCUGCUU------GUUGCAACUGUUGGUAGUUGCAACU----AGUUGGCAAGCAGCAACA
((.(........).)).....((((((((((((.(..(((..(((....))).------((((((((((....)))))))))))----))..))))))))))))). ( -39.70, z-score =  -2.81, R)
>consensus
GCAGAAUAAUUACCGCAACAAGUUGCUGCUUGCUCUCCUGAUGGCUGCUGCUC_____AGUUGCAACUGUUGGUAGUUGCUAGUUGCAAGUUGGCAAGCAGCAACA
((.(........).)).....(((((((((((((..(.((.((((.((((((...................)))))).))))....)).)..))))))))))))). (-28.12 = -29.43 +   1.31)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 20,824,924 – 20,825,030
Length 106
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 85.26
Shannon entropy 0.23620
G+C content 0.47398
Mean single sequence MFE -37.03
Consensus MFE -27.08
Energy contribution -27.95
Covariance contribution 0.87
Combinations/Pair 1.04
Mean z-score -2.36
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.923598
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20824924 106 - 27905053
UAUUGCUGCUUGCCAACUUGCAACUAGCAACUACCAACAGUUGCAACUAGCAGGAGCAGCAGCCAUCAAGAGAGCAAGCAGCAACUUGUUGCGGUAAUUAUUCUGC
..((((((((((((..(((((.....((((((......)))))).....))))).((....))........).)))))))))))......((((........)))) ( -35.60, z-score =  -1.64, R)
>droSec1.super_33 86216 106 - 478481
UGUUGCUGCUUGCCAACUUGCAACUAGCAACUACUAAGAGUUGCAACUAGCAGGAGCAGCAGCCAUCAGGAGAGCAAGCAGCAACUUGUUGCGGUAAUUAUUCUGC
.(((((((((((((..(((((.....((((((......)))))).....)))))........((....)).).)))))))))))).....((((........)))) ( -39.20, z-score =  -1.65, R)
>droYak2.chr3R 3158472 97 + 28832112
UGUUGCUGCUUGCCAACGAGCAACUACCAACUAGCAAC--UAGCAACU-------GUUGCAACCAUCAGGAAAGCAAGCAGCAACUUGUUGCGGUAAUUAUUCUGC
.((((((((((((......(((((......((((...)--))).....-------)))))..((....))...)))))))))))).....((((........)))) ( -33.80, z-score =  -2.69, R)
>droEre2.scaffold_4820 3241954 96 + 10470090
UGUUGCUGCUUGCCAACU----AGUUGCAACUACCAACAGUUGCAAC------AAGCAGCAGCCAUCAGGAGAGCAAGCAGCAACUUGUUGCGGUAAUUAUUCUGC
.(((((((((((((..((----.(((((((((......)))))))))------..((....))....))..).)))))))))))).....((((........)))) ( -39.50, z-score =  -3.46, R)
>consensus
UGUUGCUGCUUGCCAACUUGCAACUAGCAACUACCAACAGUUGCAACU_____GAGCAGCAGCCAUCAGGAGAGCAAGCAGCAACUUGUUGCGGUAAUUAUUCUGC
.((((((((((((.............((((((......))))))...........((....))..........)))))))))))).....((((........)))) (-27.08 = -27.95 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:42:08 2011